Last updated 4 October 2020

SARS-CoV-2 and COVID-19

For a recent comprehensive review of COVID-19, see (Wiersinga, JAMA)

EPIDEMIOLOGY

Transmission Dynamics. Person-to-person transmission documented with mean incubation period is ~5.8 days (95th %ile 9.7-14.2 days), serial interval 7.5 days, reproductive number approximately 2.2 (Li, NEJM; McAloon, BMJ Open; Li, MedRxiv); serial interval and reproduction number (R0) are not fixed properties of an outbreak but change with the implementation of control measures, particularly case isolation (Ali, Science); Inter-individual contact data can be used to estimate R0 in health care facilities to inform infection control measures (Temime, Clin Infect Dis)

Families. Family clusters have been observed (Chan, Lancet); estimated transmission risk ranges from 12-22% among household contacts, higher in adults/spouses and lower in children (Li, Clin Infect Dis; Jing, Lancet Infect Dis; Madewell, MedRxiv); family gatherings may facilitate community spread (Ghinai, MMWR); cats may be infected and exhibit asymptomatic transmission to other cats, but it is unknown if they can transmit SARS-CoV-2 to humans (Halfmann, NEJM); cats and ferrets are susceptible to SARS-CoV-2 infection but dogs, pigs, chickens and ducks do not support efficient replication (Shi, Science)

Children. Infection is common in children but most are asymptomatic or mild, including early neonatal infections (Cai, Clin Infect Dis; Lu, NEJM; Dong, Pediatrics; Qiu, Lancet Infect Dis; Zeng, JAMA Pediatr; Wei, JAMA; Castagnoli, JAMA Pediatr; Parri, NEJM), and children are considered less susceptible to SARS-CoV-2 than adults (Viner, JAMA Pediatr); incidence of COVID-19 in children aged 5-11 is about twice what it is for children aged 12-17 (Leeb, MMWR); a study in India found that children of all ages can become infected with SARS-CoV-2 and spread the virus to others (Laxminarayan, Science); current knowledge of COVID-19 in children summarized in (Shane, JPIDS); reduced COVID-19 disease in children may relate to differences in more robust innate immunity, ACE2 expression, cross-protection from endemic seasonal coronaviruses, Th2 immune responses, eoshinophilia, non-specific effects of vaccines, greater memory T cell diversity and lower levels of inflammatory cytokines (Pierce, Sci Transl Med; Steinman, PNAS; Felsenstein, Clin Immunol); a serosurvey in Seattle found <1% of children to be seropositive, and most were asymptomatic (Dingens, MedRxiv); symptom-based screening failed to detect 45% of SARS-CoV-2-infected children in a French study (Poline, Clin Infect Dis); on the other hand, a study of hospitalized patients in Italy without COVID-19 symptoms found lower rates of PCR positivity in children compared with adults (1% vs 9%) (Milani, JAMA Pediatr); most children requiring hospitalization for COVID-19 have comorbidities (Shekerdemian, JAMA Pediatr); most COVID-19-related deaths in the U.S. in individuals ≤21 years of age have occurred in Hispanic, Black or Native Americans and individuals with comorbid conditions (Bixler, MMWR); obesity is associated with worse clinical outcomes in children as in adults (Zachariah, JAMA Pediatr); children may still contribute to transmission and have viral loads comparable to adults (Jones, Charite); duration of viral shedding in symptomatic and Last updated 4 October 2020 asymptomatic children is comparable (Han, JAMA Pediatr); young children (< 5 yrs) can have high upper respiratory tract viral loads despite mild symptoms (Heald-Sargent, JAMA Pediatr; Baggio, Clin Infect Dis; Yonker, J Pediatr) and may remain PCR-positive for longer periods than adults (median 32 days for children 6-15 years of age), but may fail to develop neutralizing antibodies (Bahar, MedRxiv); contact tracing of outbreaks associated with child care facilities in Utah found that young children (some of whom were asymptomatic) played a role in transmission to household contacts, including adults (Lopez, MMWR); adolescents and young adults may be more likely to have asymptomatic infection and contribute to transmission in the general population (Liao, The Innovation); school re-opening is a controversial issue- current information suggests that primary schools and daycare may have a limited impact on community COVID-19 spread but secondary/high schools may be more challenging unless community transmission levels are low and safeguards are instituted (Goldstein, MedRxiv); contact tracing in South Korea found 12% of household contacts to have COVID-19, with highest rates for contacts of school-aged chldren (19%) and lower rates in contacts of chldren aged 0-9 during school closure (5%) (Park, Emerg Infect Dis contacts); child-to-child transmission has been unusual since reopening of German schools with institution of facemask use and enhanced room ventilation (Ehrhardt, Euro Surveill); a recent association with Kawasaki Disease-like inflammatory syndrome called “MIS-C” or Multisystem Inflammatory Syndrome in Children has been reported (Jones, Hosp Pediatr; Riphagen, Lancet; Licciardi, Pediatrics; Levin, NEJM; Felsenstein, Lancet Rheumatol); MIS-C characterized by shock, cardiac dysfunction, abdominal pain and markedly elevated inflammatory markers, is rare but needs to be distinguished from severe COVID-19 or Kawasaki disease (Godfred-Cato, MMWR); children meeting MIS-C criteria have distinctive demographic and clinical features depending on whether they are PCR- or antibody-positive (Swann, BMJ); children with MIS-C vs severe COVID- 19 may be distinguished by differences in TNFα and IL-10 levels (Diorio, J Clin Invest); immune profiles in children with MIS-C show evidence of inflammation, cellular activation and mucosal immune dysregulation along with the production of multiple autoantibodies (Gruber, Cell); tends to occur in older children compared with classical Kawasaki disease and has a higher rate of cardiac involvement and macrophage-activation syndrome, often treated with IVIG, corticosteroids and sometimes other immunomodulators such as tocilizumab or anakinra (Verdoni, Lancet; Feldstein, N Engl J Med; Riollano-Cruz, J Med Virol; Pain, Lancet Rheumatol); the prognosis for children treated with IVIG with or without steroids appears to be generally favorable (Belhadjer, Circulation), but PICU admission is frequently required, and long-term outcomes are uncertain (Davies, Lancet Child Adolesc Hlth; Ahmed, EClinMed); Gi involvement is common in children with MIS-C of all ages but younger children are more likely to have mucocutaneous involvement while older children are more likely to have cardiac involvement (Dufort, N Engl J Med); children with MIS-C are usually seropositive but sometimes PCR- negative, consistent with an immune-mediated process, possibly involving autoantibodies (Rowley, Nat Rev Immunol; Perez-Toledo, MedRxiv; Consiglio, Cell); SARS-CoV-2 binding and neutralizing Ab correlate with MIS-C and measures of inflammation (Rostad, Pediatrics); SARS- CoV-2 spike protein has a motif similar to superantigens which may trigger T cell activation in MIS-C (Cheng, PNAS); children of African ancestry may be at increased risk (Toubiana, BMJ); elevated cytokines are observed (IL2R, IL16, IL-18, CXCL9) (Cheung, JAMA), but patterns of cytokine production, T cell subsets and biomarkers distinguish MIS-C from Kawasaki Disease Last updated 4 October 2020 and Macrophage Activation Syndrome (Lee, J Clin Invest; Consiglio, Cell); cytotoxic T-cell dysregulation with exhaustion of CD8+ T cells and CD56dim CD57+ NK cells are observed in MIS- C (Beckmann, MedRxiv); complications include myocardial injury, shock and coronary artery aneurysms (Whittaker, JAMA), but the epidemiology differs from classical Kawasaki’s Disease (McCrindle, JAMA)

Asymptomatic Transmission. Asymptomatic or pre-symptomatic transmission makes an important contribution to SARS-CoV-2 spread (Rothe, NEJM; Yu, J Infect Dis; Bai, JAMA; Tong, Emerg Infect Dis; Li, Science; Xia, MedRxiv; Tao, MedRxiv; Qian, Clin Infect Dis; Wei, MMWR; Cheng, JAMA Intern Med; Furukawa, Emerg Infect Dis; Huff, Clin Infect Dis; Hao, Nature); a systematic review estimates that 15% of infections are truly asymptomatic but 40-60% of new infections are transmitted from presymptomatic individuals (Buitrago-Garcia, MedRxiv), whereas another review concluded that as many as 40-45% of SARS-CoV-2 infections may be asymptomatic (Oran, Ann Intern Med); asymptomatic individuals are estimated to be infectious for 6.5-9.5 days, with presymptomatic shedding lasting for 1-4 days-- viral loads are similar in asymptomatic and symptomatic individuals (Lee, JAMA Intern Med; Ra, Thorax); some models suggest that most transmission is mediated by presymptomatic individuals with a small contribution from asymptomatic individuals (Li, Science; Moghadas, PNAS); the window of transmission centers around the time of symptom onset and extends from 2-3 days before or after, with approximately 40% of transmissions occurring prior to symptom onset in the index case (Ferretti, MedRxiv); methods used to measure asymptomatic/presymptomatic transmission (case studies, viral dynamics, serial interval) are subject to different methodological limitations and bias, but in aggregate provide compelling evidence of asymptomatic and presymptomatic transmission (Savvides, MedRxiv); presymptomatic transmission is further supported by comparison of the transmission interval and incubation period in China, Japan and Singapore (Nishiura, Int J Infect Dis; Tindale, MedRxiv); over half of the PCR-positive residents of Life Care Center of Kirkland were asymptomatic on initial testing, and viral load did not correlate with the presence of symptoms (Kimball, MMWR; Arons, NEJM), which has also been noted in Italy (Cereda, ArXiv); symptom screening found to be inadequate for case detection in skilled nursing facilities, so early surveillance recommended (Roxby, JAMA Intern Med); in a study of 11 Maryland LTCFs, universal screening found that 55% of PCR- positive cases were asymptomatic (Bigelow, JAMA Intern Med); SARS-CoV-2 spread prior to symptom onset or by patients with mild atypical symptoms has been documented (Bohmer, Lancet Infect Dis), and possible transmission by hand shaking and face-to-face contact by a presymptomatic individual reported (Hijnen, Emerg Infect Dis); contact tracing and testing revealed 20% of secondary cases to be asymptomatic at the time of first clinical assessment (Bi, Lancet Infect Dis); 23% of a cohort of asymptomatic PCR-positive contacts remained asymptomatic and some were able to transmit SARS-CoV-2 to others despite lack of symptoms and a normal CT scan (Wang, Clin Infect Dis); a prospective study found that patients with asymptomatic infection cleared their infections more rapidly but secondary transmission was still observed Chau, Clin Infect Dis); 43% of SARS-CoV-2-positive persons detected in population-based screening in Iceland denied symptoms (Gudbjartsson, NEJM), and most asymptomatic patients identified on the Diamond Princess cruise ship remained asymptomatic Last updated 4 October 2020

(Sakurai, NEJM); containment measures, movement restrictions and increased awareness may shorten the window of transmission (Zhang, Lancet Infect Dis)

Superspreaders. Superspreader events appear to be associated with explosive growth and sustained transmission of COVID-19 (Frieden, Emerg Infect Dis); modeling suggests that superspreading results when a presymptomatic index case with a high viral load has a high number of exposed contacts in an indoor space (Goyal, MedRxiv); closed environments may promote superspreading, as transmission is 19-times more likely in a closed environment than in open air (Nishiura, MedRxiv), and possible aerosol transmission has occurred in crowded and poorly ventilated enclosures (Li, MedRxiv); ~10-20% of individuals appear to be responsible for ~80% of secondary transmission (Endo, Wellcome Open Res) and social exposures produce more secondary cases than family or workplace exposures (Adam, Nat Med); modeling suggests that interventions targeting superspreading (reducing personal contact number, social clustering) can have a major impact on community transmission (Nielsen, MedRxiv); genomic analysis of a superspreading event in Boston associated with a conference identified more than 90 linked cases in Massachusetts and perhaps up to 20,000 cases worldwide (Lemieux, MedRxiv); out of 318 outbreaks outside of Hubei province, only 1 occurred outdoors; most occurred in homes or transport, but the largest occurred in a shopping mall (Qian, MedRxiv); 87% of attendees at a choir rehearsal in Skagit County were infected by a single presymptomatic index patient, resulting in 2 deaths (Hamner, MMWR), and a high attack rate was also observed in church-related events in Arkansas (James, MMWR); singing generates airborne droplets that do not settle rapidly and may follow ambient airflow (Bahl, Clin Infect Dis); modeling of the Skagit Valley Chorale superspreading event indicates that indoor environment controls such as enhanced ventilation, filtration and UV disinfection could reduce the extent of transmission (Miller, Indoor Air); a 44% attack rate was observed among attendees of an overnight camp in which mask use and social distancing were not observed (Szablewski, MMWR); a single asymptomatic traveler was the index case in an outbreak involving more than 70 persons (Liu, Emerg Infect Dis); transmission in a poorly-ventilated bus suggests airborne spread in which 23 persons became infected by a single index individual (Shen, JAMA Intern Med); transmission risk in train passengers was found to correlate with co- travel time and seats adjacent to index cases (Hu, Clin Infect Dis); transmission was demonstrated on an international flight to secondary cases seated within 2 rows of an index case (Hoehl, JAMA Publ Hlth); fecal aerosols generated from a plumbing system is thought to have been responsible for an outbreak affecting 3 families in an apartment building (Kang, Ann Intern Med); most super-spreading events occur outside of household settings (Xu, Clin Infect Dis) and include crowded workplace settings such as call centers (Park, Emerg Infect Dis); an analysis of 61 COVID-19 case-clusters found that heavy breathing in close proximity to other persons (karaoke parties, cheering at clubs, conversing in bars, exercising in gyms) were high risk activities; the authors recommend avoiding the “three Cs”: closed poorly-ventilated spaces, crowds and close-contact settings; 41% of identified primary cases were asymptomatic/presymptomatic at the time of transmission (Furuse, Emerg Infect Dis); an air conditioning system was believed to potentiate the spread of airborne droplets in a restaurant- associated outbreak (Lu, Emerg Infect Dis); a synthesis of current data suggests a graded Last updated 4 October 2020 assessment based on ventilation, density, face covering, duration of exposure and activity is more predictive of exposure risk than an arbitrary physical distance (e.g., 6 feet) (Jones, BMJ)

Viral Shedding. High pharyngeal viral shedding on day zero is seen with a subsequent decline, more like influenza than SARS (He, Nat Med; Zou, NEJM; To, Lancet Infect Dis), but some patients may continue to be PCR-positive (Lan, JAMA), PCR-positivity persists for 7-12 days in mild-moderate cases but longer in severe cases (Wu CROI presentation https://special.croi.capitalreach.com/arc/audD3b/o1)

Washington State. First US cases in Washington State described (Holshue, NEJM; Arentz, JAMA); COVID-19 detected in all 50 states by early March, and genomic epidemiology suggested the importance of cryptic domestic spread (Fauver, MedRxiv; Bedford, Science); however, contrary to the conclusions of Bedford et al., phylogenetic outbreak simulations suggest that the initial Jan. 2020 SARS-CoV-2 introduction into WA state was not transmitted further, but rather a second introduction of a similar but non-identical virus occurred in Feb. 2020 and led to the regional outbreak—these and similar observations suggest that rapid public health interventions were able to successfully prevented some early SARS-CoV-2 introductions from taking hold and that more aggressive control measures could have prevented later introductions from leading to sustained outbreaks (Worobey, Science); in contrast, genomic analysis indicates the separate and unrecognized introduction of at least seven different SARS- CoV-2 lineages into California (Deng, Science); surveillance by the Seattle Flu Study detected early SARS-CoV-2 circulation (Chu, NEJM); seroprevalence in Puget Sound region 1.1% compared to 6.9% in NYC (Mar 23-Apr 1) (Havers, JAMA Intern Med); Life Care Center of Kirkland outbreak ended up involving 101 residents, 50 HCWs and 16 visitors (McMichael NEJM); links with other LTCFs involving shared staff or patients were identified; mortality in the initial group of hospitalized patients at the UW-affiliated hospitals as been high (33%), possibly because of advanced age (median 69 years) and frequent comorbidities (hypertension, cardiovascular disease, diabetes); two dominant SARS-CoV-2 clades circulating in WA hospital system associated with similar clinical outcomes (Nakamichi, MedRxiv)

Community Prevalence. Early COVID-19 pandemic in the U.S. was dominated by older adults but subsequent months have seen an increase in infections among younger adults (Boehmer, MMWR); high prevalence found when screening homeless shelter residents and staff in Boston, Seattle and San Francisco (Baggett, JAMA; Mosites, MWR); most PCR-positive cases in Seattle homeless shelters were asymptomatic and detected during surge testing events, with sleeping in communal space a risk factor (Rogers, Ann Intern Med); a mobile community, crowding, asymptomatic transmission and lack of face coverings are also thought to contribute to the high rates of COVID-19 in homeless shelters (Tobolowsky, MMWR); numerous outbreaks with rapid transmission have occurred in meat and poultry processing facilities, where physical distancing is not possible and workers frequently share workspace, transportation and housing (Waltenburg, MMWR; Steinberg, MMWR), and 4,913 cases of COVID-19 with 20 deaths have been reported in 115 U.S. facilities (Dyal, MMWR); surveys estimated SARS-CoV-2 seroprevalence to be 2.8% in Santa Clara County (Bendavid, MedRxiv) and 4.65% in LA County (Sood, JAMA), which was unexpectedly high, but concerns have been raised regarding sampling Last updated 4 October 2020 bias, inconsistency with rates of SARS-CoV-2 spread and mortality in other communities, and the likelihood of false-positive results, and another Bay Area serosurvey found only 0.26% in patients hospitalized for non-respiratory indications and 0.1% in blood donors (Ng, MedRxiv); antibody positivity in U.S blood donors has risen over time (1.8% overall) (Dodd, JAMA); cross- sectional serologic data from U.S. dialysis faclities suggest that less than 10% of the adult population seroconverted during the first pandemic wave and less than 10% of seroconverters were diagnosed (Anand, Lancet); may already have been spreading in France in late December (Deslandes, Int J Antimicrob Agents); evidence for multiple introductions of SARS-CoV-2 into NYC from Europe and other parts of the U.S. (Gonzalez-Reiche, Science); 122,300 excess deaths in US as of May 30 exceeds the 95,235 deaths officially attributed to COVID-19 and probably represents a more accurate estimate of the burden of the pandemic (Weinberger, JAMA Intern Med)

Nursing Homes. Skilled nursing facilities are particularly vulnerable to COVID-19, and residents are at risk for severe outcomes (Patel, Clin Infect Dis nursing homes; Fisman, JAMA Netw Open); screening of residents and staff of care homes have found comparable viral loads in symptomatic, pre-symptomatic, or asymptomatic individuals (Ladhani, EClinMed); aggressive surveillance and control measures are recommended in this setting (Roxby, MMWR; Roxby, JAMA Intern Med); mass testing of residents and staff following the detection of SARS-CoV-2 in long-term care facilities identified many asymptomatic cases and facilitated timely interventions to prevent further transmission (Telford, MMWR; Taylor, MMWR)

Cruise Ships. Recent outbreaks on cruise ships resulted in more than 800 infections and 10 deaths (Moriarty, MMWR); an analysis of Americans in a cruise ship outbreak found that sharing a cabin with an asymptomatic or symptomatic index case was associated with a 63-81% risk of acquisition, compared to 17% in individuals without infected cabinmates, demonstrating the importance of close quarters and asymptomatic/pre-symptomatic transmission (Plucinski, Clin Infect Dis); on the Diamond Princess cruise ship, 74% of infections were asymptomatic, and asymptomatic individuals were the source of 69% of all infections (Emery, eLife)

Seasonal Factors. Inverse relationship observed between temperature/humidity and transmission (Wang, MedRxiv; Ma, MedRxiv; Oliveiros, MedRxiv; Araujo, MedRxiv; Neher, MedRxiv; Sajadi, JAMA Network Open; Bukhari, SSRN); vitamin D deficiency correlates with severity in men (De Smet, MedRxiv); a large UK database found no correlation between vitamin D levels and COVID-19 (Hastie, Eur J Nutr), but others have found low 25(OH)-vitamin D levels to be associated with an increased risk of COVID-19 (Merzon, FEBS J), and a retrospective single-center cohort study found that probable vitamin D-deficient status correlated with increased risk of COVID-19 acquisition (Meltzer, JAMA Netw Open)

Environmental Stability. SARS-CoV-2 may remain detectable in aerosols for at least 3 hours and is more stable on plastic/steel than on copper/cardboard; inactivated by 70% ethanol, 0.5% hydrogen peroxide or 0.1% bleach but less reliably by benzalkonium chloride or chlorhexidine (Kampf, J Hosp Infect; van Doremalen, NEJM)

Last updated 4 October 2020

Possible Effects of BCG. Attributable mortality is lower in BCG vaccine-using countries (Miller, MedRxiv; Shet, MedRxiv); however, the purported relationship between BCG and COVID-19 susceptibility has been criticized because of testing, time and selection bias (Szigeti, MedRxiv) and failure to control for confounding by population age (Kirov, MedRxiv); BCG-vaccinated or unvaccinated adults in Israel had similar rates of COVID-19 infection (Hamiel, JAMA); a clinical trial may be required to definitively determine whether BCG vaccination confers protection against COVID-19 (Escobar, PNAS)

VIROLOGY

SARS-CoV-2 Virus. Description of SARS-CoV-2 (Zhu, NEJM; Lu, Lancet; Wu, Nature)

Relation to Other Coronaviruses. 88-96% similarity to bat coronaviruses (Zhou, Nature); the closest match to SARS-CoV-2 to date is an isolate from a bat collected in Yunnan Province in China, but this isolate has low sequence identity in the receptor-binding domain of the Spike protein (Zhou, Curr Biol); pangolin suggested as reservoir host (Zhang, Curr Biol; Lam, Nature; Xiao, Nature), used for food and traditional Chinese medicine, but pangolin coronaviruses lack a furin cleavage site found in SARS-CoV-2 and pangolin coronaviruses are genetically related but distinct from SARS-CoV-2 (Liu, PLoS Pathog); SARS-CoV-2 receptor binding motif appears to have arisen from recombination with pangolin coronaviruses (Li, Sci Adv); features of coronaviruses associated with higher pathogenicity are enhanced nuclear localization signals in the nucleocapsid protein and inserts in the spike glycoprotein (Gussow, PNAS); recent phylogenetic data are most consistent with an origin for SARS-CoV-2 in Rhinolophus spp. bats, most likely from Yunnan province in China (Latinne, BioRxiv); the sarbecovirus lineage giving rise to SARS-CoV-2 appears to have been circulating unnoticed in bats for decades (Boni, Nat Microbiol)

Binding. Structure of spike protein and binding to ACE2 (Wrapp, Science; Yan, Science; Hoffmann, Cell; Walls, Cell), which is encoded by an interferon-stimulated gene (Ziegler, Cell); the distribution of tissue ACE2 expression may explain a variable distribution of viral load in the respiratory tract-- ACE2 is most highly expressed in the nose, ciliated epithelium and type 2 pneumocytes (Hou, Cell); ACE2 is also expressed in cornea, GI tract, liver, heart, kidney, testis (Sungnak, Nat Med); productive infection of human gut epithelial cells has been demonstrated (Lamers, Science); lower nasal ACE2 expression in children might relate to their lower incidence of severe illness (Bunyavanich, JAMA); an analysis of ACE2 conservation has been used to predict the likelihood that other mammals may serve as intermediate hosts for SARS-CoV-2 (Damas, PNAS); SARS-CoV-2 spike protein interacts with both heparan sulfate and ACE2 on the surface of cells, which can be antagonized by heparin and may account for some of the therapeutic benefit of heparin (Clausen, Cell)

Cell Biology. A membrane-spanning molecular pore complex has been identified in the SARS- CoV-2 replication compartment that might be a therapeutic target (Wolff, Science)

Last updated 4 October 2020

Furin Cleavage. Furin-like cleavage site in the spike glycoprotein may broaden cell tropism (Coutard, Antiviral Res)

Sequence Variants. Increasing SARS-CoV-2 diversification observed (Castells, J Med Virol); subtypes with possible differences in transmissibility or virulence have been identified (Tang, Nat Sci Rev; Xi, MedRxiv; Su, BioRxiv). and designations of discrete SARS-CoV-2 lineages have been proposed (Rambaut, Nat Microbiol); a Δ382 ORF8 deletion SARS-CoV-2 variant detected in Singapore and other countries appears to be associated with milder illness and less hypoxia (Young, Lancet); the D614G spike variant has become the dominant pandemic form of SARS- CoV-2, growing to higher titers in culture, attaining higher viral loads in patients, and perhaps exhibiting enhanced fitness in communities (Korber, Cell); G614 spike variant may correlate with a higher case-fatality rate (Becerra-Flores, IJCP); a review of 80 S protein variants and 26 glycosylation site modifications has confirmed that D614G variants are more infectious, but other variants are also more or less infectious, some are resistant to neutralizing Ab, and glycosylation variants also affect infectivity (Li, Cell); S protein G614 and ORF1ab L4715 variants correlate with country-wide fatality rates— notably, WA state has a relative low fatality rate and a lower incidence of both alleles (Toyoshima, J Hum Genet); pseudovirus expressing D614G spike protein infects ACE2-expressing cells more efficiently (Zhang, BioRxiv); D614G variant shifts protein conformation toward an ACE2 binding-competent state and increases infectivity (Yukovetskiy, Cell); greater infectivity in vitro may be attributable to more efficient proteolysis of the D614G mutant S protein (Hu, BioRxiv; Daniloski, BioRxiv), although an analysis of descendants of SARS-CoV-2 sequenced isolates with recurrent mutations did not provide support for higher transmissibility (van Dorp, BioRxiv), and distinct viral lineages identified early in the Wuhan outbreak did not appear to be associated with different degrees of virulence— host factors (age, lymphocyte count, cytokines) appeared to correlate better with clinical outcomes (Zhang, Nature); patients in Chicago were found to have three distinct clades of SARS-CoV-2; clade 1 related to NYC was associated with higher viral loads, clade 3 is related to WA State isolates (Lorenzo-Redondo, MedRxiv)

Immune Response. The distinctive immune responses to SARS-CoV-2 play a major role in disease severity and mortality (Vabret, Immunity), and disease severity results from an aberrant immune response rather than viral burden (Broggi, Science); transcriptional analysis of host responses in NP swab samples show type I interferon/IL-6-dependent inflammatory responses and activation of complement and coagulation pathways (Ramlall, Nat Med); proinflammatory cytokine production, T cell exhaustion/apoptosis and endothelial activation are associated with a more severe clinical course (De Biasi, Nat Commun; Bouadma, MedRxiv); increased antibody- secreting cells (ASCs), follicular helper T cells (TFH cells), activated CD4+/CD8+ T cells and IgM/IgG SARS-CoV-2-binding antibodies were observed in a patient with non-severe COVID-19 prior to recovery, suggesting that they might correlate with favorable outcomes and protective immunity (Thevarajan, Nat Med); however, others have found that CD4+ T cell responses to SARS-CoV-2 are robust but do not necessarily correlate with viral clearance or milder illness (Thieme, Cell Rep Med); coordinated CD4+/CD8+ T cell and Ab responses are associated with milder outcomes (Moderbacher, Cell); virus-specific T cells detected in recovered patients correlate with neutralizing Ab titers (Ni, Immunity); reappearance of effector and memory T Last updated 4 October 2020 cells correlates with recovery (Odak, MedRxiv); SARS-CoV-2-specific CD4+ and CD8+ T cell responses are detected in convalescing COVID-19 patients, but also to a lesser extent in in unexposed individuals, which may represent cross-reactivity with seasonal respiratory coronaviruses (Grifoni, Cell; Weiskopf, Sci Immunol; Braun, Nature), and pre-existing memory CD4+ T cells that with cross-reactivity to common cold coronaviruses and SARS-CoV-2 have been detected in SARS-CoV-2-unexposed individuals (Mateus, Science); T cells recognizing spike proteins of endemic seasonal coronaviruses also recognize spike protein of SARS-CoV-2 (Woldemeskel, J Clin Invest); pre-existing T-cell responses were found in 81% of unexposed individuals, and cross-reactive peptides with common cold coronaviruses were identified (Nelde, Nat Immunol); recent documented infection with an endemic coronavirus is associated with less severe COVID-19 (Sagar, J Clin Invest); although many questions presently remain, pre- existing T cell immunity to SARS-CoV-2 may be related to prior endemic coronavirus exposure and could have important implications for clinical and vaccine outcomes (Sette, Nat Rev Immunol); possible immunopathological mechanisms include antibody-dependent enhancement and promotion of Th2 responses (Peeples, PNAS); the immune signature associated with SARS-CoV-2 infection includes both protective and pathological responses (CXCL10/IP10, T cell proliferation, basophil/plasmacytoid DC depletion (Laing, MedRxiv); elevation of HLA-DR CD11c inflammatory monocytes with expression of interferon-stimulated genes is associated with mild COVID-19, and depletion of CD14low CD16high monocytes with accumulation of HLA-Drlow classical monocytes, increased immature neutrophils and elevated calprotectin is associated with severe COVID-1 (Silvin, Cell; Schulte-Schrepping, Cell); the presence of unconventional T cells (mucosa-associated invariant/MAIT, γδ and invariant NK/INKT) and expression of CD69 has correlated with disease severity (Jouan, J Exp Med), and circulating NK cells expressing perforin, NKG2C and Ksp37 correlate with severe disease (Maucourant, Sci Immunol)

Immune Evasion. Transcriptomic response suggests a muted antiviral response compared to other respiratory viruses (Blanco-Melo, Cell); relatively weak induction of interferon responses is observed (Chu, Clin Infect Dis; O’Brien, Clin Infect Dis) and SARS-CoV-2 may have unique mechanisms to evade type I interferon responses (Sa Ribero, PLoS Pathog); the protein encoded by ORF3b is reported to be a type I interferon antagonist that is more potent than its SARS-CoV- 2 ortholog (Konno, Cell Rep); however, SARS-CoV-2 is sensitive to type I IFN responses in cultured cells, although it does not elicit them (Lokugamage, BioRxiv)-- early interferon responses are associated with coronavirus clearance, while delayed responses are associated with viral persistence and inflammation (Park, Cell Host Microbe); an impaired type I IFN response is associated with higher blood viral loads, inflammatory cytokine production and disease progression (Hadjadj, Science); a loss-of-function mutation in TLR7 associated with a loss of type I/II interferon responses is associated with severe COVID-19 (Van Der Made, JAMA), and genetic defects or autoantibodies directed against type I interferon increase susceptibility to severe COVID-19 (Bastard, Science; Zhang, Science); in a mouse model, type III IFNλ produced lung DCs induces barrier damage, suggesting potential risks from the therapeutic use of type III IFN (Broggi, Science); immunophenotyping indicates that severe cases exhibit a combination of type I IFN responses co-existent with TNF/IL-1beta-driven inflammation (Lee, Sci Immunol); marked T cell activation, senescence, exhaustion and TH17 skewing may be Last updated 4 October 2020 observed (De Biasi, Nat Commun); STAT2 signaling appears to play a role in both antiviral defense and immunopathology in a hamster model, suggesting that immunomodulators may potentially have mixed effects (Boudewijns, BioRxiv); T cell exhaustion and depletion are seen in other subacute viral infections and are not unique to COVID-19 (Vardhana, J Exp Med); one contributing factor in lymphopenia may be deficient IL-2-JAK1-STAT5 signaling (Shi, Cell Death Dis); SARS-CoV-2 appears to compromise effective CD8+ T cell activation (Habel, PNAS); single- cell RNA sequencing of PBMCs correlated a heterogenous interferon response, HLA class II down regulation and a developing neutrophil population with respiratory failure (Wilk, Nat Med); immune profiling of patients with COVID-19 or influenza found profound immunosuppression in most patients with COVID-19 with a small subset developing a hyper- inflammatory phenotype associated with respiratory failure (Mudd, MedRxiv); immune profiling may identify patients progressing to severe illness-- recovering patients express growth factors, whereas deteriorating patients simultaneously express multiple cytokine/chemokine patterns (Lucas, Nature); production of inflammatory cytokines in COVID- 19 inversely correlates with cytotoxic perforin-expressing NK and CD3+ T cells (Bordoni, Clin Infect Dis); transcriptional profiling of immune cells shows type I interferon and inflammatory responses, but effector T cells are associated with recovery, whereas dysregulated inflammatory responses, reduced HLA-DR and immune exhaustion with a skewed T cell receptor repertoire are associated with severe illness (Arunachalam, Science; Zhang, Nat Immunol)

Complement Activation. Viral N protein induces complement activation, which may contribute to acute lung injury (Gao, MedRxiv); see also discussion of complement inhibition under TREATMENT below

Interaction with Olfactory Epithelium. Sustentacular cells in the olfactory neuroepithelium express the ACE2 receptor and TMPRSS2 protease required for viral attachment and entry (Bilinska, ACS Chem Neuro; Fodoulian, BioRxiv); this may help to explain COVID-19-associated anosmia

Animal Models. Syrian hamsters can be used to study transmission, pathogenesis, treatment and immunization (Chan, Clin Infect Dis); SARS-CoV-2 replicates throughout the respiratory tract in a macaque model and recapitulates features of moderate human COVID-19 (Rockx, Science; Munster, Nature); causes interstitial pneumonia in transgenic mice expressing human ACE2 (Bao, Nature; Jiang, Cell); transgenic mice expressing ACE2 from the cytokeratin-18 promoter develop SARS-CoV-2 infection with severe lung inflammation (Winkler, Nat Immunol); a mouse-adapted model in which the spike protein and ACE2 protein have been modified to allow efficient interaction recapitulates SARS-CoV-2 replication in the respiratory tract, more severe illness in aged mice, and protection by IFNλ (Dinnon, Nature); replication-deficient adenoviruses encoding human ACE2 allow productive respiratory tract infections in mice which can be mitigated by neutralizing Ab (Hassan, Cell)

Autopsy Pathology. Autopsy findings in patients with COVID-19-associated ARDS shows edema, proteinaceous exudate, focal reactive pneumocyte hyperplasia, patchy inflammatory Last updated 4 October 2020 cellular infiltration, and multinucleate giant cells consistent with diffuse alveolar damage similar to SARS/MERS (Xu, Lancet Respir Med; Liu, J Med Virol); dysmorphic infected pneumocytes form the syncytia, and infected endothelial cells are associated with macro- and micro-thrombi (Bussani, MedRxiv); distinctive patterns of lung pathology have been classified as: (a) epithelial (with diffuse alveolar damage), (b) vascular (microvascular damage and thrombosis), (c) hemophagocytosis, (d) immune cell depletion, and (e) fibrosis, but multiple patterns may exist concurrently or sequentially, with virus demonstrated within endothelial cells and pneumocytes (Polak, Mod Pathol; Bösmüller, Virchows Arch; Hanley, Lancet Microbe); virus in pneumocytes and ciliated airway cells is seen during the acute phase of lung injury but not during the organizing phase of alveolar damage (Schaefer, Mod Pathol); only sporadic presence of SARS- CoV-2-infected cells is present at autopsy, whereas extensive thrombi and neutrophilic plugs are continuously present in multiple organs, suggesting that immunomodulation may be more effective than antiviral therapy in late disease (Schurink, Lancet Microbe); spleens and lymph nodes show lymphocyte depletion and virus-infected macrophages producing IL-6 (Feng, MedRxiv), which are implicated in the pathogenesis of the so-called “cytokine storm” (Merad, Nat Rev Immunol); the striking presence of capillary congestion and microthrombi is generally but not always restricted to the lungs (Fox, Lancet Respir Med; Dolhnikoff, J Thromb Haemost; Carsana, Lancet Infect Dis; Marini, JAMA suppl; Menter, Histopathology; Calabrese, Virchows Archiv); excessive platelet/neutrophil activation and microvascular thrombi with neutrophil “NETS” in lungs/heart/kidneys correlate with disease severity and fatal outcomes (Nicolai, Circulation); some patients show pulmonary septal capillary injury with complement/fibrin deposition in the microvasculature rather than classic ARDS (Magro, Transl Res); endothelial infection by SARS-CoV-2 may promote microvascular dysfunction and thrombosis (Varga, Lancet) and play a central role in severe vascular complications (Teuwen, Nat Rev Immunol), although the “viral-like particles” described in EM by Varga et al. may actually be rough endoplasmic reticulum (Goldsmith, Lancet; Varga, Lancet reply); different pathological patterns in different geographic regions is presently unexplained: autopsies of Washington State patients, many of whom were from a long-term care facility, reported diffuse alveolar damage and virus in type I and II pneumocytes but no microthrombi (Bradley, Lancet), and a series from Germany predominantly showed alveolar damage (Schaller, JAMA), whereas another reported evidence of widespread endothelial inflammation, thrombosis with microangiopathy, and intussceptive angiogenesis (Ackermann, NEJM); a NYC autopsy series also showed microthrombi and large pulmonary emboli, hemophagocytosis, and the presence of viral particles (Bryce, MedRxiv); clinically unsuspected deep venous thrombosis and pulmonary embolism have also been noted (Wichmann, Ann Intern Med); SARS-CoV-2 also reported in kidneys, liver, heart and brain (Puelles, NEJM)

CLINICAL

Incubation Period. Incubation period usually 4-5 days, most within 14 days (Chan, Lancet; Lauer, Ann Intern Med); incubation period may range up to 24 days in exceptional cases (Nie, J Infect Dis)

Last updated 4 October 2020

Usual Clinical Presentation. As many as 40-45% of SARS-CoV-2 infections may be asymptomatic (Oran, Ann Intern Med); male > female, median age 49 years, fever, cough, myalgia, fatigue, dyspnea, lymphopenia, ARDS, cardiac injury; myalgias, confusion, headache, sore throat, coryza, chest pain, secondary infection infrequent (Huang, Lancet; Chen, Lancet; Wang, JAMA; Xu, BMJ; Guan, NEJM); prolonged fever beyond 7 days after symptom onset is a risk factor for adverse outcomes, and a saddleback fever may also be accompanied by hypoxia but is associated with better outcomes (Ng, OFID); symptoms most associated with mild COVID- 19 are cough, sore throat, fever, diarrhea, headache, myalgias/arthralgias, fatigue, and disturbance of smell or taste, whereas more severe illness is associated with breathlessness, anorexia, confusion, chest pain and high fever (Struyf, Cochrane Rev); rates of hospitalization and mortality higher in men (Garg, MMWR; Lewnard, BMJ; Prieto-Alhambra, MedRxiv); females may be more susceptible to infection but less likely to develop severe disease or death (Qian, Clin Infect Dis gender); males exhibit higher inflammatory responses (IL-8, IL-18, CCL5, non- classical monocytes) and lower levels of T cell activation (Takahashi, Nature); SARS-CoV-2- positive patients in the ED are more likely to report fever, fatigue or myalgias, and to have lymphopenia/CXR infiltrates (Shah, MedRxiv); another series found predictors of COVID-19 to include exposure history, fatigue, leukopenia or lymphopenia and ground glass opacities on imaging (Mao, Lancet Digital Health); “silent” hypoxia with minimal symptoms may be a sign of impending deterioration (Wilkerson, Am J Emerg Med), and subjective dyspnea is not sufficiently sensitive to exclude hypoxemia in patients with COVID-19, supporting the utility of home oximetry to monitor patients for disease progression (Berezin, MedRxiv)

Other Signs and Symptoms. A prospective study of 16,749 people with COVID-19 in the UK found distinct respiratory, systemic and enteric presentations (Docherty, MedRxiv), and extrapulmonary involvement in COVID-19 includes the heart, kidneys, GI tract, liver, CNS and skin (Gupta, Nat Med); may present with mild URI symptoms, particularly in young healthy persons (Arashiro, Emerg Infect DIs; Woelfel, Nature); GI symptoms infrequent in some series but may be the primary presenting symptoms in a subset of patients (Pan, Am J Gastroenterol; D’Amico, Clin Gastroenterol Hepatol) and can include abdominal pain in absence of fever (Gahide, Clin Med); a systematic review found that only 12% of patients with COVID-19 have GI symptoms but 41% have viral RNA detected in GI tract (Parasa, JAMA Network Open); GI symptoms may be associated with milder illness (Nobel, Gastroenterology; Han, Am J Gastroenterol; Buscarini, MedRxiv) but have also been reported to be a risk factor for hospitalization and complications (Cholankeril, Gastroenterology; Mao, Lancet Gastroenterol Hepatol); gastrointestinal complications in patients with critical illness include mesenteric ischemia, GI bleeding, pancreatitis, ileus and Ogilvie syndrome (el Moheb, JAMA); >85% of patients with mild-moderate COVID-19 may report alteration or loss of taste/smell (Iacobucci, BMJ; Lechien, Eur Arch Oto-Rhinol Laryngol; Spinato, JAMA; Luers, Clin Infect Dis; Mercante, JAMA Otolaryngol); loss of taste/smell is the fourth most common COVID-19 symptom and has the highest (83%) positive predictive value (Dawson, Clin Infect Dis); most patients with anosmia/dysgeusia recover quickly (Levinson, MedRiv), and 89% of patients with altered taste or smell had experienced improvement or resolution by 4 weeks (Boscolo-Rizzo, JAMA Otolaryngol); recommendations for assessment and treatment of persistent olfactory dysfunction have been made (Whitcroft, JAMA); ocular signs may include conjunctival Last updated 4 October 2020 hyperemia, chemosis, epiphora or ocular secretions (Wu, JAMA Ophthalmol); cutaneous findings include acral erythema/pernio/chilblains, vesicular eruptions, urticaria, morbilliform/maculopapular rash, papulosquamous lesions and livedo or necrosis (Casas, Br J Dermatol; de Masson, JAAD); the pathogenesis of COVID-19-associated chilblains is uncertain but vasculitis is variably present in biopsy material, sometimes with immunohistochemical evidence of SARS-CoV-2 (Colmenero, Br J Dermatol; Herman, JAMA Dermatol); retiform purpura is only seen in critical cases (Freeman, MedRxiv)

Post-COVID-19 Symptoms. A majority of patients report persistent symptoms after hospital discharge, particularly fatigue, dyspnea and arthralgia (Carfi, JAMA); a survey found that 35% of symptomatic adults had not yet returned to their usual state of health 2-3 wks after diagnosis, including young adults without comorbidities (Tenforde, MMWR); more than half of individuals recovering from COVID-19 may still experience fatigue at 10 weeks after initial symptoms, and this is independent of illness severity (Townsend, MedRxiv); emerging reports are describing a subset of patients with “long-haul COVID” characterized by prolonged symptoms of poor mentation, sleep disturbance, exercise intolerance, autonomic symptoms, and sometimes low- grade fever/lymphadenopathy (Nath, Neurology)

Course of Asymptomatic or Pre-symptomatic Infections. Pre-symptomatic cases detected on screening usually result in mild disease (Wang, J Infect Dis); the estimated proportion of asymptomatic infections varies from 11-45% (Beale, MedRxiv; Oran, Ann Intern Med); patients with asymptomatic SARS-CoV-2 infections have less depression of CD4+ T cell counts and shorter duration of viral shedding (Yang, JAMA Network Open)

Fever. Although fever is a common feature of COVID-19, only half of Seattle patients requiring ICU admission for severe COVID-19 were febrile on admission (Bhatraju, NEJM); a biphasic illness is seen in severe cases, with fever at the onset of illness and again in the second week of illness at the time of acute deterioration and ARDS (https://youtu.be/Om9VTacb6VM; Kujawski, Nat Med), and a biphasic need for intubation (on day 3-4 and again on around day 9 after symptom onset) (Argenziano, BMJ); in patients with acute deterioration, viral load may indicate whether antiviral or immunomodulatory therapy is more likely to be beneficial (Lescure, Lancet Infect Dis; Joynt, Lancet Infect Dis)

Laboratory Findings. A variety of hematologic, biochemical, inflammatory and coagulation biomarkers have been identified (Henry, Clin Chem Lab Med; Ponti, Crit Rev Clin Lab Sci); lymphopenia (Tan, MedRxiv), eosinopenia (Li, MedRxiv) and elevated NLR (neutrophil-to- lymphocyte ratio, Qin, Clin Infect Dis; Liu, J Infect) are predictive of more severe illness; increasing RDW (red blood cell distribution width) during hospitalization correlates with morality risk (Foy, JAMA Netw Open); a score based on demographic features, vital signs and common laboratory tests (lymphocyte count, creatinine, CRP, LDH) is reported to have 80% sensitivity and 76% specificity in predicting the likelihood of severe respiratory failure (Bartoletti, Clin Microbiol Infect); elevated LDH, ferritin, LFTs, IL-2R/IL-6/IL-10/TNFα and reduced CD4+/CD8+ T cells are common (Chen, J Clin Invest; Pedersen, J Clin Invest; Wang, JCI Insight), and patients with elevated inflammatory markers are more likely to require respiratory Last updated 4 October 2020 support (Manson, Lancet Rheumatol); procalcitonin may be elevated; lymphopenia, elevated D- dimer ≥2.0 mcg/ml, CRP, procalcitonin predictive of mortality (Paranjpe, MedRxiv; Zhang, J Thromb Haemost); soluble urokinase plasminogen activator (suPAR) has been suggested as an early predictor of respiratory failure (Rovina, Crit Care); an international consortium of 96 hospitals has integrated clinical and laboratory data for 27,584 cases and suggests that D-dimer levels may be more indicative of persistent illness than CRP (Brat, NPJ Digit Med)

Hypercoagulable State. Abnormal coagulation parameters are common and associated with increased mortality risk (Tang, J Thromb Haemost; Lillicrap, J Thromb Haemost; Violi, Throm Haemost); coagulopathy, endothelial damage, complement activation, macrophage activation/hyperferritinemia, platelet activation, renin-angiotensin dysregulation and inflammation may contribute to thrombosis (Connors, Blood; Java, JCI Insight; Hanff, Am J Hematol); endothelial cell infection may play a central role in COVID-19 manifestations in the lungs, heart, brain, kidney, vasculature and skin (Libby, Eur Heart J); inflammatory thrombotic process primarily in the lungs is common to SARS and COVID-19 (McGonagle, Lancet Rheumatol); patients with critical COVID-19 develop multiple perfusion defects consistent with diffuse circulatory dysfunction and microthrombi (Beenen, Thromb Res); anti-phospholipid antibodies or lupus anticoagulant may be detected in the setting of coagulopathy and multifocal thrombosis (Zhang, NEJM; increased platelet activation and aggregation has been reported (Manne, Blood); Harzallah, J Thromb Haemost; Bowles, NEJM); thromboelastography more consistent with an inflammatory hypercoagulable state than with DIC (Panigada, J Thromb Haemost; Spiezia, Thromb Haemost; Lawicki, MedRxiv) and correlates with thrombotic events; markers of endotheliopathy (e.g., VWF antigen, soluble thrombomodulin) are commonly elevated and correlate with mortality (Goshua, Lancet Haematol); hypercoagulability may result from increased angiotensin II expression, resulting in increased expression of plasminogen activator inhibitor C-1, as well as from COVID-19-related inflammation (Mortus, JAMA Network Open); 8% of non-ICU patients hospitalized with COVID-19 and 23% of ICU patients develop venous thromboembolism (Nopp, Rev Thromb Haemost); ~30% incidence of thrombotic complications in ICU patients with COVID-19 (Klok, Thromb Res); 16% of patients hospitalized with COVID-19 in a large NYC cohort had a thrombotic event, and elevated D-dimer at presentation was predictive (Bilaloglu, JAMA); pulmonary arterial thrombosis may be observed in fatal cases despite prophylactic anticoagulation (Lax, Ann Intern Med); high risk of venous thromboembolism and pulmonary embolism in patients with severe COVID-19, with adverse outcomes (Lodigiani, Thromb Res), even on therapeutic anticoagulation (Llitjos, J Thromb Haemost; Ren, Circulation; Zhang, Circulation); most patients admitted to ICU with COVID-19 may have DVT (Nahum, JAMA Network Open; Voicu, JACC)

Radiographic Findings. Chest CT shows multifocal ground-glass opacities, but findings overlap with other causes of viral pneumonitis (Chung, Radiology; Zhou, AJR; Shi, Lancet Infect Dis; Li, AJR); most discriminating chest CT features of COVID-19 pneumonia are peripheral distribution, ground glass opacities and vascular thickening (Bai, Radiology); other chest CT findings include air-bronchograms, crazy paving pattern, consolidation, patchy infiltrates, spider-web sign, or cord-like and nodular lesions; pleural thickening sometimes seen but lymphadenopathy and pleural efflusions are rare (Zhu, J Med Virol); may be abnormal in asymptomatic individuals Last updated 4 October 2020

(Hu, Sci China Life Sci); consensus guidelines for the use of chest imaging are available (Rubin, Radiology); electrical impedance tomography suggests distinctive pulmonary physiology in some patients with severe COVID-19 with more ventilated/nonperfused units, consistent with vasculopathy (Mauri, Crit Care Med)

Ultrasound. Lung ultrasound may show pleural thickening, B lines and consolidation (Peng, Intensive Care Med)

Risk Factors and Outcomes. Case-Fatality Rate is estimated to be ~1.38% with a strong age- gradient (Verity, MedRxiv; Wu, Nature Med; Yang, MedRxiv fatality risk); crude CFR in US and Canada was 5.4% and 4.9%, respectively, and estimated to be 1.6% and 1.78% after adjustment for survival and reporting bias (Abdollahi, CMAJ); patients admitted to ICU within 1 week of symptom onset have higher mortality, perhaps indicative of more rapid disease progression (Azoulay, Intensive Care Med); higher CFR reported in Italy, attributable to more patients ≥70 years of age (Onder, JAMA); the age-adjusted median case-fatality rate in 9 countries was determined to be 1.9%-- variability amont 95 countries was 13 times greater than could be accounted for by age differences along (Sudharsanan, Ann Intern Med); age-specific infection fatality ratios vary widely across countries and may provide an indication of population immunity (O’Driscoll, MedRxiv); low levels of national preparedness and population characteristics such as obesity, age and GDP are associated with national caseload and mortality (Chaudhry, EClinMed); mean time from symptom onset to hospital discharge or death is 18.1 days (Byrne, BMJ Open); most deaths occur in patients with co-morbidities including cardiovascular/pulmonary disease and diabetes (Wu, JAMA; Zhou, Lancet; Guan, MedRxiv; COVID-19 Response Team, MMWR), but frailty may be a better predictor of mortality than age or comorbidity (Hewitt, Lancet Public Hlth); some young adults (aged 18-34) with COVID-19 experience adverse outcomes, particularly in individuals who are Black or Hispanic and individuals with obesity, hypertension or diabetes (Cunningham, JAMA Intern Med); risk factors for mechanical ventilation and death include male sex, age, non-White race, obesity, chronic kidney/liver disease, cardiovascular disease, cancer and dementia (Fried, Clin Infect Dis; Harrison, PLoS Med; Ioannou, JAMA Netw Open; Jackson, Clin Infect Dis); risk stratification on the basis of age, sex, comorbidities, respiratory rate, O2 saturation, level of consciousness, urea and CRP (“4C Mortality Score”) can predict mortality with AUC 0.77-0.79 (Knight, BMJ); another risk calculator is based on age, nursing home residence, comorbidities, obesity, respiratory symptoms, respiratory rate, fever, lymphocyte count, albumin, troponin, CRP (Garibaldi, Ann Intern Med); a large UK study analyzing health records of >17 million adults found a strong correlation between mortality and age, sex, obesity, diabetes, recent diagnosis of malignancy and organ transplant (Williamson, Nature); even modestly increased BMI is associated with increased risk of hospitalization (Hamer, PNAS), and obesity is associated with a markedly higher risk of death in male patients less than 60 years of age (Tartof, Ann Intern Med); large increases in mortality from heart disease, diabetes and other conditions coincide with the COVID-19 pandemic, potentially due to delayed access to health care or extra-respiratory manifestations of COVID-19 (Woolf, JAMA); better glucose control was associated with more favorable clinical outcomes in diabetics with COVID-19 (Zhu, Cell Metab); illness may be more severe in Blacks (Gold, MMWR); higher in-hospital mortality in Blacks hospitalized with COVID- Last updated 4 October 2020

19 has been attributed to demographic characteristics and greater severity at presentation (Price-Haywood, NEJM), and the disproportionate impact of COVID-10 on racial and ethnic minorities may be due to long-standing disparities that result in a higher prevalence of chronic medical conditions and lower health care access (Tai, Clin Infect Dis); Black racial background remained an independent predictor of hospital mortality even after adjustment for demographic and clinical confounders in one study (Perez-Guzman, Clin Infect Dis), but another study of 11,210 patients with COVID-19 at 92 U.S. hospitals did not detect a difference in mortality between hospitalized Black and White patients after adjustment for sociodemographic factors and comorbidities (Yehia, JAMA Netw Open); Black race is associated with risk of COVID-19 and hospitalization but not ICU admission (Munoz-Price, JAMA Netw Open); outcomes in racial/ethnic minorities are not worse after adjustment for age, sex, socioeconomic status and comorbidities (Kabarriti, JAMA Netw Open); risk of PCR-positivity higher in non-English speaking individuals/immigrants (Kim, JAMA Netw Open); higher levels of TMPRSS2 protease expression in Blacks may also be a contributing factor to racial disparaties in COVID-19 burden (Bunyavanich, JAMA racial ethnic); a 50kb gene cluster on chromosome 3 inherited from Neanderthals and carried by half of people from South Asia and ~16% of people in Europe is associated with higher risk of respiratory failure from COVID-19 (Zeberg, Nature); although CFR is highest in older patients, a substantial number of patients aged 20-64 are requiring hospitalization and ICU admission (COVID-19 Response Team, MMWR; Myers, JAMA); hypoxemia is independently associated with mortality (Xie, Mayo Clin Proc) and monitoring of oxygen saturation (SpO2/FiO2) has been recommended (Von Vopelius-Feldt, MedRxiv); dyspnea, ARDS and cardiac injury (elevated troponin T) are associated with fatal outcomes (Chen, BMJ; Guo, JAMA Cardiol; Gupta, JAHA); hyperkalemia, acute kidney injury and hypoxic encephalopathy may also be seen; a New York study of 5,449 patients admitted to a New York hospital system with COVID-19 found acute kidney injury in 37%, temporally associated with respiratory failure, which carried a poor prognosis (35% died, 39% still hospitalized) (Hirsch, Kidney Int; another NYC study found that most COVID-19 patients in the ICU developed acute kidney injury, and 35% required dialysis (Argenziano, BMJ); mortality in patients requiring ICU admission may be ~25% or more (Grasselli, JAMA); high SOFA score is predictive of mortality (OR 5.65; Zhou, Lancet); 28-day survival of 61% has been reported in patients requiring ICU admission (Wang, AJRCCM); reported mortality in patients requiring mechanical ventilation has varied widely from 17-88%, but it is unclear whether patient populations are comparable and some estimates may be inflated due to incomplete follow-up (Richardson, JAMA; Auld, MedRxiv; Petrilli, BMJ; Docherty, MedRxiv; Ziehr, NEJM); pooled ICU mortality in a meta- analysis of 10,150 patients was 41.6% (Armstrong, Anaesthesia); out of 2,215 patients admitted to ICUs in the US, 40% died, but the risk-adjusted proportion of patients who died varied widely among institutions, from 7-81% (Gupta, JAMA Intern Med); out of 3,988 COVID- 19 patients admitted to ICUs in Lombardy, Italy, 87% required invasive mechanical ventilation and 53% died in-hospital (Grasselli, JAMA Intern Med); 22% of COVID-19 patients at two NYC hospitals were critically ill; at follow-up, 79% required mechanical ventilation, 39% had died and 37% remained hospitalized (Cummings, Lancet); a nationwide study in Germany, which did not have a shortage of ICU beds, found 53% in-hospital mortality for patients who required invasive mechanical ventilation, which rose to 72% in those 80 years or older (Karagiannidis, Lancet Respir Med); patients requiring mechanical ventilation frequently require vasopressor support Last updated 4 October 2020

(Goyal, NEJM); risk factors for severe illness and mortality are age, obesity, comorbidities, dyspnea/tachypnea, hemoptysis, hypotension, loss of consciousness, O2 sat <88% and elevated D-dimer/IL-6/ferritin/CRP/NLR, azotemia/elevated LFTs/troponin (Petrilli, BMJ; Lighter, Clin Infect Dis; Wang, MedRxiv; Liang, JAMA Intern Med; Mikami, J Gen Intern Med); from Feb-Apr 2020, COVID-19 was calculated to have caused 21 times more deaths than seasonal influenza in NYC (Faust, MedRxiv); individuals with the type A-positive blood group are more likely to have respiratory failure, and type O has a protective effect; (Ellinghaus, NEJM; Zhao, Clin Infect Dis ABO); a 3p21.31 gene cluster was also identified as a possible genetic susceptibility locus

Cardiac Complications. Pre-existing cardiovascular disease is a risk factor for more severe disease, and COVID-19 can have a variety of cardiovascular complications (Driggin, JACC; Guzik, Cardiovasc Res); cardiac injury more common in severe illness (Hui, MedRxiv), which can be accompanied by arrhythmias and may be due to the presence of ACE2 on cardiac myocytes (Zheng, Nat Rev Cardiol; Wang, JAMA clinical); patients presenting with acute ST-elevation myocardial infarction in the setting of COVID-19 had lower lymphocyte counts and elevations of troponin T, D-dimer and CRP along with evidence of multivessel thrombosis and poorer outcomes (Choudry, JACC); in vitro infection of human cardiac cells results in sarcomeric fragmentation and anucleate cells parallelling findings from autopsy specimens from COVID-19 patients (Perez-Bermejo, BioRxiv); cardiac pathology in COVID-19 ranges from interstial macrophage infiltration to multifocal lymphocytic myocarditis (Basso, Eur Heart J); evidence of cardiac injury may be seen in ~22% of critically ill patients with COVID-19 (Clerkin, Circulation); cardiac injury is an independent risk factor for in-hospital mortality (Shi, JAMA Cardiology); 58% increase in out-of-hospital cardiac arrest observed during the COVID-19 outbreak in Italy (Baldi, NEJM); 14% of critically ill patients have in-hospital cardiac arrest, and only 7% survive to hospital discharge with preseved neurological status (Hayek, BMJ); cor pulmonale may occur, most likely due to thromboembolic disease (Creel-Bulos, NEJM); stress cardiomyopathy (also called Takotsubo syndrome) can be a complication of COVID-19 (Jabri, JAMA Network Open); cardiac MRI may detect abnormalities in patients recently recovered from COVID-19, suggesting potential cardiovascular complications, but the long-term consequences of these findings are unknown (Puntmann, JAMA Cardiol; Rajpal, JAMA Cardiol)

Neurologic Complications. Neurologic abnormalities are not uncommon but may result from indirect mechanisms (Mao, JAMA Neurol); endothelial injury may lead to disruption of the blood-brain barrier and inflammatory disruption of neuronal function (Iadecola, Cell); studies of human brain organoids, transgenic mice and human autopsy specimens suggest that SARS-CoV- 2 may be able to infect neurons under certain conditions, perhaps in areas of focal ischemia (Song, BioRxiv); acute CVA may be a presentation of COVID-19, including patients <50 yrs of age (Oxley, NEJM); ischemic stroke is an unusual complication of COVID-19 and most cases are cryptogenic (Yaghi, Stroke); Guillain-Barré Syndrome has been reported (Toscano, NEJM); other neurologic presentations include headache, impaired consciousness, dizziness, seizures and encephalopathy (Zubair, JAMA Neurol; Ellul, Lancet Neurol; Paterson, Brain); neuropsychiatric presentations include acute psychosis (Varatharaj, Lancet Psychiatr; Agarwal, J Neurol); neuropathology of patients who died with COVID-19 found evidence of acute hypoxic injury but no encephalitis or evidence of infection of neurons, glia, endothelium or immune cells Last updated 4 October 2020

(Solomon, NEJM); microvascular and hypoxic injury are the most characteristic neuropathological findings (Jaunmuktane, Acta Neuropathol)

Cytokine Storm. “Cytokine storm” and elevated IL-6 levels produced by macrophages seen in severe illness (Wang, Clin Infect Dis; Chen, MedRxiv; Wang (2), MedRxiv; Yang, MedRxiv; Moore, Science; Tay, Nat Rev Immunol; Merad, Nat Rev Immunol; Pearce, Exp Opin Ther Target), although some have questioned characterizing the hyperinflammatory state in COVID- 19 as a “cytokine storm” since IL-6 levels are considerably less markedly elevated compared to sepsis/ARDS (Sinha, JAMA Intern Med; Kox, JAMA); IL-6 levels ≥80 pg/ml associated with 22- fold increased risk of respiratory failure (Herold, J Allerg Clin Immunol); elevated IL-6 and TNFα are predictive of severe disease and death and can inform the use of immunomodulatory agents (Del Valle, Nat Med)

Immunocompromised Hosts. Rates of hospitalization in patients on immunosuppressive therapy in NYC were comparable to the general population (Haberman, NEJM); some immunocompromised populations have been reported to have a generally favorable prognosis (Minotti, J Infect; Tschopp, Am J Transpl), but a higher case-fatality rate has been observed for patients with cancer in NYC (Mehta, Cancer Discov), and kidney transplant recipients in NYC had a high early mortality (28% at 3 wks) (Akalin, NEJM); others have reported that immunocompromised patients (autoimmune disease, cancer, organ transplant) are less likely to develop moderate-severe ARDS (Monreal, Res Sq preprint); overall mortality in hospitalized SOT recipients with COVID-19 is 20.5%, comparable to the general population (Kates, Clin Infect Dis); patients with cancer are more likely to develop severe illness, particularly if they have recently received chemotherapy (Kuderer, Lancet; Tian, Lancet Oncol; Yang, Lancet Oncol; Garassino, Lancet Oncol); a multicenter study involving 66 Italian hospitals found worse outcomes in patients with hematologic malignancies (standardized mortality ratio 2.04) (Passamonti, Lancet Haematol); nevertheless, outcomes in hematopoietic cell transplant and CAR-T therapy recipients are generally favorable (Shah, J Clin Invest); among cancer patients with COVID-19, age ≥65 and treatment with immune checkpoint inhibitors are risk factors for hospitalization and severe outcomes (Robilotti, Nat Med); clinical presentation in patients with HIV is variable and largely dependent on other comorbidities (Blanco, Lancet HIV; Gervasoni, Clin Infect Dis; Vizcarra, Lancet HIV) and HIV-infected patients of Black ethnicity may be at higher risk for severe outcomes (Childs, Clin Infect Dis); a multicenter registry of patients with HIV found that severe COVID-19 infections correlated with age, low CD4 counts and comorbidities such as hypertension and chronic lung disease, but not with HIV viremia or antiretroviral regimen (Dandachi, Clin Infect Dis); liver fibrosis may be a risk factor for COVID-19 severity and mortality (Sterling, J Infect Dis)

Pregnancy. Only very rare evidence of intrauterine or transplacental transmission (Chen, Lancet; Schwartz, Arch Pathol Lab Med; Chen, NEJM), but pregnant women have an increased risk of hospitalization, ICU admission and mechanical ventilation (Ellington, MMWR); severe COVID-19 in pregnancy can be associated with adverse pregnancy outcomes including preterm delivery, pregnancy loss and maternal death (Delahoy, MMWR); higher risk of pre-eclampsia in pregnant women with COVID-19 (Ahlberg, JAMA); comorbidities, high maternal age and high Last updated 4 October 2020

BMI are risk factors for more severe COVID-19 in pregnancy (Allotey, BMJ); transplacental transmission from a viremic mother who was infected in the third trimester and developed placental infection (Vivanti, Nat Commun); in another case of congenital SARS-CoV-2 infection, the newborn did well (Kirtsman, CMAJ); detection of antibodies including IgM in newborns of SARS-CoV-2-infected mothers has also suggested possible in utero infection, but virus was not detected (Dong, JAMA; Zeng, JAMA; Kimberlin, JAMA); may be an increased risk of preterm delivery (Mullins, Ultrasound Obstet Gynecol; Wang, Clin Infect Dis) and pregnancy loss has also been reported (Galang, Obstet Gynecol); a case of preeclampsia in the 2nd trimester associated with placental infection reported (Hosier, MedRxiv); 88% of COVID-positive pregnant women admitted for delivery during the NYC epidemic were asymptomatic (Sutton, NEJM); breastfeeding by SARS-CoV-2-positive mothers appears to be safe if appropriate precautions are taken (Salvatore, Lancet Child Adolesc Health); in a small series of breastfeeding women who had COVID-19, viable virus was not detected in breast milk even though viral RNA was detected in one sample (Chambers, JAMA)

Impact on Surgical Outcomes. Asymptomatic patients with COVID-19 who undergo elective surgery may have unexpectedly poor outcomes, with 44% requiring ICU care and 21% mortality (Lei, EClinicalMedicine); a higher incidence of post-operative pulmonary complications is seen in patients with perioperative COVID-19 (COVIDSurg Collaborative, Lancet); this warrants routine pre-operative screening

LABORATORY DIAGNOSIS

Diagnostic Tests. Diagnostic testing plays an extremely important role in COVID-19 control, but there are still major unmet needs in the domestic diagnostic pipeline (Cheng, Ann Intern Med; Caruana, Clin Microbiol Infect); PCR/Ab test performance is reviewed in (Jarrom, BMJ EBM); testing availability in the U.S. has been uneven and inadequate (Schneider, NEJM); although the emergency use authorization (EUA) process for diagnostics has been workable, the FDA has recently suggested that a more centrally coordinated approach to development and validation of novel diagnostics should be considered for future pandemics (Shuren, NEJM); controversies in COVID-19 diagnostics include the use of PCR for test-of-cure, reporting Ct values, pooling specimens, deployment of research personnel to perform clinical testing, and widespread screening of asymptomatic populations to allow societal reopening (Binnicker, J Clin Microbiol); in low prevalence settings, such as screening studies, sample pooling can conserve PPE and testing reagents (Hogan, JAMA; Lohse, Lancet Infect Dis; Yelin, Clin Infect Dis); modeling suggests that diagnostic testing was a major limiting factor in limiting the assessment of transmission during the initial weeks of the outbreak in the U.S. (Perkins, PNAS); demographic data, labs (CRP, LDH, ferritin, neutrophil/lymphocyte counts) and x-ray/CT can be used for a presumptive diagnosis of COVID-19 with 96% sensitivity and 95% specificity (Kurstjens, Clin Chem Lab Med); RT-PCR is the standard method for SARS-CoV-2 detection, and sensitive commercial assays are available (Zhen, J Clin Microbiol); IDSA diagnostic guidelines have been published (Hanson, IDSA guidelines); point-of-care (POC) tests are under development or being assessed (Loeffelholz, Emerg Microbes Infect; Joung, NEJM; Gibani, Lancet Microbe) and a few Last updated 4 October 2020 have received emergency use authorization (Dinnes, Cochrane Database); answers to FAQs may be found in (Fang, Clin Infect Dis)

Clinical Specimens for Viral Detection by Nucleic Acid Amplification Tests (NAAT). Sequential utility of specimen types: upper respiratory specimens more sensitive early in illness, lower respiratory tract specimens more sensitive later, fecal specimens remain positive the longest (Song, J Med Virol); some false negatives are probably due to improper sampling technique (Piras, Otolaryngol Head Neck Surg); PCR of Sputum or BALF is more sensitive than upper respiratory specimens (Wang, JAMA: Han, Lancet Infect Dis; Lin, MedRxiv; Loeffelholz, Emerg Microbes Infect; Cheng, Ann Intern Med; Wu, Travel Med Infect Dis) and parallels higher viral load in sputum compared to nasopharyngeal or throat swabs (Zou, NEJM; Yu, Clin Infect Dis); viral load at the time of presentation shows some correlation with disease severity and prognosis (Liu, Lancet Infect Dis; Pujadas, Lancet Respir Med; Magleby, Clin Infect Dis; Westblade, Cancer Cell), although not all have observed a relationship between initial viral load and clinical progression or mortality (Argyropoulos, Am J Pathol); differences observed in the sensitivity of primer-probe sets used to detect SARS-CoV-2, with E gene (Charité), ORF1 (HKU) and N1 (US CDC) more sensitive than RdRp-SARSr (Charité) (Vogels, MedRxiv); panels with multiple RT-PCR targets can mitigate the risk of loss of sensitivity due to genomic variants (Penarrubia, IJID); most commercial assays are comparably sensitive and specific (Lieberman, J Clin Microbiol), but the Abbott ID NOW rapid NAAT assay is reported to have lower specificity than conventional PCR assays (Basu, J Clin Microbiol)

Limitations of PCR. Sensitivity of RT-PCR is highest during first few days of symptoms (Kucirka, Ann Intern Med); a negative NP/OP swab does not rule-out COVID-19 (Winichakoon, J Clin Microbiol; Long, Eur J Radiol; Woloshin, NEJM); yield of re-testing depends on local prevalence (Green, MedRxiv; Long, Clin Infect Dis; Williams, MedRxiv); PCR assays may revert to positive in a minority of patients, clinical significance of this is unknown (Yuan, Clin Infect Dis) but patients who re-test positive have no obvious signs of disease recurrence, progression or transmission (An, MedRxiv); it has been suggested that widespread surveillance with an insensitive but rapid and widely available test might be an effective approach for limiting COVID-19 community spread (Mina, NEJM), but concerns have been raised about the practicality of such an approach (Pettengill, J Clin Microbiol), and it has been argued that proposed strategies based on repeated self-testing are unsound and likely to fail because of problems from both false-positives and false-negatives (Deeks, BMJ); false-positives from screening of low prevalence populations may be highly disruptive (Surkova, Lancet Respir Med), so rapid confirmation of positive test results would be very important

Other Specimens. Virus detected in urine, blood, anal swabs, saliva (To, Clin Infect Dis; Peng, MedRxiv; Tang, J Clin Microbiol; Caulley, Ann Intern Med); has been detected in breast milk, but the clinical significance is uncertain (Tam, Clin Infect Dis); self-collected tongue, nasal, saliva or mid-turbinate swabs appear comparable to health care worker-collected nasopharyngeal swabs and can reduce PPE use and patient discomfort (Tu, NEJM; Wehrhahn, MedRxiv; Kojima, MedRxiv; Wyllie, NEJM; Williams, J Clin Microbiol; Jamal, MedRxiv; Berenger, MedRxiv; Wong, Clin Infect Dis; McCulloch, JAMA Netw Open), although some have found mid-turbinate swabs Last updated 4 October 2020 to be less sensitive than nasopharyngeal swabs (Pinninti, Clin Infect Dis); viral loads in saliva reportedly comparable to those in nasopharyngeal swabs and may be detected up to 20 days post-symptom onset, correlating with illness severity (Khurshid, MedRxiv; McCormick-Baw, J Clin Microbiol), but others have found lower sensitivity or viral load in saliva (Becker, MedRxiv) or oropharyngeal swab samples (Hung, Lancet Infect Dis; Patel, Clin Infect Dis); assays that can sensitively detect SARS-CoV-2 in saliva without extraction or special collection devices might improve the accessibility of diagnostic testing and relieve demands on reagents and PPE (Vogels, MedRxiv; Ranoa, BioRxiv); self-collected saliva sampling can facilitate mass screening (Yokota, Clin Infect Dis); viremia/RNAemia correlates with disease severity, lymphopenia, organ damage, inflammation/elevated IL-6, ICU admission and in-hospital mortality (Fajnzylber, MedRxiv; Chen, MedRxiv; Xu, Clin Infect Dis RNAemia; Hagman, Clin Infect Dis; Veyer, Clin Infect Dis; Prebensen, Clin Infect Dis; Hogan, Clin Infect Dis)

Viral Shedding. Nasopharyngeal viral load declines over time regardless of clinical severity (Huang, Clin Infect Dis); PCR may continue to detect viral RNA for weeks (Ridgway, ICHE), but cultures of respiratory secretions in patients with mild illness become negative after 8 days (Woelfel, Nature); respiratory samples from COVID-19 patients with ≥8 days of symptoms are often culture-negative, suggesting a lack of infectivity despite PCR-positivity (Bullard, Clin Infect Dis), and correlate with lower quantitative PCR values (E gene Ct ≥24); one study has found viral shedding to last for 0-20 days post-symptom onset, with viral loads >7 log10 RNA copies/mL associated with detection of infectious virus, and a neutralizing Ab titer ≥1:20 associated with the absence of infectious SARS-CoV-2 (Van Kampen, MedRxiv); others have reported that the ability to recover virus in culture correlates with viral loads of 5.4-6.0 log10 genome copies/mL (Huang, J Clin Microbiol), and lower loads may not represent the presence of intact genomes; a Ct value >30 is suggestive of a non-infectious sample (Jefferson, MedRxiv); one study has defined a relationship between Ct value and likelihood of culture-positivity, ranging from 0% (Ct 34) to 50% (Ct 29) to 100% (Ct 18) (La Scola, Eur J Clin Micro Infect Dis); duration of viral shedding correlates with illness severity, even though neutralizing Ab may be detected after 10d post-symptom onset and tend to be higher in severe cases (Wang, J Clin Invest); more severely ill patients may continue to exhibit detectable viral RNA in lower respiratory tract specimens for weeks to months (Huang, AJRCCM; Zheng, BMJ; Xiao, Clin Infect Dis; Wajnberg, Lancet Microbe; Xiao, J Clin Virol), and more prolonged shedding of cultivable virus has been reported in patients with more severe illness (Folgueira, MedRxiv), but persistent viral PCR positivity is not associated with recurrent symptoms or transmission (Wu, JAMA Network Open); PCR-positivity occasionally persists for months (92 days; Wang, Medicine); viral RNA can also be found in stool for weeks; although there is currently little evidence of fecal-oral transmission (Pan, Lancet infect Dis; Gu, Gastroenterology; Wu, Lancet Gastroenterol Hepatol; Chan, Ann Intern Med; Cheung, Gastrotenterology; Xu, Nat Med), culturable SARS-CoV-2 has been recovered from fecal samples (Wang, JAMA; Xiao, Emerg Infect Dis), and virions have been observed by electron microscopy in intestinal tissue (Qian, Clin Infect Dis intestine)

Co-Infections. Co-infections may be present (Lin, Sci China Life Sci; Kim, JAMA), but a study of 162 consecutive patients in Italy found few respiratory co-infections with SARS-CoV-2, Last updated 4 October 2020 suggesting possible viral interference (Calcagno, Clin Microbiol Infect); see also Co-Infections section under TREATMENT below

Adjunctive Role of CT Scanning. Chest CT may show abnormalities even when PCR is negative (Fang, Radiology; Ai, Radiology); however, in low prevalence regions, positive predictive value of RT-PCR is far greater than that of chest CT (Kim, Radiology); chest findings consistent with COVID-19 may be detected as an incidental finding when patients with atypical presentations undergo spine/neck or abdomen/pelvis CT scanning (Hossain, Radiology); dual-energy CT may detect regions of decreased perfusion surrounded by a halo of higher perfusion indicative of disrupted pulmonary vasoregulation (Lang, Lancet Infect Dis)

Serology. Many issues relating to serologic testing remain to be defined (Theel, J Clin Microbiol; Cheng, Ann Intern Med serology; Hanson, IDSA guidelines), and serological tests will have important applications at both individual and population levels (Bryant, Sci Immunol); guidance for the use and interpretation of serologic testing has been published (Van Caeseele, CMAJ); limited clinical and experimental data suggest that recovery from COVID-19 may confer immunity to reinfection (Kircaldy, JAMA); it has recently been clearly shown that true reinfection with different strains of SARS-CoV-2 can occur, and the subsequent infection is usually but not always milder (To, Clin Infect Dis; Tillett, Lancet Infect Dis); the patient with asymptomatic reinfection lacked neutralizing Ab on second presentation but rapidly developed a neutralizing Ab response (To, Clin Infect Dis antibody); another case report of reinfection with milder clinical course was associated with the D614G variant and a poor neutralizing antibody response to the primary infection (Goldman, MedRxiv); other possible reinfections have been reported (Duggan, Am J Emerg Med), and an analysis of subjects with seasonal common cold coronaviruses suggests that immunity is short-lived (Edridge, Nat Commun), with reinfections often occurring 12 months later; Ab begins to be detected as viral load declines (Sethuraman, JAMA), so a combination of RT-PCR and serology may enhance case detection (Guo, Clin Infect Dis; Zhao, Clin Infect Dis 2; Zhang, J Infect Dis; Miller, FASEB J); serologic tests vary in sensitivity and specificity, ranging from 68-93% sensitivity for IgM and 65-100% for IgG, with high specificity for most assays (98%) (Okba, MedRxiv; Whitman, Nat Biotechnol; Caini, MedRxiv); validated serologic assays appear to have high sensitivity and specificity (Paiva, BioRxiv); pooled sensitivity is higher for chemiluminescent immunoassays (98%) than for ELISAs (84%), with 97- 99.7% specificity (Bastos, BMJ), while point-of-care serologic tests have approximately 52-68 % sensitivity and 96-100% specificity (Bond, J Infect Dis); IgG more sensitive than IgM (Dittadi, MedRxiv), but IgM and IgG exhibit similar initial kinetics (Jin, Int J Infect Dis; Xiang, Clin Infect Dis); IgA has lower specificity (Traugott, J Infect Dis); nearly 50% of symptomatic patients in NYC were IgG-positive (Reifer, Diagn Microbiol Infect Dis); seroconversion occurs 5-14d after symptom onset in hospitalized patients with COVID-19 (Grzelak, Sci Transl Med); sensitivity of serology is only 30% after 1 week but rises to over 90% in week 3 (Deeks, Cochrane; Long, Nat Med; To, Lancet Infect Dis; Lou, MedRxiv; Traugott, J Infect Dis); based on aggregate data, IgG from 25d-60d post-symptom onset would be an optimal window in which to test for prior exposure (Benny, MedRxiv); some have found that Ab titers correlate with disease severity (Zhao, Clin Infect Dis; Ou, MedRxiv), while others have found that titers inversely correlate with viral load but not necessarily with clinical outcomes (Ren, Clin Infect Dis); community Last updated 4 October 2020 seroprevalence comparable in children/middle-aged adults and lower in older adults (Stringhini, Lancet); commercial assays exhibit considerable variation in sensitivity and specificity (Lassauniere, MedRxiv), but SARS-CoV-2 serological tests in general do not appear to cross- react with seasonal coronaviruses (Amanat, Nat Med); antibodies directed to the receptor- binding domain (RBD) of the spike protein correlate with neutralizing antibodies (Premkumar, Sci Immunol); Ab directed against multiple sites on the S-protein, not only the receptor-binding domain, appear to be able to neutralize SARS-CoV-2 (Brouwer, Science); neutralizing antibodies prevent viral engagement with the ACE2 receptor by steric hindrance (Ju, Nature) and protect hamsters from SARS-CoV-2 challenge (Rogers, Science); antibodies capable of cross- neutralization of SARS-CoV and SARS-CoV-2 have been identified from B cells obtained from an individual with prior SARS (Wec, Science); neutralizing Ab may be detected within 6 days of diagnosis (Suthar, MedRxiv), but titers are variable in recovered patients and correlate with CRP and lymphopenia (Wu, JAMA Intern Med neutralizing Ab); although most patients develop neutralizing Ab, higher titers correlate with more severe clinical illness (Wang, Clin Infect Dis neutralizing Ab; Wang, BioRxiv); most convalescent sera do not contain high titers of neutralizing antibodies, although some RBD-specific antibodies have potent antiviral activity (Robbiani, Nature); assays for Ab to nucleocapsid protein may be more sensitive than assays of Ab to spike protein (Burbelo, J Infect Dis); however, anti-spike Ab may correlate with recovery, whereas anti-nucleocapsid Ab may correlate with progression (Atyeo, Immunity); 28% of blood donors in Lombardy had evidence of COVID-19 infection, but few had high titers of neutralizing antibodies (Percivalle, Euro Surveill); mild COVID-19 is associated with a more delayed Ab response with lower titers of neutralizing Ab (Rijkers, MedRxiv); false negative serologies may result from waning antibody levels, and sensitivity of serology in subclinical infection is presently unknown, but seroconversion may not occur in some asymptomatic infections or may be less durable (Zhang, Emerg Microbes Infect; Long, Nat Med asymptomatic); 20% of PCR- positive cases in a children’s and women’s hospital failed to seroconvert by 3 weeks (Brandstetter, Ped Allerg Immunol), but subclinical seroconversion was observed among HCWs and patients in a pediatric dialysis unit (Hains, JAMA); 2-9% of individuals in one study failed to seroconvert; non-seroconverters tend to be young with fewer comorbidities (Staines, MedRxiv); antibody titers do not necessarily mean immunity, and protection may be transient (Huang, MedRxiv; Edridge, MedRxiv), but SARS-CoV-2 infection protects macaques from rechallenge (Chandrashekar, Science), suggesting that natural infection elicits protective immunity; in an outbreak on a fishing boat with an 85% attack rate, 3 individuals with baseline neutralizing antibodies did not become infected, suggesting that neutralizing antibodies from prior infection are associated with immunity to re-infection (Addetia, J Clin Microbiol); the durability of antibody responses is uncertain-- although seroconversion is observed in most symptomatic individuals, Ab responses may wane by 3 mos post-infection (Seow, MedRxiv); only 42% of seropositive HCWs still had detectable antibodies 60 days later, and symptomatic individuals are more likely to remain seropositive (Patel, JAMA antibodies); a longitudinal survey of convalescent plasma samples found titers of neutralizing anti-RBD antibodies to wane within 4 months of symptom onset (Perreault, Blood); others have found IgG titers to stabilize at relatively high levels for 3 months or longer (Wu, MedRxiv sustained humoral response; Ripperger, MedRxiv), and a serosurvey in Iceland found that antibodies against SARS-CoV-2 did not decline within 4 months of diagnosis (Gudbjartsson NEJM antibody); IgG targeting RBD Last updated 4 October 2020 correlates with neutralizing Ab and can still be detected 75d post-symptom onset (Iyer, MedRxiv), but SARS-CoV-2 antibodies decline rapidly in persons with mild COVID-19 (half-life 36d, Ibarrondo, NEJM); predominantly Th1 T cell responses appear early in patients with severe COVID-19 and increase over time (Weiskopf, Sci Immunol), but others have found stronger Th1 T cell responses to correlate with better outcomes (Sattler, J Clin Invest); some patients with mild COVID-19 develop T cell responses without seroconversion (Gallais, MedRxiv), and robust memory T cell responses have been reported in both seronegative and seropositive individuals with asymptomatic or mild COVID-19 (Sekine, Cell); although antibody responses may be relatively short-lived, T cell responses appear to be more lasting (Altmann, Sci Immunol); long lasting memory T cell responses are detected in patients following SARS or COVID-19 (Le Bert, Nature)

Biosafety. Clinical lab safety recommendations have been published (Iwen, Am J Clin Pathol)

TREATMENT

Investigational Agents. A large number of potential therapeutic agents is under investigation (Sanders, JAMA); although many therapeutic trials for COVID-19 have been initiated, many are overlapping and potentially underpowered (Kouzy, JAMA Netw Open); the importance of maintaining standards in clinical research despite the urgency of a pandemic has been emphasized (London, Science); timing of antiviral, immunomodulatory and anticoagulant interventions must take into account the sequential progression of illness from viral to pulmonary to inflammatory and hypercoagulable phases of illness (Liu, Circulation; Siddiqi, J Heart Lung Transpl; Matheson, Science; Schiffer, OFID); whether investigational or approved, treatment decisions must carefully consider the individual physiology of the patient and the timing of the intervention, with guidance from biomarkers and immunophenotype (Fang, Clin Infect Dis evidence; Garcia-Vidal, Clin Infect Dis; Hall, Clin Infect Dis; Mathew, Science); cytokine profiles (IL-6, IL-8, TNFα, IL1β, GM-CSF, IL-10, I-33, IFNγ) can be used to select patients for immunomodulatory therapy (Burke, Respir Res); modeling based on viral dynamics indicates that antiviral therapy is likely to be helpful only if administered very early but is unlikely to have a major effect in severe patients (Gonçalves, MedRxiv); immunostimulation may be beneficial early, while immunosuppression is required later (Jamilloux, Autoimmun Rev)

Immunostimulators. Interferon/ribavirin/lopinavir-ritonavir was superior to lopinavir-ritonavir alone (Hung, Lancet); early reports of inhaled interferon-beta are reportedly promising (https://clinicaltrials.gov/ct2/show/NCT04385095); IL-7 has been reported to restore lymphocyte count and function in patients with COVID-19 (Laterre, JAMA Netw Open)

Remdesivir. Remdesivir is a potent inhibitor of SARS-CoV-2 RNA-dependent RNA polymerase (Gordon, J Biol Chem) that causes chain termination (Yin, Science) and is active in vitro (Wang, Cell Res); effective when given prophylactically or therapeutically in a macaque model of MERS- CoV (de Wit, PNAS) and when given early in a macaque model of COVID-19 (Williamson, BioRxiv); results of compassionate use of remdesivir reported in 63 patients (Grein, NEJM): Last updated 4 October 2020 clinical improvement observed in 68%, and 57% of intubated patients were able to be extubated, but no control group or viral load measurement, and adverse events seen in 60% (including elevated LFTs); a double-blind placebo-controlled RCT in China found no benefit from remdesivir, although there was a trend toward more rapid clinical improvement in patients with symptoms ≤ 10 days (Wang, Lancet); however, a randomized trial in 1,059 patients with COVID-19 and evidence of pulmonary involvement found that remdesivir shortened the median time to recovery from 15 to 11 days, with a trend toward reduced mortality that did not achieve significance (HR 0.70, 95% CI 0.47-1.04) (Beigel, NEJM); a review of the RCT data has concluded that low certainty evidence suggests that remdesivir may reduce time to improvement and decrease mortality but probably has no important impact on the need for invasive ventilation and may have little effect on hospital LOS (Rochwerg, BMJ); a 5 day course of remdesivir appears to be as effective as 10 days (Goldman, NEJM); an open label RCT in 596 patients with moderate COVID-19 showed a higher likelihood of improved clinical status in those receiving 5d of remdesivir but failed to show improved clinical status in those receiving 10d remdesivir (Spinner, JAMA)—many questions about remdesivir remain, including the optimal population to treat, the optimal duration of therapy, the effect on discrete clinical outcomes and the effect in combination with steroids (McCreary, JAMA)

Chloroquine/Hydroxychloroquine/Azithromycin. Hydroxychloroquine inhibits SARS-CoV-2 replication in vitro (Yao, Clin Infect Dis; Liu Cell DIscovery); anecdotal reports of clinical benefit of chloroquine/hydroxychloroquine (Gao, Biosci Trends); a non-randomized French open-label trial reported evidence of an anti-viral effect in vivo, particularly in combination with azithromycin (Gautret, MedRxiv/Int J Antimicrob Agents); a follow-up report from the same group reported only 4% poor outcomes with <1% deaths in 1,061 patients treated early with HCQ/AZ, and no adverse cardiac outcomes, but again there was no control group (Million, Travel Med Infect Dis); in contrast, a small RCT of hydroxychloroquine failed to show a beneficial effect on viral clearance or clinical resolution (Chen, J Zhejiang Univ), while another RCT involving 62 patients observed more rapid clinical resolution and fewer patients progressing to severe illness in hydroxychloroquine recipients (Chen, MedRxiv HCQ); a subsequent larger study by the French authors has reported a good virologic and clinical outcome in 72 of 74 additional recipients of combination therapy, but without a control group (Gautret, unpublished); concerns have been raised regarding the paper by Gautret, et al. and the use of hydroxychloroquine to treat COVID-19 outside research protocols (Kim, Ann Intern Med; Hulme, MedRxiv; Yazdany, Ann Intern Med); a different French group was unable to demonstrate rapid viral clearance in 11 patients receiving the same regimen of hydroxychloroquine and azithromycin, and one patient had treatment discontinued due to QT prolongation (Molina, Med Mal Infect); the addition of azithromycin to hydroxychloroquine in patients with severe COVID-19 did not improve clinical outcomes (Furtado, Lancet); some supporting data reported from a multicenter retrospective observational study in Michigan (n=2,541), in which hydroxychloroquine use was associated with reduced mortality (13.5% vs 26.4%), but treatment was non-randomized (Arshad, IJID); hydroxychloroquine 480 mg/d x 5d in patients hospitalized with COVID-19 was associated with lower mortality (aHR 0.70) in a large retrospective study in Belgium (n=8,075; Catteau, Int J Antimicrob Agents); hydroxychloroquine is suggested to act as an ionophore that enhances zinc entry into cells, and the addition of zinc Last updated 4 October 2020 to hydroxychloroquine/azithromycin was reported to reduce mortality in a retrospective observational study (Carlucci, MedRxiv); acute renal failure is a risk factor for QTc prolongation on hydroxychloroquine/azithromycin, but baseline QTc is not (Chorin, Nat Med); based on PK studies of hydroxychloroquine in patients with COVID-19, a loading dose of 800 mg followed by 200mg BID for 7 days has been suggested (Perinel, Clin Infect Dis)

Additional Studies of Hydroxychloroquine. A growing body of evidence is failing to support a clinical benefit of hydroxychloroquine or chloroquine in COVID-19, with or without azithromycin; an FDA emergency use authorization for hydroxychloroquine was criticized as polically motivated and was subsequently revoked as increasing numbers of studies suggested that the drug was ineffective (Thomson, JAMA); an RCT of 504 patients with confirmed mild- moderate COVID-19 failed to detect a benefit of hydroxychloroquine with or without azithromycin (Calvacanti, NEJM); the RECOVERY trial involving 4,716 patients hospitalized with COVID-19 found that hydroxychloroquine was associated with a reduced likelihood of being discharged from the hospital alive at 28d (60.3% vs 62.8%) (Horby, MedRxiv); a double-blind placebo-controlled RCT found that prophylactic hydroxychloroquine fails to prevent symptomatic infection after SARS-CoV-2 exposure (Boulware, NEJM); an RCT of hydroxychloroquine vs placebo in 423 patients with early mild COVID-19 failed to demonstrate a significant impact on symptom severity (Skipper, Ann Intern Med); an RCT of hydroxychloroquine in China (n=75 per group) failed to detect an effect on viral clearance (Tang, BMJ); an open-label multicenter RCT in Spain found that early hydroxychloroquine treatment failed to reduce nasopharyngeal viral load or shorten the time to symptom resolution (Mitja, Clin Infect Dis); a retrospective French study (n=181) of patients with COVID- 19 and hypoxemia found no significant reduction in ICU transfers, ARDS or mortality (Mahevas, MedRxiv)—8 patients had to discontinue hydroxychloroquine due to QTc prolongation or AV block; a retrospective of 368 VA patients found higher mortality in recipients of hydrochloroquine (27.8%) or hydrochloroquine plus azithromycin (22.1%) compared to no hydrochloroquine (11.4%), although selection bias and residual confounding cannot be excluded (Magagnoli, MedRxiv); receipt of hydroxychloroquine and/or azithromycin was not associated with lower mortality in 1438 patients hospitalized with COVID-19 in New York State, but patients were not randomized (Rosenberg, JAMA); an observational study of 1,446 consecutive patients in a NYC medical center failed to detect a benefit of hydroxychloroquine on prevention of intubation or death (Geleris, NEJM); chronic HCQ does not prevent COVID-19 or severe/fatal outcomes in patients treated for rheumatologic diseases (Mathian, Ann Rheum Dis; Gendelman, Autoimmun Rev; Konig, Ann Rheum Dis; Gentry, Lancet Rheumatol); analysis of more than 30,000 individuals taking hydroxychloroquine for RA/SLE found no evidence of protection against COVID-19 mortality (Rentsch, MedRxiv); HCQ was ineffective in hamster and macaque models of SARS-CoV-2 infection (Rosenke, BioRxiv; Kaptein, BioRxiv)

Tocilizumab and Other Immunomodulators. Multiple targets for immunomodulatory therapeutic intervention (Alijotas-Reig, Autoimmune Rev); possible benefits of tocilizumab (IL- 6RA) or other immunomodulators in patients with severe illness or cytokine storm, improving oxygenation and reducing the need for mechanical ventilation (Liu, MedRxiv; Xu, PNAS; Mehta, Lancet; Price, Chest; McCarthy, Respirology), although clinical responses may be variable (Luo, J Last updated 4 October 2020

Med Virol); preliminary results or Roche phase III COVACTA trial of tocilizuman failed to meet its primary endpoint, although a positive trend in time to discharge was observed (Roche, Covacta press release); retrospective studies have found lower mortality in tocilizumab recipients (Roumier, MedRxiv; Klopfenstein, Med Mal Infect; Somers, MedRxiv) and a reduced risk of invasive ventilation or death and shorter duration of vasopressor support (Guaraldi, Lancet Rheumatol; Kewan eClinicalMedicine); an observational study involving patients with critical COVID-19 in 13 New Jersey hospitals found tocilizumab administration (n=210) to be associated with lower mortality (HR 0.64) (Biran, Lancet Rheumatol); a retrospective study from Spain found a tocilizumab treatment to be associated with lower mortality, but not combination therapy with corticosteroids (Rodriguez-Bano, Clin Microbiol Infect); a meta-analysis of 10 observation studies found 12% mortality reduction with tocilizumab that has not yet been confirmed in RCTs (Malgie, Clin Infect Dis); reconciling the differences in observational and RCT data reported thus far are likely to require additional trial data (Campochiaro, Lancet Rheumatol); 2 patients treated with tociluzumab still progressed to macrophage activation syndrome, and one developed viral myocarditis (which may have resulted from immunosuppression) (Radbel, Chest); elevations in D-dimer following tocilizumab have also been reported (Price, Chest); Il-6-driven immune dysregulation with macrophage activation syndrome and impaired antigen presentation is partially rescued by tocilizumab, with an increase in lymphocyte count and HLA-DR expression (Giamarellos-Bourbolis, Cell Host Microbe); however, IL-6 inhibition is associated with an increased risk of secondary infections (Kimmig, MedRxiv; Somers, MedRxiv); other IL-6 antagonists like sarulimab have also been associated with clinical improvement and reduced O2 requirement (De Lusignan, Lancet Infect Dis; Gremese, eClinMed), and siltuximab was associated with a decline in CRP but variable clinical responses (Gritti, MedRxiv); Leronlimab (CC5-blocking Ab) given to patients with critical COVID-19 and elevation of IL-6/CCR5 was followed by a rapid decline in inflammatory biomarkers and reduced viral load (Patterson, MedRxiv); IL-1 is upstream of IL-6 production, and early IL-1 receptor blockade with anakinra can also reduce CRP, oxygen requirements and days of ventilatory support (Cauchois, PNAS); anakinra was associated with clinical improvement in 72% of patients with hyper-inflammation in the setting of COVID-19 (Cavalli, Lancet Rheumatol), as well as reduced need for ventilation and lower mortality (Huet, Lancet Rheumatol); a pilot study suggested an improvement in inflammatory parameters and clinical outcomes in recipients of baricitinib (JAK kinase inhibitor with both immunomodulatory and antiviral actions) (Cantini, J Infect); baricitiniib was associated with recovery in 11 of 15 patients with moderate-severe COVID-19, but superinfections and thrombotic events were also reported (Titanji, Clin Infect Dis); a reduction in IL-1/IL-6/TNFα with more rapid development of specific Ab has also been observed following baricitinib treatment (Bronte, MedRxiv); the JAK/STAT inhibitor ruxolitinib has been suggested to arrest disease progression in a pilot study of patients with severe COVID-19 (Capochiani, Front Med); combined JAK1/2 (ruxolitinib) and complement (eculizumab) inhibition has been reported to result in clinical improvement and reduced evidence of coagulopathy (Giudice, Front Pharmacol); acalabrutinib, a Bruton’s tyrosine kinase inhibitor, appeared to reduce inflammation and improve oxygenation in patients with severe COVID-19 (Roschewski, Sci Immunol); a small RCT of colchicine reported reduced progression in hospitalized patients (Deftereos, JAMA Network Open); a retrospective study found lower mortality in patients receiving statins after propensity score matching Last updated 4 October 2020

(Zhang, Cell Metab); anecdotal reports suggest that infusion of regulatory T (Treg) cells may be beneficial in patients with ARDS (Gladstone, Ann Intern Med)

Lopinavir-Ritonavir. No benefit from lopinavir-ritonavir seen in severe COVID-19 (Cao, NEJM); interferon/ribavirin/lopinavir-ritonavir was superior to lopinavir-ritonavir (Hung, Lancet); pharmacokinetic analyses suggest that plasma lopinavir concentrations are inadequate to limit SARS-CoV-2 replication (Smolders, Antiviral Ther)

Treatment of Coagulopathy. ISTH and other societies have endorsed interim guidance on recognition and management of COVID-19-related coagulopathy (Thachil, J Thromb Haemost; Bikdeli, JACC); anticoagulation may be beneficial in patients with coagulopathy and marked D- dimer elevation (Tang 2, J Thromb Haemost); an observational study found that systemic anticoagulation correlated with improved survival in patients requiring mechanical ventilation (Paranjpe, JACC); therapeutic anticoagulation may be more effective in preventing mortality in hospitalized patients (Nadkami, JACC), and therapeutic anticoagulation was associated with a lower mortality compared to prophylactic anticoagulation in ventilated ICU patients (Trinh, MedRxiv); improved oxygenation in response to therapeutic heparin (Negri, MedRxiv) or tissue plasminogen activator (tPA) (Wang, J Thromb Haemost; Poor, Clin Transl Med); heparin may have an antiviral effect in addition to its activity as an anticoagulant (Clausen, Cell); coagulation studies may guide the need for intensive anticoagulation (Panigada, J Thromb Haemost; Ranucci, J Throm Haemost; Connors, J Thromb Haemost; Connors, Blood), but serious thrombotic events may still occur despite anticoagulation (Helms, Intensive Care Med); circulating endothelial cells, a sign of endothelial damage, are detected in patients with COVID- 19 but appear to be reduced in patients receiving therapeutic anticoagulation (Khider, J Thromb Haemost); detection of circulating endothelial cells correlates with ICU admission, inflammatory cytokines and other evidence of illness severity (Guervilly, Clin Infect Dis)

Complement Inhibition. Complement activation is a common feature of severe COVID-19 and may contribute to inflammation, thrombotic microangiopathy and tissue injury (Campbell, Circulation; Ciceri, Crit Care Resusc; Magro, Transl Res; Risitano, Nat Rev Immunol; Lo, J Immunol); activated complement and tissue factor from neutrophil extracellular traps (NETs) are proposed to drive thrombus formation (Skendros, J Clin Invest); a longitudinal immunophenotyping study correlated C5a/C5aR1 levels with disease severity, implicating complement cascade activation in severe COVID-19 (Carvelli, Nature); anecdotal evidence suggests that complement inhibition can improve oxygenation and reduce inflammation (Gao, MedRxiv)

Corticosteroids. Possible benefits of low-dose corticosteroids have been suggested (Wu, JAMA Intern Med; Wang, MedRxiv), but caveats have also been raised (Russell, Lancet; Shang, Lancet); an early short-course of 0.5-1.0 mg/kg/d methylprednisolone x 3d was associated with clinical improvement and a shorter LOS (Fadel, Clin Infect Dis), and a retrospective analysis with propensity score-matched cohorts suggested reduced in-hospital mortality in patients receiving corticosteroids (Cruz, MedRxiv); however, an RCT of methylprednisolone in 416 hospitalized Brazilian patients with COVID-19 failed to show a mortality benefit (Jeronimo, Clin Last updated 4 October 2020

Infect Dis); the open-label RECOVERY trial involving 6,425 patients hospitalized with COVID-19 found that dexamethasone was associated with lower 28d mortality (23% vs 26%), particularly in those requiring mechanical ventilation (29% vs 41%) (Horby, NEJM), so corticosteroids are now the standard of care for hospitalized patients with severe COVID-19; three additional RCTs, that were halted after announcement of the RECOVERY trial results, collectively provide support for a benefit from corticosteroids in critical COVID-19 (Angus, JAMA; Tomazini, JAMA; Dequin, JAMA); a meta-analysis of data from 7 RCTs concluded that systemic corticosteroids reduces 28-day mortality in patients with critical COVID-19 (Sterne, JAMA); a systematic review of RCT data to date concludes that corticosteroids probably reduce mortality and mechanical ventilation but effectiveness of other interventions is uncertain (Siemieniuk, BMJ), and another living systematic review has strongly recommended corticosteroids in severe/critical COVID-19 but not in non-severe COVID-19 (Lamontagne, BMJ); a large observational study did not suggest that inhaled corticosteroids are protective (Schultze, Lancet Respir Med)

Convalescent Plasma. Possible benefit reported in an uncontrolled trial of convalescent plasma with viral neutralizing activity (Shen, JAMA); in another study, convalescent plasma with neutralizing Ab titers >1:640 was administered to 10 patients with severe COVID-19; clinical improvement was observed with falling viral load, rising lymphocyte counts, improved O2 saturation, and decreased CRP (Duan, PNAS); however, 6 patients with severe COVID-19 received convalescent plasma and cleared their virus, but 5 of them died nevertheless (Zeng, J Infect Dis); convalescent plasma was associated with improved oxygen requirements and survival (for non-intubated patients) compared to historical matched controls (Liu, MedRxiv); an RCT showed a trend toward more rapid clinical improvement that failed to reach significance, possibly because of early termination (Li, JAMA); convalescent plasma may be more beneficial if administered prior to the need for endotracheal intubation (Liu, MedRxiv); an uncontrolled trial of convalescent plasma found that it is safe in severe COVID-19, and 76% of recipients exhibited improvement by 14 days (Salazar, Am J Pathol); a large clinical trial of convalescent serum has been initiated (Casadevall and Pirofski, J Clin Invest; Bloch J Clin Invest); preliminary analysis found that mortality in convalescent plasma recipients inversely correlates with SARS-CoV-2 antibody levels, suggesting clinical benefit (Joyner, MedRxiv); a matched case-control study of patients from RCTs, matched-control studies and case series (n=804) reported a 57% mortality reduction in convalescent plasma recipients (Joyner, MedRxiv plasma efficacy); however, a planned RCT of convalescent plasma for patients hospitalized with COVID-19 in the Netherlands was terminated early after it was found that 80% already had high titers of neutralizing Ab on admission (Gharbharan, MedRxiv); the decision by the FDA to authorize emergency use of convalescent plasma in August 2020 is likely to have delayed a determination of whether it is effective (Estcourt, BMJ); a randomized controlled trial in India (n=464) failed to demonstrate a reduction in disease progression or mortality (14.5% in plasma recipients vs 13.5% in controls) (Agarwal, MedRxiv); the likelihood of having neutralizing Ab in donor plasma correlates with risk factors for COVID-19 severity: age, sex and hospitalization (Klein, J Clin Invest); a summary of current technologies for convalescent plasma therapy and ongoing RCTs can be found in (Focosi, Clin Microbiol Rev); although convalescent plasma is thought to work by neutralizing virus, it may also ameliorate inflammation and the hypercoagulable state of COVID-19 (Rojas, Autoimmun Rev); potential benefits of convalescent plasma include replenishing coagulation Last updated 4 October 2020 proteins and restoring ADAMTS-13 activity (Kesici, PNAS); serious adverse events are infrequent in convalescent plasma recipients, including circulatory overload, lung injury, allergic reactions (Joyner, Mayo Clin Proc)

Monoclonal Antibodies. Several monoclonal Ab to SARS-CoV-2 spike protein are poised to enter clinical trials (Marovich, JAMA); one monoclonal Ab (BD-368-2) has been shown to block ACE2 recognition by spike protein by occupying all three receptor-binding domains simultaneous (Du, Cell)

Angiotensin Converting Enzyme Inhibitors and Angiotensin Receptor Blockers. Continuation of ACE inhibitors/ARBs recommended (Patel, JAMA; Vaduganathan, NEJM), and ACEi/ARB are not a risk factor for COVID-19 or COVID-19-related admission, ICU admission or death (Mancia, NEJM; Reynolds, NEJM; de Abajo, Lancet; Mackey, Ann Intern Med; Fosbøl, JAMA); although hypertension is a risk factor for severe COVID-19, patients taking ACE inhibitors or angiotensin receptor blockers may be less likely to develop severe pneumonia (Feng, MedRxiv); continuation of ACE inhibitors or angiotensin receptor blockers is associated with reduced ICU admissions and mortality compared to discontinuation (Lam, J Infect Dis); one study found that ACE inhibitors reduced the risk of hospitalization in Medicare patients (Khera, MedRxiv); pre- hospital use of renin-angiotensin system inhibitors has a protective effect (Chen, J Am Heart Assoc)

Miscellaneous. Avoidance of ibuprofen recommended but with little basis in evidence (Day, BMJ); receipt of hypnotics has been associated with favorable outcomes (Hu, Clin Infect Dis); a retrospective study suggests that the putative immune response modifier thymosin-α1 may reverse lymphopenia and T cell exhaustion in association with a reduction in mortality in severe COVID-19 (Liu, Clin Infect Dis); Famotidine use may be associated with lower mortality (Freedberg, Gastroenterol), and famotidine use was associated with lower risk of inflammation, intubation and mortality in a retrospective single-center study, possibly due to antiinflammatory effects (Mather, Am J Gastroenterol); analysis of gene expression in bronchoalveolar lavage cells from COVID-19 patients suggests that aberrant renin-angiotensin signaling may elevate bradykinin levels and contribute to inflammatory sequelae (Garvin, eLife); ACE2 regulates des-Arg9-bradykinin turnover, and elevated bradykinin might promote pulmonary edema in severe COVID-19-- a small case-control study of a kinin B2 receptor antagonist (icatibant) suggested improved oxygenation (Van De Veerdonk, JAMA Netw Open)

Favipiravir. Treatment with favipiravir, an RNA polymerase inhibitor, was superior to lopinavir- ritonavir in promoting viral clearance and radiographic improvement in an open-label non- randomized study (Cai, Engineering); an RCT of favipiravir (n=40) vs standard or care (n=20) found that favipiravir accelerated viral clearance and resolution of fever (Ivashchenko, MedRxiv); patients in both arms also received inhaled IFN-α; nebulized IFN-α2b has been used in China and reported to reduce viral shedding in the respiratory tract in parallel with reduced inflammatory markers (Zhou, medRxiv); favipiravir has weak antiviral activity in a hamster model (Kaptein, BioRxiv)

Last updated 4 October 2020

Arbidol. Arbidol is a broad spectrum antiviral that blocks cell entry of enveloped viruses; a small trial found more rapid resolution of viral load and laboratory abnormalities in recipients of arbidol compared to recipients of lopinavir/ritonavir (Zhu, J Infect)

Treatment of Co-infections. Although ventilator-associated pneumonia and other nosocomial infections may occur with prolonged hospitalization, bacterial co-infection appears to be relatively infrequent; nevertheless, broad-spectrum antibiotics are frequently administered (Rawson, Clin Infect Dis; Lansbury, J Infect; Adler, Lancet); a Michigan study found that empiric antibacterials were given to 57% of patients (with substantial variation among institutions) hospitalized with COVID-19, but only 3.5% had a confirmed community-onset bacterial infection (Vaughn, Clin Infect Dis); patients may appear septic but have only a 1.6% bacteremia rate, and overutilization of blood cultures can exceed lab capacity (Sepulveda, MedRxiv) ; invasive pulmonary aspergillosis may occur as a late and often lethal complication, particularly in Europe (Van Arkel, AJRCCM; Bartoletti, Clin Infect Dis; Thompson, OFID)

Management of ARDS. General guidance for the treatment of severe COVID-19-associated ARDS has been pubished (Matthay, Lancet Respir Med; Phua, Lancet Respir Med); some European intensivists have stressed differences between ARDS and COVID-19, recommending the use of the lowest possible PEEP to avoid worsening lung injury (Gattinoni, AJRCCM; Gattinoni, Crit Care; Marini JAMA; Ceruti, MedRxiv; Price, Eur Heart J); a high incidence of barotrauma in mechanically ventilated COVID-19 patients is seen compared to conventional ARDS, associated with increased mortality (McGuinness, Radiology); ARDS per se is not necessarily associated with the hyperinflammatory phenotype (Sinha, Lancet Respir Med), but those with reduced lung compliance accompanied by elevated D-dimer have higher mortality (Grasselli, Lancet Respir Med); patients with COVID-19 and ARDS show immunological differences compared to non-COVID-19-associated ARDS, including profound lymphopenia and elevated chemokine levels (CCL3, CCL4, CCL19, CLL5) that highlight the involvement of myeloid cells (Hue, Am J Respir Crit Care Med); hospitalized patients with COVID-19 exhibit anomalous reductions in the volume of small pulmonary blood vessels consistent with vasoconstriction or microvascular thrombosis (Lins, MedRxiv), which correlates with hypoxemia (De Backer, MedRxiv); severe hypoxemia with preserved lung compliance and elevated deadspace is suggested to represent a distinctive subtype of ARDS with prominent hypercoagulability, thrombosis, and vascular pathology/perfusion abnormalities warranting specific interventions (Rello, Eur Respir J; Mangalmurti, AJRCCM; Patel, AJRCCM); others favor standard ARDS protocols (Ziehr, AJRCCM; Berlin, NEJM; Barbeta, Annals ATS); a multicenter trial found more ventilator-free days and lower mortality in COVID-19 ICU patients treated with non-invasive positive pressure ventilation when possible and protocolized ARDS care (Janz, Chest); prone positioning improves oxygenation in a subset of hypoxemic COVID-19 patients (Elharrar, JAMA); 90-day mortality in patients requiring ECMO is 38% (Barbaro, Lancet)

IDSA Guidelines. IDSA has published treatment guidelines regarding hydroxychloroquine/azithromycin, lopinavir/ritonavir, corticosteroids, tocilizumab and convalescent plasma (Bhimraj, Clin Infect Dis)

Last updated 4 October 2020

PREVENTION

Travel Restrictions. Travel restrictions gain time but only effective if combined with measures to reduce community transmission (Chinazzi, Science; Wells, PNAS; Kucharski, Lancet Infect Dis)

Social Distancing. Social distancing can be effective (Anderson, Lancet; Cowling, MedRxiv) and is more effective in reducing demand for ICU beds if instituted early (Li, MedRxiv); an analysis of 149 countries or regions found that physical distancing is associated with a 13% reduction in COVID-19 incidence (Islam, BMJ); statewide social distancing measures are associated with lower rates of increase in cases and attributable mortality (Siedner, PLoS Med); another study of 211 U.S. counties found social distancing to be the most important determinant of reproduction number, with a 70% reduction in visits to nonessential businesses associated with a fall in R0 < 1 in nearly all cases (Rubin, JAMA Netw Open); social distancing reduced the likelihood of symptomatic COVID-19 in soldiers exposed to SARS-CoV-2, possibly due to reduced viral inocula (Bielecki, Clin Infect Dis); experience in King County indicates that strong intervention can stop the exponential rise in infections (Klein, working paper; Randhawa, JAMA); drastic social distancing interventions in Wuhan drove the effective reproductive number from 3.86 to 0.32 (Wang, MedRxiv) and less dramatically in WA/CA (Lewnard, BMJ); a combination of distancing, self-isolation and contact tracing is more likely to result in R0<1 than any measure alone (Kucharski, Lancet Infect Dis); however, modeling suggests that contact tracing is most useful when case rates are low but can easily become overwhelmed as epidemics accelerate (Gardner, MedRxiv); analysis of contact survey data in China indicates that social distancing alone may be sufficient to control COVID-19; school closures may delay and reduce peak incidence (Zhang, Science), although some modeling studies suggest a limited impact of interventions targeting children on transmission (Davies, Nat Med); statewide school closures have been associated with reductions in COVID-19 incidence and mortality, although confounding by other interventions cannot be excluded (Auger, JAMA; Brauner, MedRxiv); the safest way to reopen schools is to reduce or eliminate community transmission and create robust testing and surveillance capabilities (Levinson, NEJM); targeted nonpharmaceutical interventions such as banning large gatherings and closing schools and high-risk businesses is associated with R0<1 even in the absence of a stay-at-home order (Brauner, MedRxiv); lockdown in France reduced R0 from 2.90 to 0.67 but is predicted to only result in infection of 4.4% of the population, far short of the requirement for herd immunity (Salje, Science); similarly, seroprevalence was only 5% in Spain, one of the European countries most affected by the pandemic, and at least one-third of infections were asymptomatic (Pollan, Lancet); similarly, surveys indicate only 3.2-3.8% seropositivity in Wuhan (Xu, Nat Med serology) and 2.7% in Hong Kong (To, Lancet Microbe); however, 44% of 28,523 individuals in NYC with known or probably COVID-19 exposure were seropositive (Reifer, Diagn Microbiol Infect Dis); social distancing combined with visitor restriction and hand hygiene has been effective in limiting COVID-19 spread in a senior indepencent and assisted living setting (Roxby, MMWR); the impact of social interventions on case numbers has a delay of about two weeks (Dehning, Science); non-pharmaceutical interventions are estimated to have prevented 62 million COVID- 19 infections in China, South Korea, Italy, Iran, France and the US alone (Hsiang, Nature); a Last updated 4 October 2020 parallel study estimated that 3.1 million deaths were averted by interventions in Europe (Flaxman, Nature); low income workers are less able to self-isolate and quarantine-- PCR/serologic screening in San Francisco determined that SARS-CoV-2 was continuing to circulate, mostly asymptomatically, among low-income Latinx persons despite a shelter-in-place ordinance (Chamie, Clin Infect Dis)

Beyond Social Distancing. Sustained suppression is likely to be more effective than mitigation (Ferguson, Imperial College report); temporary non-pharmaceutical interventions may ultimately be ineffective unless accompanied by reinforcement of critical care capacity to ensure adequate care for the most severely ill patients until more definitive strategies (vaccines, new therapeutics, aggressive contact tracing and quarantine) can be implemented (Kissler, DASH); one proposal for eventual restoration of social interaction suggests sequential phases in which widespread surveillance, testing and containment capabilities are established, followed by the application of effective vaccines or therapeutics and the bolstering of public health infratructure (Gottlieb, AEI); experiences on college campuses have been highly variable, with rapid increases in cases associated with student gatherings and congregate living settings both on- and off-campus (Wilson, MMWR); in one model, rapid testing every 2 days and strict behavioral interventions were required to keep R0<2.5 in a college campus setting (Paltiel, JAMA Netw Open); modeling predicts that recurrent wintertime SARS-CoV-2 outbreaks may occur, requiring repeated episodes of social distancing through 2022 (Kissler, Science); other models suggest that tailored strategies combining sheltering of high-risk age groups and distancing by the rest of the population might substantially curtail transmission (Wilder, PNAS); intensive control strategies require extensive diagnostic capability; delays in testing or tracing are likely to substantially reduce the effectiveness of contact tracing (Kretzschmar, MedRxiv); near real-time genome sequencing may enhance recognition of transmission links (Rockett, Nat Med; Oude Munnink, Nat Med); monitoring SARS-CoV-2 in wastewater can be used to perform community surveillance (Peccia, Nat Biotechnol); current gaps in diagnostic testing include widespread surveillance, screening of asymptomatic persons and monitoring shedding in convalescence (Cheng, Ann Intern Med), although it has been argued that even inaccurate tests may be useful in the surveillance setting (Ramdas, Nat Med); ~60% of the population may need to be immune for adequate herd immunity (Altmann, Lancet); modeling suggests that attempted mitigation strategies to allow the development of “herd immunity” are not feasible and carry a risk of overwhelming the health care system if not accompanied by carefully calibrated social distancing (Brett, PNAS); a CIDRAP report describes three potential pandemic scenarios (peaks & valleys/fall peak/slow burn) (Moore, CIDRAP); comparison of public health measures and epidemic activity in different countries suggests that countries should only ease restrictions once robust systems to monitor infection activity are in place, including contact tracing, and face mask usage shows a positive correlation with lower transmission rates (Han, Lancet)

Vaccines. Potential vaccine platforms include RNA, DNA, recombinant proteins, viral vector- based vaccines, live attenuated virus and inactivated virus (Amanat, Immunity; Lurie, NEJM; Krammer, Nature); current leading vaccine candidates are being developed by Moderna, BioNTech/Fosun/Pfizer, Merck/IAVI, J&J/Janssen and AstraZeneca/Oxford University Last updated 4 October 2020

(O’Callaghan, JAMA); an analysis of 18,514 sequenced viral genomes found limited diversity and suggested that a single vaccine could cover currently circulating SARS-CoV-2 lineages (Dearlove, PNAS); the FDA has been urged to adhere to its usual rigorous approach to evaluation in assessing candidate COVID-19 vaccines (Avorn, JAMA); challenges include elicitation of durable immunity and potential immune enhancement (Peeples, PNAS); vaccine hypersensitivity has been shown experimentally for spike protein Ab in SARS and MERS but has not been shown or excluded for SARS-CoV-2 (Ulrich, Cytometry); although dengue-like antibody-dependent enhancement (ADE) is unlikely, vaccine-associated hypersensitivity (VAH) reactions have been seen in challenged animals previously vaccinated against SARS/MERS and need to be carefully monitored (Halstead, J Infect Dis); potential mechanisms of vaccine-induced immunopathology or antibody-dependent enhancement discussed in (Lee, Nat Microbiol); an inactivated vaccine candidate has been shown to induce neutralizing Ab in mice, rats and non-human primates, neutralizes different strains, and protects macaques from challenge without evidence of antibody-dependent enhancement (Gao, Science); a recombinant vaccine based on the receptor binding domain of the S protein is immunogenic and elicits protetive responses in non- human primates correlated with neutralizing Ab and CD4 T cell responses (Yang, Nature); the Oxford ChAdOx1 adenovirus-based vaccine is protective in a macaque model (van Doremalen, BioRxiv), but two episodes of transverse myelitis have recently caused a delay in a clinical trial of the Oxford/AstraZeneca vaccine (https://www.telegraph.co.uk/news/2020/09/20/human- trials-oxford-vaccine-hold-us-spinal-cord-disease-fears/); a single intranasal dose of a chimpanzee adenovirus-vectored vaccine encoding pre-fusion stabilized spike protein (ChAd- SARS-CoV-2 S) elicits systemic and mucosal Ab and T cell responses, and protects against viral challenge (Hassan, Cell vaccine); a DNA vaccine expressing S protein protected macaques from SARS-CoV-2 (Yu, Science); a recombinant adenovirus-vectored COVID-19 vaccine was reported to be immunogenic in human subjects (Zhu, Lancet), but pre-existing immunity to the Ad5 factor was associated with diminished antibody and T cell responses; a single dose of an Ad26-based vaccine was found to be protective against SARS-CoV-2 in macaques (Mercado, Nature); a single dose of an Ad26-based vaccine protected hamsters from SARS-CoV-2 challenge (Tostanoski, Nat Med); Russian Ad5- and Ad26-based vaccines elicited robust humoral and cellular immune responses in phase 1/2 studies (Logunov, Lancet); concerns regarding possible anomalies in the Russian vaccine study data and the authors’ reply have been published (Bucci, Lancet; Logunov, Lancet); a recombinant spike protein nanoparticle vaccine NVX-CoV2373 was found to be safe and immunogenic in phase 1/2 studies (Keech, NEJM); an inactivated whole virus vaccine was well tolerated and immunogenic in phase 1 and 2 trials (n=320) (Xia, JAMA); a phase 1 study of an mRNA vaccine found it to be safe and immunogenic, with neutralizing Ab detected in all participants (Jackson, NEJM); the mRNA-1273 vaccine elicits robust neutralizing Ab responses, protection from respiratory tract challenge and no lung pathology in non-human primates (Corbett, NEJM); comparable immune responses to mRNA-1273 are observed in older adults, but headache, fatigue and injection site pain were commonly reported adverse effects (Anderson, NEJM); a Pfizer/BioNTech lipid nanoparticle- formulated nucleoside-modified mRNA vaccine (BNT162b1) was moderately well tolerated and immunogenic in a phase 1/2 study (n=45) (Mulligan, Nature); although a Department of Defense study suggested that influenza vaccination might increase the risk of other respiratory viruses due to viral interference (Wolff. Vaccine. 2020 Jan 10;38(2):350-354), a comprehensive Last updated 4 October 2020 analysis of influenza vaccine coverage in the U.S. has actually found a protective effect in the elderly population against COVID-19 mortality (Zanettini, MedRxiv)

Models. Even with social distancing, modeling studies predict excess U.S. demand at the pandemic peak in the second week of April to be 64,175 hospital beds, 17,309 ICU beds and 19,481 ventilators, with 81,114 deaths occurring over the next 4 months; IHME model (Murray, MedRxiv https://covid19.healthdata.org/united-states-of-america) has been widely used but also criticized (Jewell, Ann Intern Med)

Health Care Workers. Health care workers are at increased risk of infection (Pan, JAMA)—as of April 9, 2020, the CDC reported 9,282 HCWs infected in the U.S. with 723 hospitalizations, 184 ICU admissions and 27 deaths (CDC MMWR HCWs), which has risen to more than 63,000 health care providers infected with 299 deaths as of 28 May 2020 (https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/cases-in-us.html); compared to the general community, frontline HCWs are at increased risk of symptomatic COVID-19 acquisition, and a national database analysis has confirmed the increased risk to HCWs (Mutambudzi, MedRxiv); seropositivity in Danish HCWs was higher than in blood donors and correlated with exposure to infected patients- 46% were asymptomatic, and loss of taste or smell were the most common symptoms (Iversen, Lancet Infect Dis); HCWs suspecting that they were exposed to SARS-CoV-2 are more likely to be seropositive (Moscola, JAMA); in a study of 99,795 HCWs and 2,035,395 community individuals, front-line HCWs had increased risk of SARS-CoV-2 acquisition compared with the general community (aHR 3.40 after adjustment for testing rates) (Nguyen, Lancet Public Hlth); however, HCWs in NYC who were provided with N95 respirators when caring for patients with COVID-19 did not have higher rates of seropositivity than the general population (Jeremias, JAMA Intern Med); although 6% of 3,248 frontline HCWs in the U.S. were seropositive for SARS-CoV-2 in one study, most were asymptomatic or minimally symptomatic, and PPE use inversely correlated with the likelihood of seropositivity, suggesting that PPE use may reduce infective dose and the likelihood of symptomatic infection (Self, MMWR); most HCWs with fatal infections have had had risk factors (older age, male, Asian or Black, comorbidities) (Hughes, MMWR); workplace acquisition by HCWs has been associated with unsuspected exposures in non-COVID-19 units and lapses in PPE compliance in nursing stations and work or break rooms (Zabarsky, Am J Infect Control); 36% of HCWs at a NYC hospital were seropositive, most of whom had minimal symptoms (Mansour, MedRxiv); even serologic testing may underestimate mild COVID-19 cases in HCWs due to low Ab titers (Eyre, MedRxiv antibodies); in another NYC study, 33% of symptomatic HCWs and 8% of asymptomatic HCWs in NYC were PCR-positive, with declining rates over time possibly reflecting efficacy of PPE (Nagler, Clin Infect Dis); an analysis of 9,684 HCWs in China also documented COVID-19 acquisition in 1%, with the highest risk during the initial days of the outbreak in hospital areas thought to be low-risk (Lai, JAMA Netw Open); infection rates among HCWs have correlated inversely with levels of PPE and are higher in hospital housekeeping/porter staff and HCWs of non-White ethnicity (Eyre, eLife); HCWs can be a source of transmission to patients: an outbreak of 66 hospital-acquired COVID-19 cases representing 15% of COVID-positive admissions was associated with a 36% case fatality rate, and HCWs were consider to be a likely source of some of the infections (Rickman, Clin Infect Last updated 4 October 2020

Dis); however, nosocomial acquisition of SARS-CoV-2 by patients is rare if rigorous infection control measures are employed (Rhee, JAMA Netw Open); most positives found in contact tracing of HCWs with COVID-19 have been asymptomatic (Mandic-Rajcevic, MedRxiv) or had atypical symptoms; one study of HCWs observed both symptomatic and asymptomatic seroconversion, but antibody levels were higher in symptomatic individuals (Shields, Thorax); time required for 95% of HCWs to be cleared was 30 days; a large outbreak in a pediatric dialysis unit resulted from an index case HCW with a high viral load (Schwierzeck, Clin Infect Dis); many asymptomatically infected HCWs may reflect community rather than hospital transmission (Treibel, Lancet); evidence suggests that PPE (masks, gloves, gowns, eye protection) and hand washing decrease HCW infection risk (Chou, Ann Intern Med); inadequate PPE increased risk, but HCWs with adequate PPE may still have increased risk (Nguyen, Lancet Public Hlth); screening of health care workers in NYC found 5% positive for SARS-CoV-2; two- thirds were asymptomatic, and prevalence was 7% higher than in non-HCW controls (Barrett, MedRxiv); random sampling of 1,032 HCWs by nasal/throat swab found 3% positive in a UK study, of whom more than half were truly asymptomatic/pauci-symptomatic, demonstrating the limitations of symptom-based preventative measures (Rivett, eLife); modeling indicates that universal PPE is more effective than testing and isolation to prevent nosocomial spread (Miller, MedRxiv); ED, Anesthesiology and Ophthalmology residents are the specialties at highest risk for COVID-19 acquisition, followed by Surgery, Psychiatry, Medicine and Pediatrics (Breazzano, MedRxiv); the need for airborne vs droplet precautions is controversial and may be based on outdated biophysical concepts of respiratory emissions (Bourouiba, JAMA); increasing evidence is pointing to airborne transmission of SARS-CoV-2 (Prather, Science), and 239 clinicians, epidemiologists, engineers and aerosol scientists have published a commentary calling for greater attention to the role of airborne SARS-CoV-2 transmission (Morawska, Clin Infect Dis); aerosol transmission is most likely to occur in poorly ventilated spaces and/or at close range (Somsen, Lancet Respir Med); modeling suggests that droplet and airborne routes of infection are more important than contact for transmission to HCWs, and airborne transmission primarily occurs when HCWs are near patients and rates of emission are high (Jones, J Occup Environ Hyg); the University of Nebraska found viral contamination of commonly used items, toilets and air samples, suggesting that airborne precautions are appropriate (Santarpia, Sci Rep); culturable virus and intact virions seen by EM could be detected in <4 µm aerosol samples in rooms housing COVID-19 patients (Santarpia, MedRxiv aerosol), and viable virus has been detected in air samples collected 15 feet away from COVID- 19 patients in the absence of aerosol-generating procedures (Lednicky, MedRxiv); Patients with COVID-19 exhale millions of SARS-CoV-2 RNA copies per hour (Ma, Clin Infect Dis); airborne SARS-CoV-2 RNA could be detected nearby patients' toilets and in areas of crowding (Liu, Nature); in another study SARS-CoV-2 RNA was detected on high touch surfaces and air samples in airborne isolation rooms despite 12 air changes per hour (Chia, Nat Commun); ~4 micron droplets generated by speaking could be detected in a closed stagnant air environment for 8-14 minutes, suggesting that SARS-CoV-2 might be transmitted by an airborne route in confined settings (Stadnytskyi, PNAS); SARS-CoV-2 RNA detected in 25% of samples from hospital heating, ventilation and HVAC systems, concerning for potential airborne spread (Horve, MedRxiv); upper-room germicidal ultraviolet fixtures might mitigate airborne transmission (Nardell, JAMA); available evidence suggests that airborne precautions will provide optimal Last updated 4 October 2020 protection for HCWs caring for patients with COVID-19 (Bahl, J Infect Dis); IDSA guidelines to protect HCWs recommend N95 or surgical masks in non aerosol-generating settings and N95 or PAPR for aerosol-generating procedures, with alternative methods in crisis settings (Lynch, IDSA Guideline), but surgical masks were ineffective at preventing infection of HCWs in a nursing home with inadequate ventilation (De Man, Clin Infect Dis); use of PPE with medical masks for patient care and N95 respirators for aerosol-generating procedures reduced but did not eliminate COVID-19 acquisition by HCWs in a French study (Contejean, Clin Infect Dis); a meta- analysis supports physical distancing, face masks (N95 > surgical masks) and eye protection to prevent SARS-CoV-2 transmission (Chu, Lancet); some advocate the use of N95 respirators for all COVID-19 inpatient care on the basis of existing evidence (Dau, Ann Intern Med), and note that none of 420 health care providers deployed to Wuhan who were given PPE including N95 respirators developed COVID-19 (Liu, BMJ); a synthesis of available information concludes that viruses may be carried by small aerosolized particles as well as by larger droplets, and HCWs should be protected from potentially infectious aerosols when working in close proximity to patients, i.e. N95 respirators with face shields or goggles, or PAPRs (Fennelly, Lancet Respir Med); only a major role for aerosols explains the observed patterns of SARS-CoV-2 transmission, but “droplet PPE” (i.e., surgical masks) actually provides protection against aerosols in the supermicron range, contributing to confusion regarding droplet vs. aerosol transmission (Jimenez, COVID-19 aerosol; Shakya, J Expos Sci Environ Epidemiol); pre-exposure prophylaxis of HCWs with hydroxychloroquine is ineffective (Abella, JAMA Intern Med)

Face Masks. The use of face masks lowers risk to health care workers— one study found no infections in HCWs using N95 masks to care for high-risk patients, whereas 10/215 HCWs not using masks while caring for patients considered low-risk were infected (Wang, J Hosp Infect); institution of universal masking at MGH was associated with a lower rate of SARS-CoV- 2 positivity in HCWs (Wang, JAMA; Brooks, JAMA); universal masking in an academic center decreased self-reported high-risk exposures of HCWs by 68%, and universal testing further decreased exposures by 77% (Walker, Clin Infect Dis); 20% of infected health care providers lack fever, cough or dyspnea as an initial symptom, suggesting that symptomatic screening may be less effective than universal masking of all health care providers (Chow, JAMA; Klompas, NEJM); inoculum size may be an important but neglected determinant of infection severity (Guallar, IJID), and individuals wearing face masks, including HCWs, may be more likely to have mild or asymptomatic infection if they become infected, due to a reduced viral inoculum (Gandhi, J Gen Intern Med; Gandhi, NEJM masks); in view of PPE shortages, N95 respirators may be decontaminated up to 3 times with UV/H2O2 vapor or up to 2 times with dry heat and re- used (Fischer MedRxiv); surgical masks worn by individuals with infections can also reduce the risk of transmission (Leung, Nat Med); facemasks reduce SARS-CoV-2 transmission in a hamster model and are more effective when the index case rather than the naîve recipient is masked (Chan, Clin Infect Dis masks); universal cloth face masks have been advocated for infection prevention in the community (Abeluck, SSRN; https://rs- delve.github.io/addenda/2020/07/07/masks-update.html), as evidence indicates that masks can prevent the spread of respiratory viruses in non-HCWs as well as in HCWs (Liang, Travel Med Infect Dis); face masks worn by the general public vary in their ability to filter expelled droplets (Fischer, Sci Adv); state policies mandating face masks are associated with a 1-2% Last updated 4 October 2020 decline in the daily COVID-19 growth rate (Lyu, Health Affairs); no transmission to 139 clients was reported from two symptomatic hair stylists working in salons in which both stylists and clients wore face coverings (Hendrix, MMWR); asymptomatic transmission means that symptom-based case detection is insensitive and supports universal face mask usage (Gandhi, NEJM); a narrative review of the benefits of public face mask-wearing may be found in (Howard, Preprints)

Fomites. Fomites may contribute to transmission in the hospital environment; SARS-CoV-2 RNA has been detected in air samples near patients and on floors, printers, keyboards, computer mice, doorknobs, telephones, trash cans, sickbed handrails, medical equipment, gloves and hand sanitizer dispensers (Ye, J Infect; Guo, Emerg Infect Dis)

EMERGENCY MANAGEMENT

Emergency Response. An overview of the principles of emergency management in the State of Washington and connections to the national emergency response infrastructure has been published (Morris, Prehosp Disast Med)

This summary was compiled by Ferric C. Fang, M.D. and does not necessarily represent the views of the University of Washington or its affiliated institutions.

Last updated 4 October 2020

Literature Cited

Abaluck J, et al. The case for universal cloth mask adoption and policies to increase the supply of medical masks for health workers. SSRN. 1 April 2020. https://ssrn.com/abstract=3567438.

Abdollahi E, et al. Temporal estimates of case-fatality rate for COVID-19 outbreaks in Canada and the United States. CMAJ. 2020 May 22. doi: 10.1503/cmaj.200711.

Abella BS, et al. Efficacy and Safety of Hydroxychloroquine vs Placebo for Pre-exposure SARS- CoV-2 Prophylaxis Among Health Care Workers: A Randomized Clinical Trial. JAMA Intern Med. 2020 Sep 30. doi: 10.1001/jamainternmed.2020.6319.

Ackermann M, et al. Pulmonary vascular endothelialitis, thrombosis, and angiogenesis in COVID-19. N Engl J Med. 2020 May 21. doi: 10.1056/NEJMoa2015432.

Adam DC, et al. Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong. Res Square. Nat Med. 2020 Sep 17. doi: 10.1038/s41591-020-1092-0.

Addetia A, et al. Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate. J Clin Microbiol. 2020 Aug 21. doi: 10.1128/JCM.02107-20.

Adler H, et al. Low rate of bacterial co-infection in patients with COVID-19. Lancet Microbe. 2020 Jun. doi: 10.1016/S2666-5247(20)30036-7.

Agarwal A, et al. Convalescent plasma in the management of moderate COVID-19 in India: An open-label parallel-arm phase II multicentre randomized controlled trial (PLACID trial). medRxiv. https://doi.org/10.1101/2020.09.03.20187252.

Agarwal P, et al. Neurological manifestations in 404 COVID-19 patients in Washington State. J Neurol. 2020 Aug 6. doi: 10.1007/s00415-020-10087-z.

Ahlberg M, et al. Association of SARS-CoV-2 Test Status and Pregnancy Outcomes. JAMA. 2020 Sep 23. doi: 10.1001/jama.2020.19124.

Ahmed M, et al. Multisystem inflammatory system in children: A systematic review. EClinicalMedicine. 2020 Sept 4. https://doi.org/10.1016/j.eclinm.2020.100527.

Ai T, et al. Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases. Radiology. 2020 Feb 26:200642. doi: 10.1148/radiol.2020200642.

Akalin E, et al. COVID-19 and kidney transplantation. N Engl J Med. 2020 Apr 24. doi: 10.1056/NEJMc2011117. Last updated 4 October 2020

Ali ST, et al. Serial interval of SARS-CoV-2 was shortened over time by nonpharmaceutical interventions. Science. 2020 Jul 21;eabc9004. doi: 109.1126/science.abc9004.

Alijotas-Reig J, et al. Immunomodulatory therapy for the management of severe COVID-19. Beyond the anti-viral therapy: A comprehensive review. Autoimmun Rev. 2020 May 3:102569. doi: 10.1016/j.autrev.2020.102569.

Allotey J, et al. Clinical manifestations, risk factors, and maternal and perinatal outcomes of coronavirus disease 2019 in pregnancy: living systematic review and meta-analysis. BMJ. 2020 Sep 1;370:m3320. doi: 10.1136/bmj.m3320.

Altmann DM, et al. What policy makers need to know about COVID-19 protective immunity. Lancet. 2020 Apr 27. https://doi.org/10.1016/S0140-6736(20)30985-5.

Altmann DM, RJ Boyton. SARS-CoV-2 T cell immunity: Specificity, function, durability, and role in protection. Sci Immunol. 2020 Jul 17. doi: 10.1126/sciimmunol.abd6160.

Amanat F, F Krammer. SARS-CoV-2 vaccines: Status report. Immunity. 2020 Apr 3. pii: S1074- 7613(20)30120-5. Doi: 10.1016/j.immuni.2020.03.007.

Amanat F, et al. A serological assay to detect SARS-CoV-2 seroconversion in humans. Nat Med. 2020 May 12. doi: 10.1038/s41591-020-0913-5.

An J, et al. Clinical characteristics of the recovered COVID-19 patients with re-detectable positive RNA test. medRxiv https://doi.org/10.1101/2020.03.26.20044222.

Anand S, et al. Prevalence of SARS-CoV-2 antibodies in a large nationwide sample of patients on dialysis in the USA: a cross-sectional study. Lancet. 2020 Sep 25. https://doi.org/10.1016/ S0140-6736(20)32009-2.

Anderson EJ, et al. Safety and Immunogenicity of SARS-CoV-2 mRNA-1273 Vaccine in Older Adults. N Engl J Med. 2020 Sep 29. doi: 10.1056/NEJMoa2028436.

Anderson RM, et al. How will country-based mitigation measures influence the course of the COVID-19 epidemic? Lancet. 2020 Mar 9. pii: S0140-6736(20)30567-5. doi: 10.1016/S0140- 6736(20)30567-5.

Angus DC, et al. Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial. JAMA. 2020 Sep 2. doi: 10.1001/jama.2020.17022.

Arashiro T, et al. COVID-19 in 2 Persons with Mild Upper Respiratory Symptoms on a Cruise Ship, Japan. Emerg Infect Dis. 2020 Jun 17;26(6). doi: 10.3201/eid2606.200452. Last updated 4 October 2020

Araujo MB, B Naimi. Spread of SARS-CoV-2 coronavirus likely to be constrained by climate. medRxiv medRxiv 2020.03.12.20034728.

Arentz M, et al. Characteristics and Outcomes of 21 Critically Ill Patients With COVID-19 in Washington State. JAMA. 2020 Mar 19. doi: 10.1001/jama.2020.4326.

Argenziano MG, et al. Characterization and clinical course of 1000 patients with coronavirus disease 2019 in New York: Retrospective case series. BMJ. 2020 May 29;369:m1996. Doi: 10.1136/bmj.m1996.

Argyropoulos KV, et al. Association of initial viral load in SARS-CoV-2 patients with outcome and symptoms. Am J Pathol. 2020 Jul 3:S0002-9440(20)30328-X. doi: 10.1016/j.ajpath.2020.07.001.

Armstrong RA, et al. Outcomes from intensive care in patients with COVID-19: a systematic review and meta-analysis of observational studies. Anaesthesia. 2020 Jun 30. doi: 10.1111/anae.15201.

Arons MM, et al. Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. N Engl J Med. 2020 Apr 24. doi: 10.1056/NEJMoa2008457.

Arshad S, et al. Treatment with hydroxychloroquine, azithromycin and combination in patients hospitalized with COVID-19. Int J Infect Dis. https://doi.org.10.1016/j.ijid.2020.06.099.

Arunachalam PS, et al. Systems biological assessment of immunity to mild versus severe COVID- 19 infection in humans. Science. 2020 Aug 11;eabc6261. doi: 10.1126/science.abc6261.

Atyeo C, et al. Distinct early serological signatures track with SARS-CoV-2 survival. Immunity. https://doi.org/10.1016/j.immuni.2020.07.020.

Auger KA, et al. Association Between Statewide School Closure and COVID-19 Incidence and Mortality in the US. JAMA. 2020 Jul 29. doi: 10.1001/jama.2020.14348.

Auld SC, et al. ICU and ventilator mortality among critically ill adults with COVID-19. medRxiv. https://doi.org/10.1101/2020.04.23.20076737.

Avorn J, A Kesselheim. Regulatory Decision-making on COVID-19 Vaccines During a Public Health Emergency. JAMA. 2020 Aug 31. doi: 10.1001/jama.2020.17101.

Azoulay E, et al. Increased mortality in patients with severe SARS-CoV-2 infection admitted within seven days of disease onset. Intensive Care Med. 2020 Aug 11;1-9. doi: 10.1007/s00134- 020-06202-3.

Last updated 4 October 2020

Baggett TP, et al. Prevalence of SARS-CoV-2 infection in residents of a large homeless shelter in Boston. JAMA. 2020 Apr 27. doi: 10.1001/jama.2020.6887.

Baggio S, et al. SARS-CoV-2 viral load in the upper respiratory tract of children and adults with early acute COVID-19. Clin Infect Dis. 2020 Aug 6;ciaa1157. doi: 10.1093/cid/ciaa1157.

Bahar B, et al. Kinetics of viral clearance and antibody production across age groups in SARS- CoV-2 infected children. medRxiv. https://doi.org/10.1101/2020.08.06.20162446.

Bahl P, et al. Airborne or droplet precautions for health workers treating COVID-19? J Infect Dis. 2020 Apr 16. doi: 10.1093/infdis/jiaa189.

Bahl P, et al. Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs. Clin Infect Dis. 2020 Sep 18;ciaa1241. doi: 10.1093/cid/ciaa1241.

Bai HX, et al. AI augmentation of radiologist performance in distinguishing COVID-19 from pneumonia or other etiology on chest CT. Radiology. 2020 Apr 27:201491. doi: 10.1148/radio.2020201491.

Bai Y, et al. Presumed asymptomatic carrier transmission of COVID-19. JAMA. 2020 Feb 21. doi: 10.1001/jama.2020.2565.

Baldi E, et al. Out-of-hospital cardiac arrest during the COVID-19 outbreak in Italy. N Engl J Med. 2020 Apr 29. doi: 10.1056/NEJMc2020418.

Bao L, et al. The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice. Nature. 2020 May 7. https://doi.org/10.1038/s41586-020-2312-y.

Barbaro RP, et al. Extracorporeal membrane oxygenation support in COVID-19: an international cohort study of the Extracorporeal Life Support Organization registry. Lancet. 2020 Sep 25. https://doi.org/10.1016/ S0140-6736(20)32008-0.

Barbata E, et al. SARS-CoV-2-induced Acute Respiratory Distress Syndrome: Pulmonary Mechanics and Gas Exchange Abnormalities. Ann Am Thorac Soc. 2020 Jun 24. doi: 10.1513/AnnalsATS.202005-462RL.

Barrett ES, et al. Prevalence of SARS-CoV-2 infection in previously undiagnosed health care workers at the onset of the U.S. COVID-19 epidemic. medRxiv. https://doi.org/10.1101/2020.04.20.20072470.

Bartoletti M, et al. Epidemiology of invasive pulmonary aspergillosis among COVID-19 intubated patients: a prospective study. Clin Infect Dis. 2020 Jul 28;ciaa1065. doi: 10.1093/cid/ciaa1065.

Last updated 4 October 2020

Bartoletti M, et al. Development and validation of a prediction model for severe respiratory failure in hospitalized patients with SARS-Cov-2 infection: a multicenter cohort study (PREDI-CO study). Clin Microbiol Infect. 2020 Aug 8;S1198-743X(20)30479-1. doi: 10.1016/j.cmi.2020.08.003.

Basso C, et al. Pathological features of COVID-19-associated myocardial injury: a multicentre cardiovascular pathology study. Eur Heart J. 2020 Sep 24;ehaa664. doi: 10.1093/eurheartj/ehaa664.

Bastard P, et al. Auto-antibodies against type I IFNs in patients with life-threatening COVID-19. Science. 2020 Sep 24;eabd4585. doi: 10.1126/science.abd4585.

Bastos ML, et al. Diagnostic accuracy of serological tests for COVID-19: Systematic review and meta-analysis. BMJ. 2020 Jun 23. 370:m2516. http://dx.doi.org/10.1136/bmj.m2516.

Basu A, et al. Performance of Abbott ID NOW COVID-19 rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution. J Clin Microbiol. 2020 May 29:JCM.01136-20.

Beale S, et al. A rapid review of the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections in community settings. medRxiv. https://doi.org/10.1101/2020.05.20.20108183.

Becerra-Flores M, T Cardozo. SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate. Int J Clin Pract. 2020 May 6;e13525. doi: 10.1111/ijcp.13525.

Becker D, et al. Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting. medRxiv. https://doi.org/10.1101/2020.05.11.20092338.

Beckmann ND, et al. Cytotoxic lymphocytes are dysregulated in multisystem inflammatory syndrome in children. medRxiv. https://doi.org/10.1101/2020.08.29.20182899.

Bedford T, et al. Cryptic transmission of SARS-CoV-2 in Washington State. Science. 2020 Sep 10. doi: 10.1126/science.abc0523..

Beenen LFM, et al. Extensive pulmonary perfusion defects compatible with microthrombosis and thromboembolic disease in severe COVID-19 pneumonia. Thromb Res. 2020 Aug 14. https://doi.org/10.1016/j.thromres.2020.08.026.

Beigel JH, et al. Remdesivir for the treatment of COVID-19—Preliminary report. N Engl J Med. 2020 May 22. doi: 10.1056/NEJMoa2007764.

Belhadjer Z, et al. Acute heart failure in multisystem inflammatory syndrome in children (MIS-C) in the context of global SARS-CoV-2 pandemic. Circulation. 2020 May 17. doi: 10.1161/CIRCULATIONAHA.120.048360. Last updated 4 October 2020

Bendavid E, et al. COVID-19 antibody seroprevalence in Santa Clara County, California. medRxiv. doi: https://doi.org/10.1101/2020.04.14.20062463.

Benny B, et al. Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection. medRxiv. https://doi.org/10.1101/2020.05.15.20103275.

Berenger BM, et al. Sensitivity of nasopharyngeal, nasal and throat swab for the detection of SARS-CoV-2. medRxiv. https://doi.org/10.1101/2020.05.05.20084889.

Berezin L, et al. The diagnostic accuracy of subjective dyspnea in detecting hypoxemia among outpatients with COVID-19. medRxiv. https://doi.org/10.1101/2020.08.10.20172262.

Berlin DA, et al. Severe COVID-19. N Engl J Med. 2020 May 15. doi: 10.1056/NEJMcp2009575.

Bhatraju PK, et al. COVID-19 in critically ill patients in the Seattle region—Case series. N Engl J Med. 30 Mar 2020. doi: 10.1056/NEJMoa2004500.

Bhimraj A, et al. Infectious Diseases Society of America guidelines on the treatment and management of patients with COVID-19 infection. Clin Infect Dis 2020 Apr 27. doi: 10.1093/cid/ciaa478.

Bi Q, et al. Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study. Lancet Infect Dis. 2020 Apr 22. https://doi.org/10.1016/S1473-3099(20)30287-5

Bielecki M, et al. Social distancing alters the clinical course of COVID-19 in young adults: A comparative cohort study. Clin Infect Dis. 2020 Jun 29;ciaa889. doi: 10.1093/cid/ciaa889.

Bigelow BF, et al. Outcomes of universal COVID-19 testing following detection of incident cases in 11 long-term care facilities. JAMA Intern Med. 2020 Jul 14. doi: 10.1001/jamainternmed.2020.3738.

Bikdeli B, et al. COVID-19 and thrombotic or thromboembolic disease: Implications for prevention, antithrombotic therapy, or follow-up. J Am Coll Cardiol. 2020 Apr 15. pii: S0735- 1097(20)35008-7.

Bilaloglu S, et al. Thrombosis in hospitalized patients with COVID-19 in a New York City health system. JAMA. 2020 Jul 20. doi: 10.1001/jama.2020.13372.

Bilinski K, et al. Expression of the SARS-CoV-2 entry proteins, ACE2 and TMPRSS2, in cells of the olfactory epithelium: Identification of cell types and trends with age. ACS Chem Neurosci. 2020 May 7. doi: 10.1021/acschemneuro.0c00210.

Last updated 4 October 2020

Binnicker MJ. Challenges and Controversies Related to Testing for COVID-19. J Clin Microbiol. 2020 Aug 12;JCM.01695-20. doi: 10.1128/JCM.01695-20.

Biran N, et al. Tocilizumab among patients with COVID-19 in the intensive care unit: A multicentre observational study. Lancet Rheumatol. 2020 Aug 14. https://doi.org/10.1016/S2665-9913(20)30277-0.

Bixler D, et al. SARS-CoV-2-Associated Deaths Among Persons Aged <21 Years - United States, February 12-July 31, 2020. MMWR Morb Mortal Wkly Rep. 2020 Sep 18;69(37):1324-1329.

Blanco JL, et al. COVID-19 in patients with HIV: clinical case series. Lancet HIV. 2020 May;7(5):e314-e316. doi: 10.1016/S2352-3018(20)30111-9.

Blanco-Melo D, et al. Imbalanced host response to SARS-CoV-2 drives development of COVID- 19. Cell. 2020 May 13;S0092-8674-(20)30489-X.

Bloch EM, et al. Deployment of convalescent plasma for the prevention and treatment of COVID-19. J Clin Invest. 2020. https://doi.org/10.1172/JCI138745.

Böhmer MM, et al. Invesetigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: A case series. Lancet Infect Dis. 2020 May 15. https://doi.org/10.1016/S1473-3099(20)30314-5.

Boehmer TK, et al. Changing Age Distribution of the COVID-19 Pandemic - United States, May- August 2020. MMWR Morb Mortal Wkly Rep. 2020 Oct 2;69(39):1404-1409. doi: 10.15585/mmwr.mm6939e1.

Bond K, et al. Evaluation of serological tests for SARS-CoV-2: Implications for serology testing in a low-prevalence setting. J Infect Dis. 2020 Aug 6;jiaa467. doi: 10.1093/infdis/jiaa467.

Boni MF, et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol. 2020 Jul 28. doi: 10.1038/s41564-020-0771-4.

Bordoni V, et al. An inflammatory profile correlates with decreased frequency of cytotoxic cells in COVID-19. Clin Infect Dis. 2020 May 15;ciaa577.

Boscolo-Rizzo P, et al. Evolution of altered sense of smell or taste in patients with mildly symptomatic COVID-19. JAMA Otolaryngol Head Neck Surg. 2020 Jul 2;e201379. doi: 10.1001/jamaoto.2020.1379.

Bosmüller H, et al. The evolution of pulmonary pathology in fatal COVID-19 disease: An autopsy study with clinical correlation. Virchows Arch. 2020 Jun 30. doi: 10.1007/s00428-020-02881-x.

Last updated 4 October 2020

Bouadma L, et al. Immune alterations during SARS-CoV-2-related acute respiratory distress syndrome. medRxiv. https://doi.org/10.1101/2020.05.01.20087239.

Boudewijns R, et al. STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters. bioRxiv. https://doi.org/10.1101.2020.04.23.056838.

Bourouiba L. Turbulent gas clouds and respiratory pathogen emissions: Potential implications for reducing transmission of COVID-19. JAMA. 26 Mar 2020. doi:10.1001/jama.2020.4756.

Bowles L, et al. Lupus anticoagulant and abnormal coagulation tests in patients with COVID-19. N Engl J Med. 2020 May 5. doi: 10.1056/NEJMc2013656.

Bradley BT, et al. Histopathology and ultrastructural findings of fatal COVID-19 infections in Washington State: a case series. Lancet. 2020 Jul 16. https://doi.org/10.1016/S0140- 6736(20)31305-2.

Brandstetter S, et al. Symptoms and immunoglobulin development in hospital staff exposed to a SARS-CoV-2 outbreak. Pediatr Allergy Immunol. 2020 May 15. doi: 10.1111/pai.13278.

Brat GA, et al. International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium. npj Digital Medicine. 2020. 3:109. https://doi.org/10.1038/s41746-020- 00308-0.

Braun J, et al. SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19. Nature. 2020 Jul 29. doi: 10.1038/s41586-020-2598-9.

Brauner JM, et al. The effectiveness of eight nonpharmaceutical interventions against COVID-19 in 41 countries. medRxiv. https://doi.org/10.1101/2020.05.28.20116129.

Breazzano MP, et al. Resident physician exposure to novel coronavirus (2019-nCoV, SARS-CoV- 2) within New York City during exponential phase of COVID-19 pandemic: Report of the New York City Residency Program Directors COVID-19 Research Group. medRxiv. https://doi:org/10.1101/2020.04.32.20074310.

Brett TS, P Rohani. Transmission dynamics reveal the impracticality of COVID-19 herd immunity strategies. Proc Natl Acad Sci USA. 2020 Sep 22;202008087. doi: 10.1073/pnas.2008087117.

Broggi A, et al. Type III interferons disrupt the lung epithelial barrier upon viral recognition. Science. 2020 Jun 11. doi: 10.1126/science.abc3545.

Bronte V, et al. Baracitinib restrains the immune dysregulation in COVID-19 patients. medRxiv. https://doi.org/10.1101.2020.06.26.20135319.

Last updated 4 October 2020

Brooks JT, et al. Universal masking to prevent SARS-CoV-2 transmission—the time is now. JAMA. 2020 Jul 14. doi: 10.1001/jama.2020.13107.

Brouwer PJM, et al. Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability. Science. 2020 Jun 15;eabc5902.

Bryant JE, et al. Serology for SARS-CoV-2: Apprehensions, opportunities, and the path forward. Sci Immunol. 2020 May 19. doi: 10.1126/sciimmunol.abc6347.

Bryce C, et al. Pathophysiology of SARS-CoV-2: Targeting of endothelial cells renders a complex disease with thrombotic microangiopathy and aberrant immune response. The Mount Sinai COVID-19 autopsy experience. medRxiv. https://doi.org/10.1101/2020.05.18.20099960.

Boulware DR, et al. A randomized trial of hydroxychloroquine as postexposure prophylaxis for COVID-19. N Engl J Med. 2020 Jun 3. doi: 10.1056/NEJMoa2016638.

Bucci E, et al. Safety and efficacy of the Russian COVID-19 vaccine: More information needed. Authors reply. Lancet. 2020 Sep 18. https://doi.org/10.1016/ S0140-6736(20)31960-7.

Buckner FS, et al. Clinical features and outcomes of 105 hospitalized patients with COVID-19 in Seattle, Washington. Clin Infect Dis. 2020 May 22:ciaa632. doi: 10.1093/cid/ciaa632.

Buitrago-Garcia DC, et al. The role of asymptomatic SARS-CoV-2 infections: Rapid living systematic review and meta-analysis. medRxiv. https://doi.org/10.1101/2020.04.25.20079103.

Bukhari Q, Y Jameel. Will coronavirus pandemic diminish by summer? 17 Mar 2020. SSRN http://dx.doi.org/10.2139/ssrn.3556998.

Bullard J, et al. Predicting infectious SARS-CoV-2 from diagnostic samples. Clin Infect Dis. 2020 May 22;ciaa638. doi: 10.1093/cid/ciaa638.

Bunyavanich S, et al. Nasal gene expression of angiotensin-converting enzyme 2 in children and adults. JAMA. 2020 May 20. doi: 10.1001/jama.2020.8707.

Bunyavanich S, et al. Racial/Ethnic Variation in Nasal Gene Expression of Transmembrane Serine Protease 2 (TMPRSS2). JAMA. 2020 Sep 10. doi: 10.1001/jama.2020.17386.

Burbelo PD, et al. Sensitivity in Detection of Antibodies to Nucleocapsid and Spike Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 in Patients With Coronavirus Disease 2019. J Infect Dis. 2020 Jun 29;222(2):206-213. doi: 10.1093/infdis/jiaa273.

Burke H, et al. Inflammatory phenotyping predicts clinical outcome in COVID-19. Respir Res. 2020 Sep 22;21(1):245. doi: 10.1186/s12931-020-01511-z.

Last updated 4 October 2020

Buscarini E, et al. Gastrointestinal symptoms as COVID-19 onset in hospitalized Italian patients. medRxiv. https://doi.org/10.1101/2020.04.20.20064873.

Bussani R, et al. Persistence of viral RNA, widespread thrombosis and abnormal cellular syncytia are hallmarks of COVID-19 lung pathology. medRxiv. https://doi.org/10.1101.2020.06.22.20136358.

Byrne AW, et al. Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases. BMJ Open. 2020 Aug 5;10(8):e039856. doi: 10.1136/bmjopen-2020-039856.

Cai J, et al. A Case Series of children with 2019 novel coronavirus infection: clinical and epidemiological features. Clin Infect Dis. 2020 Feb 28. pii: ciaa198. doi: 10.1093/cid/ciaa198.

Cai Q, et al. Experimental Treatment with Favipiravir for COVID-19: An Open-Label Control Study. Engineering. 2020. doi: https://doi.org/10.1016.j.eng.2020.03.007.

Caini S, et al. Meta-analysis of diagnostic performance of serological tests for SARS-CoV-2 antibodies and public health implications. medRxiv. https://doi.org/10.1101/2020.05.03.30084160.

Calabrese F, et al. Pulmonary pathology and COVID-19: lessons from autopsy. The experience of European pulmonary pathologists. Virchows Arc. 2020 Jul 9:1-14. doi: 10.1007/s00428-020- 02886-6.

Calcagno A, et al. Co-infection with other respiratory pathogens in COVID-19 patients. Clin Microbiol Infect. 2020 Aug 18;S1198-743X(20)30494-8. doi: 10.1016/j.cmi.2020.08.012.

Calvacanti AB, et al. Hydroxychloroquine with or without azithromycin in mild-to-moderate COVID-19. N Engl J Med. 2020 Jul 23. doi: 10.1056/NEJMoa2019014.

Campbell CM, R Kahwash. Will complement inhibition be the new target in treating COVID-19 related systemici thrombosis? Circulation. 2020 Apr 9. doi: 10.1161/CIRCULATIONAHA.120.047419.

Campocharo C, L Dagna. The conundrum of interleukin-6 blockade in COVID-19. Lancet Rheumatol. 2020 Aug 14. https://doi.org/10.1016/S2665-9913(20)30287-3.

Capochiani E, et al. Ruxolitinib Rapidly Reduces Acute Respiratory Distress Syndrome in COVID- 19 Disease. Analysis of Data Collection From RESPIRE Protocol. Front Med. 2020 Aug 4;7:466. doi: 10.3389/fmed.2020.00466.

Cantini F, et al. Baricitinib therapy in COVID-19: A pilot study on safety and clinical impact. J Infect. 2020 Apr 23. doi: 10.1016/j.jinf.2020.04.017. Last updated 4 October 2020

Cao B, et al. A Trial of Lopinavir-Ritonavir in Adults Hospitalized with Severe Covid-19. N Engl J Med. 2020 Mar 18. doi: 10.1056/NEJMoa2001282.

Carfi A, et al. Persistent symptoms in patients after acute COVID-19. JAMA. 2020 Jul 9. doi: 10.1001/jama.2020.12603.

Carlucci PM, et al. Hydroxychloroquine and azithromycin plus zinc vs hydroxychloroquine and azithromycin alone: outcomes in hospitalized patients. medRxiv. https://doi.org/10.1101/2020.05.01.20080036.

Carsana L, et al. Pulmonary post-mortem findings in a large series of COVID-19 cases from Northern Italy: a two-centre descriptive study. Lancet Infect Dis. 2020 Jun 8. doi: 10.1016/S1473-3099(20)30449-7.

Caruana G, et al. Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results. Clin Microbiol Infect. 2020 Jun 25;S1198-743X(20)30363-3.

Carvelli J, et al. Association of COVID-19 inflammation with activation of the C5a-C5aR1 axis. Nature. 2020 Jul 29. doi: 10.1038/s41586-020-2600-6.

Casadevall A, LA Pirofski. The convalescent sera option for containing COVID-19. J Clin Invest. 2020 Mar 13. pii: 138003. doi: 10.1172/JCI138003.

Casas CG, et al. Classification of the cutaneous manifestations of COVID-19: a rapid prospetive nationwide consensus study in Spain with 375 cases. Br J Dermatol. doi: 10.1111/BJD.19163.

Castagnoli R, et al. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adolescents: A systematic review. JAMA Pediatr. 2020 Apr 22. doi: 10.1001/jamapediatriics.2020.1467.

Castells M, et al. Evidence of increasing diversification of emerging SARS-CoV-2 strains. J Med Virol. 2020 May 15. doi: 10.1002/jmv.26018.

Catteau L, et al. Low-dose Hydroxychloroquine Therapy and Mortality in Hospitalized Patients with COVID-19: A Nationwide Observational Study of 8075 Participants. Int J Antimicrob Agents. 2020 Aug 24;106144. doi: 10.1016/j.ijantimicag.2020.106144.

Cauchois R, et al. Early IL-1 receptor blockade in severe inflammatory respiratory failure complicating COVID-19. Proc Natl Acad Sci USA. 2020 Jul 22;202009017. doi: 10.1073/pnas.2009017117.

Caulley L, et al. Salivary Detection of COVID-19. Ann Intern Med. 2020 Aug 28. doi: 10.7326/M20-4738. Last updated 4 October 2020

Cavalli G, et al. Interleukin-1 blockade with high-dose anakinra in patients with COVID-19, acute respiratory distress syndrome, and hyperinflammation: a retrospective cohort study. Lancet Rheumatol. 2020 May 7. https://doi.org/10.1016/S2665-9913(20)31029-6.

Cereda D, et al. The early phase of the COVID-19 outbreak in Lombardy, Italy. arXiv:2003.09320.

Ceruti S, et al. Reduced mortality and shortened ICU stay in SARS-CoV-2 patients: A low PEEP strategy. medRxiv. https://doi.org/10.1101.2020.05.03.20089318.

Chambers C, et al. Evaluation for SARS-CoV-2 in Breast Milk From 18 Infected Women. JAMA. 2020 Aug 19. doi: 10.1001/jama.2020.15580.

Chamie G, et al. SARS-CoV-2 Community Transmission disproportionately affects Latinx population during Shelter-in-Place in San Francisco. Clin Infect Dis. 2020 Aug 21;ciaa1234. doi: 10.1093/cid/ciaa1234.

Chan JF, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020 Feb 15;395(10223):514-523.

Chan JF, et al. Simulation of the clinical and pathological manifestations of Coronavirus Disease 2019 (COVID-19) in golden Syrian hamster model: implications for disease pathogenesis and transmissibility. Clin Infect Dis. 2020 Mar 26. pii: ciaa325. doi: 10.1093/cid/ciaa325.

Chan JF, et al. Surgical mask partition reduces the risk of non-contact transmission in a golden Syrian hamster model for coronavirus disease 2019 (COVID-19). Clin Infect Dis. 2020 May 30:ciaa644. doi: 10.1093/cid/ciaa644.

Chan J, et al. A pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease-19 (COVID-19). J Zhejiang Univ. 2020 Mar. doi: 10.3785/j.issn.1008- 9292.2020.03.03.

Chandrashekar A, et al. SARS-CoV-2 infection protects against rechallenge in rhesus macaques. Science. 2020 May 20:eabc4776. doi: 10.1126/science.abc4776.

Chau NVV, et al. The natural history and transmission potential of asymptomatic SARS-CoV-2 infection. Clin Infect Dis. 2020 Jun 4;ciaa711. doi: 10.1093/cid/ciaa711.

Chaudhry R, et al. A country level analysis measuring the impact of government actions, country preparedness and socioeconomic factors on COVID-19 mortality and related health outcomes. EclinicalMedicine. 2020 Aug 4. https://doi.org/10.1016/j.eclinm.2020.100464.

Last updated 4 October 2020

Chen C, et al. SARS-CoV-2-positive sputum and feces after conversion of pharyngeal samples in patients with COVID-19. Ann Intern Med. 2020 Mar 30. doi: 10.7326/M20-0991.

Chen C, et al. Mortality and Pre-Hospitalization use of Renin-Angiotensin System Inhibitors in Hypertensive COVID-19 Patients. J Am Heart Assoc. 2020 Aug 18;e017736. doi: 10.1161/JAHA.120.017736.

Chen G, et al. Clinical and immunologic features in severe and moderate Coronavirus disease 2019. J Clin Invest. 2020. https://doi.org/10.1172/JCI137244.

Chen H, et al. Clinical characteristics and intrauterine vertical transmission potential of COVID- 19 infection in nine pregnant women: a retrospective review of medical records. Lancet. 2020 Mar 7;395(10226):809-815.

Chen L, et al. Clinical characteristics of pregnant women with COVID-19 in Wuhan, China. N Engl J Med. 2020 Apr 17. doi: 10.1056/NEJMc2009226.

Chen N, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020 Feb 15;395(10223):507-513.

Chen T, et al. Clinical characteristics of 113 deceased patients with coronavirus disease 2019: retrospective study. BMJ 26 Mar 2020;368:m1091. doi: 10.1136/bmj.m1091.

Chen X, et al. Detectable serum SARS-CoV-2 viral load (RNAaemia) is closely associated with drastically elevated interleukin 6 (IL-6) level in critically ill COVID-19 patients. medRxiv 2020.02.29.20029520.

Chen Z, et al. Efficacy of hydroxychloroquine in patients with COVID-19: results of a randomized clinical trial. MedRxiv. https://doi.org/10.1101/2020.03.22.20040758.

Cheng HY, et al. Contact tracing assessment of COVID-19 transmission dynamics in Taiwan and risk at different exposure periods before and after symptom onset. JAMA Intern Med. 2020 May 1. doi: 10.1001/jamainternmed.2020.2020.

Cheng MH, et al. Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. Proc Natl Acad Sci USA. 2020 Sep 28;202010722. doi: 10.1073/pnas.2010722117.

Cheng MP, et al. Diagnostic testing for severe acute respiratory syndrome-related coronavirus- 2: A narrative review. Ann Intern Med. 2020 Apr 13. doi: 10.7326/M20-1301.

Cheng MP, et al. Serodiagnostics for severe acute respiratory syndrome-related coronavirus-2: A narrative review. Ann Intern Med. 2020 Jun 4. doi: 10.7326/M20-2854.

Last updated 4 October 2020

Cheung EW, et al. Multisystem inflammatory syndrome related to COVID-19 in previously healthy children and adolescents in New York City. JAMA. 2020 Jun 8. doi: 10.1001/jama.2020.10374.

Cheung KS, et al. Gastrointestinal manifestations of SARS-CoV-2 infection and virus load in fecal samples from the Hong Kong cohort and systematic review and meta-analysis. Gastroenterology. 2020 Apr 3. pii: S0016-5085(20)30448-0. doi: 10.1053/j.gastro.2020.03.065.

Chia PY, et al. Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients. Nat Commun. 2020 May 29;11(1):2800. doi: 10.1038/s41467-020-16670-2.

Childs K, et al. Hospitalized patients with COVID-19 and HIV: A case series. Clin Infect Dis. 2020 May 27:ciaa657. doi: 10.1093/cid/cia657.

Chinazzi M, et al. The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak. Science. 2020 Mar 6. pii: eaba9757. doi: 10.1126/science.aba9757.

Cholankeril G, et al. Association of digestive symptoms and hospitalization in patients with SARS-CoV-2 infection. Am J Gastroenterol. https://doi.org/10.1053/j.gastro.2020.04.008.

Chorin E, et al. The QT interval in patients with SARS-CoV-2 infection treated with hydroxychloroquine/azithromycin. Nat Med. 2020 Apr 24. https://doi.org/10.1038/s41591-020- 0888-2.

Chou R, et al. Epidemiology of and risk factors for coronavirus infection in health care workers: A living rapid review. Ann Intern Med. 2020 May 5;M20-1632. doi: 10.7326/M20-1632.

Choudry FA, et al. High Thrombus Burden in Patients With COVID-19 Presenting With ST- Segment Elevation Myocardial Infarction. J Am Coll Cardiol. 2020 Sep 8;76(10):1168-1176. doi: 10.1016/j.jacc.2020.07.022.

Chow EJ, et al. Symptom screening at illness onset of health care personnel with SARS-CoV-2 infection in King County, Washington. JAMA. 2020 Apr 17. doi: 10.1001/jama.2020.6637.

Chu DK, et al. Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis. Lancet. 2020 Jun 1:S0140-6736(20)31142-9.

Chu H, et al. Comparative replication and immune activation profiles of SARS-CoV-2 and SARS- CoV in human lungs: an ex vivo study with implications for the pathogenesis of COVID-19. Clin Infect Dis. 2020 Apr 9. pii: ciaa410. doi: 10.1093/cid/ciaa410.

Chu HY, et al. Early detection of COVID-19 through a citywide pandemic surveillance program. N Engl J Med. 2020 May 1. doi: 10.1056/NEJMc2008646. Last updated 4 October 2020

Chung M, et al. CT Imaging Features of 2019 Novel Coronavirus (2019-nCoV). Radiology. 2020 Apr;295(1):202-207.

Ciceri F, et al. Microvascular COVID-19 lung vessels obstructive thromboinflammatory syndrome (MicroCLOTS): an atypical acute respiratory distress syndrome working hypothesis. Crit Care Resusc. 2020 Apr 15.

Clausen TM, et al. SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2. Cell. 2020 Sep 10. https://doi.org/10.1016/j.cell.2020.09.033.

Clerkin KJ, et al. COVID-19 and cardiovascular disease. Circulation. 2020 May 19;141(20):1648- 1655.

Colmenero I, et al. SARS-CoV-2 Endothelial Infection Causes COVID-19 Chilblains: Histopathological, Immunohistochemical and Ultraestructural Study of 7 Paediatric Cases. Br J Dermatol. 2020 Jun 20. doi: 10.1111/bjd.19327.

Connors JM, JH Levy. Thromboinflammation and the hypercoagulability of COVID-19. J Thromb Haemost. 2020 Apr 17. doi: 10.1111/jth.14849.

Connors JM, JH Levy. COVID-19 and its implications for thrombosis and anticoagulation. Blood. 2020 Apr 27. doi: 10.1182/blood.2020006000.

Consiglio CR, et al. The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19. Cell. 2020 Sept 3. https://doi.org/10.1016/j.cell.2020.09.016.

Contejean A, et al. Comparing dynamics and determinants of SARS-CoV-2 transmissions among health care workers of adult and pediatric settings in central Paris. Clin Infect Dis. 2020 Jul 15;ciaa977. doi: 10.1093/cid/ciaa977.

Corbett KS, et al. Evaluation of the mRNA-1273 Vaccine against SARS-CoV-2 in Nonhuman Primates. N Engl J Med. 2020 Jul 28. doi: 10.1056/NEJMoa2024671.

Coutard B, et al. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antiviral Res. 2020 Apr;176:104742.

COVID-19 Response Team. Severe outcomes among patients with Coronavirus disease 2019 (COVID-19)—United States, February 12-March 16, 2020. MMWR Morb Mortal Wkly Rep. 2020 Mar 27;69(12):343-346.

Last updated 4 October 2020

COVID-19 Response Team. Preliminary estimates of the prevalence of selected underlying health conditions among patients with Coronavirus disease 2019—United States, February 12- March 28, 2020. MMWR Morb Mortal Wkly Rep. 2020 Apr 3;69(13):382-386..

COVID-19 Response Team. Characteristics of health care personnel with COVID-19—United States, February 12-April 9, 2020. MMWR Morb Mortal Wkly Rep. 2020 Apr 14. https://www.cdc.gov/mmwr/volumes/69/wr/mm6915e6.htm?s_cid=mm6915e6_w.

COVIDSurg Collaborative. Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study. Lancet. 2020 Jul 4;396(10243):27-38.

Cowling BJ, et al. Impact assessment of non-pharmaceutical interventions against COVID-19 and influenza in Hong Kong: an observational study. medRxiv 2020.03.12.20034660.

Creel-Bulos C, et al. Acute cor pulmonale in critically ill patients with COVID-19. N Engl J Med. 2020 May 6. doi: 10.1056/NEJMc2010459.

Cruz AF, et al. Impact of glucocorticoid treatment in SARS-CoV-2 infection mortality: A retrospective controlled cohort study. medRxiv. https://doi.org/10.1101/2020.05.22.20110544.

Cummings MJ, et al. Epidemiology, clinical course, and outcomes of critically ill adults with COVID-19 in New York City: a prospective cohort study. Lancet. 2020 May 19. https://doi.org/10.1016/S0140-6736(20)31189-2.

Cunningham JW, et al. Clinical Outcomes in Young US Adults Hospitalized With COVID-19. JAMA Intern Med. 2020 Sep 9. doi: 10.1001/jamainternmed.2020.5313.

Damas J, et al. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proc Natl Acad Sci USA. 2020 Aug 21;202010146. doi: 10.1073/pnas.2010146117.

D’Amico F, et al. Diarrhea during COVID-19 infection: pathogenesis, epidemiology, prevention and management. Clin Gastroenterol Hepatol. 2020 Apr 8. pii: S1542-3565(20)30481-X. doi: 10.1016/j.cgh.2020.04.001.

Dandachi D, et al. Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19. Clin Infect Dis. 2020 Sep 9;ciaa1339. doi: 10.1093/cid/ciaa1339.

Daniloski Z, et al. The D614G mutation in SARS-CoV-2 spike increases transduction of multiple human cell types. bioRxiv. https:doi.org/10.1101/2020.06.14.151357.

Last updated 4 October 2020

Dau NQ, et al. Why N95 should be the standard for all COVID-19 inpatient care. Ann Intern Med. 2020 Jun 29. doi: 10.7326/M20-2623.

Davies NG, et al. Age-dependent effects in the transmission and control of COVID-19 epidemics. Nat Med. 2020 Jun 16. doi: 10.1038/s41591-020-0962-9.

Davies P, et al. Intensive care admissions of children with paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) in the UK: a multicentre observational study. Lancet Child Adolesc Health. 2020 Jul 9. https://doi.org/10.1016/S2352- 4642(20)30215-7.

Dawson P, et al. Loss of taste and smell as distinguishing symptoms of COVID-19. Clin Infect Dis. 2020 Jun 21;ciaa799. doi: 10.1093/cid/ciaa799.

Day M. COVID-19: Ibuprofen should not be used for managing symptoms, say doctors and scientists. BMJ. 2020 Mar 17;368:m1086. doi: 10.1136/bmj.m1086.

De Abajo FJ, et al. Use of renin-angiotensin-aldosteroine system inhibitors and risk of COVID-19 requiring admission to hospital: a case-population study. Lancet. 2020 May 14. https://doi.org/10.1016/S0140-6736(20)31031-8.

De Backer W, et al. CT-derived measurements of pulmonary blood volume in small vessels and need for oxygen in COVID-19 patients. medRxiv. https://doi.org/10.1101.2020.06.03.20121483.

De Biasi S, et al. Marked T cell activation, senscence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia. Nat Commun. 2020 Jul 6;11(1):3434. doi: 10.1038/s41467- 020-17292-4.

De Lusignan S, et al. Risk Factors for SARS-CoV-2 Among Patients in the Oxford Royal College of General Practitioners Research and Surveillance Centre Primary Care Network: A Cross- Sectional Study. Lancet Infect Dis. 2020 May 15;S1473-3099(20)30371-6.

De Man P, et al. Outbreak of COVID-19 in a nursing home associated with aerosol transmission as a result of inadequate ventilation. Clin Infect Dis. 2020 Aug 28;ciaa1270. doi: 10.1093/cid/ciaa1270.

De Masson A, et al. Chilblains are a common cutaneous finding during the COVID-19 pandemic: a retrospective nationwid study from France. J Am Acad Dermatol. 2020 May 4. doi: 10.1016/jaad.2020.04.161.

De Smet D, et al. Vitamin D deficiency as risk factor for severe COVID-19: a convergence of two pandemics. medRxiv. https://doi.org/10.1101/2020.05.01.20079376.

Last updated 4 October 2020

De Wit E, et al. Prophylactic and therapeutic remdesivir (GS-5734) treatment in the rhesus macaque model of MERS-CoV infection. Proc Natl Acad Sci USA. 2020 Feb 13. pii: 201922083. doi: 10.1073/pnas.1922083117.

Dearlove B, et al. A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Proc Natl Acad Sci USA. 2020 Aug 31;202008281. doi: 10.1073/pnas.2008281117.

Deeks JJ, et al. Antibody tests for identification of current and past infection with SARS-CoV-2. Cochrane Database Syst Rev. 2020 Jun 25;6:CD013652. doi: 10.1002/14651858.CD013652.

Deeks JJ, et al. Operation Moonshot proposals are scientifically unsound. BMJ. 2020 Sep 22;370:m3699. doi: 10.1136/bmj.m3699.

Deftereos SG, et al. Effect of Colchicine vs Standard Care on Cardiac and Inflammatory Biomarkers and Clinical Outcomes in Patients Hospitalized With Coronavirus Disease 2019: The GRECCO-19 Randomized Clinical Trial. JAMA Netw Open. 2020 Jun 1;3(6):e2013136. doi: 10.1001/jamanetworkopen.2020.13136.

Dehning J, et al. Inferring change points in the spread of COVID-19 reveals the effectiveness of interventions. Science. 2020 May 14:eabb9789.

Delahoy MJ, et al. Characteristics and maternal and birth outcomes of hospitalized pregnant women with laboratory-confirmed COVID-19—COVID-NET, 13 states, March 1-August 22, 2020. MMWR Morb Mortal Wkly Rep. 2020 Sep 16. https://www.cdc.gov/mmwr/volumes/69/wr/mm6938e1.

Del Valle DM, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020 Aug 24. doi: 10.1038/s41591-020-1051-9.

Deng X, et al. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science. 2020 Jul 31;369(6503):582-587. doi: 10.1126/science.abb9263.

Dequin PF, et al. Effect of Hydrocortisone on 21-Day Mortality or Respiratory Support Among Critically Ill Patients With COVID-19: A Randomized Clinical Trial. JAMA. 2020 Sep 2. doi: 10.1001/jama.2020.16761.

Deslandes A, et al. SARS-CoV-2 was already spreading in France in late December 2019. Int J Antimicrob Agents. 2020 May 3. https://doi.org/10.1016/j.ijantimicag.2020.106006.

Di Giambenedetto S, et al. Still much to learn about the diagnostic role of SARS-CoV-2 antibody detection. Clin Infect Dis. 2020 May 2. doi: 10.1093/cd/ciaa532.

Dingens AS, et al. Seroprevalence of SARS-CoV-2 among children visiting a hospital during the initial Seattle outbreak. medRxiv. https://doi.org/10.1101.2020.05.26.20114124.

Last updated 4 October 2020

Dinnes J, et al. Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS- CoV-2 infection. Cochrane Database Syst Rev. 2020 Aug 26;8:CD013705. doi: 10.1002/14651858.CD013705.

Dinnon 3d KH et al. A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures. Nature. 2020 Aug 27. doi: 10.1038/s41586-020-2708-8.

Diorio C, et al. Multisystem inflammatory syndrome in children and COVID-19 are distinct presentations of SARS-CoV-2. J Clin Invest. 2020 Jul 30;140970. doi: 10.1172/JCI140970.

Dittadi R, et al. Early antibody response to SARS-CoV-2. medRxiv. https://doi.org/10.1101/2020.05.19.20099317.

Docherty AB, et al. Features of 16,749 hospitalised UK patients with COVID-19 using the ISARIC WHO clinical characterisation protocol. medRxiv. https://doi.org/10.1101.2020.04.23.20076042.

Dodd RY, et al. Change in Donor Characteristics and Antibodies to SARS-CoV-2 in Donated Blood in the US, June-August 2020. JAMA. 2020 Sep 14. doi: 10.1001/jama.2020.18598.

Dolhnikoff M, et al. Pathological evidence of pulmonary thrombotic phenomena in severe COVID-19. J Thromb Haemost. 2020 Apr 15. doi: 10.1111/JTH.14844.

Dong L, et al. Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn. JAMA. 26 Mar 2020. Doi:10.1001/jama.2020.4621.

Driggin E, et al. Cardiovascular considerations for patients, health care workers, and health systems during the COVID-19 pandemic. J Am Coll Cardiol. 2020 May 12;75(18):2352-2371.

Du S, et al. Structurally resolved SARS-CoV-2 antibody shows high efficacy in severely infected hamsters and provides a potent cocktail pairing strategy. Cell. 2020 Sep 10. https://doi.org/10.1016/j.cell.2020.09.035.

Duan K, et al. Effectiveness of convalescent plasma therapy in severe COVID-19 patients. Proc Natl Acad Sci USA. 2020 Apr 6. pii: 202004168. doi: 10.1073/pnas.2004168117.

Dufort EM, et al. Multisystem inflammatory syndrome in children in New York State. N Engl J Med. 2020 Jun 29. doi: 10.1056/NEJMoa2021756.

Duggan NM, et al. A case report of possible novel coronavirus 2019 reinfection. Am J Emerg Med. 2020 Jul 4:S0735-6757(20)30583-0. doi: 10.1016/j.ajem.2020.06.079.

Last updated 4 October 2020

Dyal JW, et al. COVID-19 among workers in meat and poultry processing facilities – 19 states, April 2020. MMWR Morb Mortal Wkly Rep. 2020 May 8:69(18). doi: 10.15585/mmwr.mm6918e3.

Edridge AWD, et al. Seasonal coronavirus protective immunity is short-lasting. Nat Med. 2020 Sep 14. doi: 10.1038/s41591-020-1083-1.

Ehrhardt J, et al. Transmission of SARS-CoV-2 in children aged 0 to 19 years in childcare facilities and schools after their reopening in May 2020, Baden-Württemberg, Germany. Euro Surveill. 2020 Sep;25(36). doi: 10.2807/1560-7917.ES.2020.25.36.2001587.

El Moheb M, et al. Gastrointestinal Complications in Critically Ill Patients With and Without COVID-19. JAMA. 2020 Sep 24. doi: 10.1001/jama.2020.19400.

Elharrar X, et al. Use of prone positioning in nonintubated patients with COVID-19 and hypoxemic acute respiratory failure. JAMA. 2020 May 15;e208255.

Ellinghaus D, et al. Genomewide association study of severe COVID-19 with respiratory failure. N Engl J Med. 2020 Jun 17. doi: 10.1056/NEJMoa2020283.

Ellington S, et al. Characteristics of Women of Reproductive Age With Laboratory-Confirmed SARS-CoV-2 Infection by Pregnancy Status - United States, January 22-June 7, 2020. MMWR Morb Mortal Wkly Rep. 2020 Jun 26;69(25):769-775.

Ellul MA, et al. Neurological associations of COVID-19. Lancet Neurol. 2020 Jul 2. https://doi.org/10.1016/S1474-4422(20)30221-0.

Emery JC, et al. The contribution of asymptomatic SARS-CoV-2 infections to transmission on the Diamond Princess cruise ship. Elife. 2020 Aug 24;9:e58699. doi: 10.7554/eLife.58699.

Endo A, et al. Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. Wellcome Open Res. 2020 Apr 09. https://doi.org/10.12688/wellcomeopenres. 15842.1.

Escobar LE, et al. BCG vaccine protection from severe coronavirus disease 2019 (COVID-19). Proc Natl Acad Sci USA. 2020 Jul 9;202008410. doi: 10.1073/pnas.2008410117.

Estcourt LJ, DJ Roberts. Convalescent plasma for COVID-19. BMJ. 2020 Sep 15;370:m3516. doi: 10.1136/bmj.m3516.

Eyre DW, et al. Differential occupational risks to healthcare workers from SARS-CoV-2 observed during a prospective observational study. eLife. 2020 Aug 21;9:e60675. doi: 10.7554/eLife.60675.

Last updated 4 October 2020

Eyre DW, et al. Stringent thresholds for SARS-CoV-2 IgG assays result in underdetection of cases reporting loss of taste/smell. medRxiv. https://doi.org/10.1101/2020.07.21.20159038.

Fadel R, et al. Early short course corticosteroids in hospitalized patients with COVID-19. Clin Infect Dis. 2020 May 19;ciaa601.

Fajnzylber JM, et al. SARS-CoV-2 viral load is associated with increased disease severity and mortality. medRxiv. https://doi.org/10.1101.2020.07.15.20131789.

Fang FC, et al. The laboratory diagnosis of COVID-19—Frequently asked questions. Clin Infect Dis. 2020 Jun 8:ciaa742. doi: 10.1093/cid/ciaa742.

Fang FC, Schooley RT. Treatment of COVID-19 – Evidence-based or personalized medicine? Clin Infect Dis. 2020 Jul 15:ciaa996. doi: 10.1093/cid/ciaa996.

Fang Y, et al. Sensitivity of chest CT for COVID-19: Comparison to RT-PCR. Radiology. 2020 Feb 19:200432. doi: 10.1148/radiol.2020200432.

Faust JS, C del Rio. Relative disease burdents of COVID-19 and seasonal influenza in New York City, February 1 – April 18, 2020. medRxiv. https://doi.org/10.1101/2020.04.22.20073551.

Fauver JR, et al. Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology. medRxiv doi: https://doi.org/10.1101/2020.03.25.20043828.

Feldstein LR, et al. Multisystem inflammatory syndrome in U.S. children and adolescents. N Engl J Med. 2020 Jun 29. doi: 10.1056/NEJMoa2021680.

Felsenstein S, CM Hedrich. COVID-19 in children and young people. Lancet Rheumatol. 2020 Jun 29. https://doi.org/10.1016/S2665-9913(20)3-212-5.

Felsenstein S, CM Hedrich. COVID-19 in children and young people. Clin Immunol. 2020 Sep 6;220:108588. doi: 10.1016/j.clim.2020.108588.

Fennelly KP, et al. Particle sizes of infectious aerosols: Implications for infection control. Lancet Respir Med. 2020 Jul 24. https://doi.org/10.1016/S2213-2600(20)30323-4.

Feng Z, et al. The use of adjuvant therapy in preventing progression to severe pneumonia in patients with coronavirus disease 2019: A multicenter data analysis. medRxiv. https://doi.org/10.1101/2020.04.08.20057539.

Feng Z, et al. The novel severe respiratory syndrome coronavirus 2 (SARS-CoV-2) directly decimates human spleens and lymph nodes. medRxiv. https://doi.org/10.1101/2020.03.27.20045427.

Last updated 4 October 2020

Ferguson NM, et al. Impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcar demand. Imperial College COVID-19 Response. 16 March 2020.

Ferretti L, et al. The timing of COVID-19 transmission. medRxiv. https://doi.org/10.1101.2020.09.04.20188516.

Fischer EP, et al. Low-cost measurement of facemask efficacy for filtering expelled droplets during speech. Sci Adv. 2020 Aug 7. doi: 10.1126/sciadv.abd3083.

Fischer RJ, et al. Assessment of N95 respirator decontamination and re-use for SARS-CoV-2. medRxiv. https://doi.org/10.1101/2020.04.11.20062018.

Fisher KA, et al. Community and close contact exposures associated with COVID-19 among symptomatic adults ≥ 18 years in 11 outpatient health care facilities—United States, July 2020. MMWR Morb Mortal Wkly Rep. 2020 Sept 11. doi: http://dx.doi.org/10.15585/mmwr.mm6936a5.

Fisman DN, et al. Risk factors associated with mortality among residents with coronavirus disease 2019 (COVID-19) in long-term care faciliities in Ontario, Canada. JAMA Netw Open. 2020 Jul 1:3(7):e2015957.

Flaxman S, et al. Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe. Nature. 2020 Jun 8. doi: 10.1038/s41586-020-2405-7.

Focosi D, et al. Convalescent Plasma Therapy for COVID-19: State of the Art. Clin Microbiol Rev. 2020 Aug 12;33(4):e00072-20. doi: 10.1128/CMR.00072-20.

Fodoulian L, et al. SARS-CoV-2 receptor and entry genes are expressed by sustentacular cells in the human olfactory neuroepithelium. bioRxiv. doi: https://doi.org/10.1101/2020.03.31.013268.

Folgueira MD, et al. Persistent SARS-CoV-2 replication in severe COVID-19. medRxiv. https://doi.org/10.1101/2020.06.10.20127837.

Fosbøl EL, et al. Association of Angiotensin-Converting Enzyme Inhibitor or Angiotensin Receptor Blocker Use With COVID-19 Diagnosis and Mortality. JAMA. 2020 Jun 19;e2011301. doi: 10.1001/jama.2020.11301.

Fox SE, et al. Pulmonary and cardiac pathology in African American patients with COVID-19: an autopsy series from New Orleans. Lancet Respir Med. 2020 May 27. doi: 10.1016/S2213- 2600(20)30243-5.

Last updated 4 October 2020

Foy BH, et al. Association of Red Blood Cell Distribution Width With Mortality Risk in Hospitalized Adults With SARS-CoV-2 Infection. JAMA Netw Open. 2020 Sep 1;3(9):e2022058. doi: 10.1001/jamanetworkopen.2020.22058.

Freedberg DE, et al. Famotidine Use is Associated with Improved Clinical Outcomes in Hospitalized COVID-19 Patients: A Propensity Score Matched Retrospective Cohort Study. Gastroenterology. 2020 May 22;S0016-5085(20)34706-5. doi: 10.1053/j.gastro.2020.05.053.

Freeman EE, et al. The spectrum of COVID-19-associated dermatologic manifestations: An international registry of 716 patients from 31 countries. medRxiv. https://doi.org/10.1101/2020.05.24.20111914.

Fried MW, et al. Patient Characteristics and Outcomes of 11,721 Patients with COVID19 Hospitalized Across the United States. Clin Infect Dis. 2020 Aug 28;ciaa1268. doi: 10.1093/cid/ciaa1268.

Frieden TR, CT Lee. Identifying and Interrupting Superspreading Events-Implications for Control of Severe Acute Respiratory Syndrome Coronavirus 2. Emerg Infect Dis. 2020 Jun;26(6):1059- 1066. doi: 10.3201/eid2606.200495.

Furtado RHM, et al. Azithromycin in addition to standard of care versus standard of care alone in the treatment of patients admitted to the hospital with severe COVID-19 in Brazil (COALITION II): a randomised clinical trial. Lancet. 2020 Sep 4. https://doi.org/10.1016/ S0140- 6736(20)31862-6.

Furukawa NW, et al. Evidence supporting transmission of severe acute respiratory syndrome coronavirus 2 while presymptomatic or asymptomatic. Emerg Infect Dis. 2020 Jul;26(7):e201595. doi: 10.3201/eid2607.201595.

Furuse Y, et al. Clusters of coronavirus disease in communities, Japan, January-April 2020. Emerg Infect Dis. 2020 June 10. doi: 10.3201/eid2609.202272.

Gahide G, et al. COVID-19 patients presenting with afebrile acute abdominal pain. Clin Med. 2020 Apr 27. doi: 10.7861/clinmed.2020-0150.

Galang RR, et al. Severe coronavirus infections in pregnancy: A systematic review. Obstet Gynecol. 2020 Jun 16. doi: 10.1097/AOG.0000000000004011.

Gallais F, et al. Intrafamilial exposure to SARS-CoV-2 induces cellular immune response without seroconversion. medRxiv. https://doi.org/10.1101.2020.06.21.20132449.

Gandhi M, et al. Asymptomatic transmission; the Achilles’ heel of current strategies to control COVID-19. N Engl J Med. 2020 May 28;382(22):2158-2160.

Last updated 4 October 2020

Gandhi M, et al. Masks do more than protect others during COVID-19: Reducing the inoculum of SARS-CoV-2. J Gen Intern Med. 2020 Jul 31;1-4. doi: 10.1007/s11606-020-06067-8.

Gandhi M, GW Rutherford. Facial Masking for Covid-19 - Potential for "Variolation" as We Await a Vaccine. N Engl J Med. 2020 Sep 8. doi: 10.1056/NEJMp2026913.

Gao J, et al. Breakthrough: Chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies. Biosci Trends. 2020 Mar 16;14(1):72-73.

Gao T, et al. Highly pathogenic coronavirus N protein aggravates lung injury by MASP-2- mediated complement over-activation. medRxiv. 2020.03.29.20041962.

Gao Q, et al. Rapid development of an inactivated vaccine candidate for SARS-CoV-2. Science. 2020 May 6. doi: 10.1126/science.abc1932.

Garassino MC, et al. COVID-19 in patients with thoracic malignancies (TERAVOLT): First results of an international, registry-based, cohort study. Lancet Oncol. 2020 Jun 12;S1470- 2045(20)30314-4.

Garcia-Vidal C, et al. Personalized therapy approach for hospitalized patients with COVID-19. Clin Infect Dis. 2020 Jul 10;ciaa964. doi: 10.1093/cid/ciaa964.

Gardner B, AM Kilpatrick. Contact tracing efficiency, transmission heterogeneity, and accelerating COVID-1 19 epidemics. medRxiv. https://doi.org/10.1101/2020.09.04.20188631.

Garg S, et al. Hospitalization rates and characteristics of patients hospitalized with laboratory- confirmed coronavirus disease 2019—COVID-NET, 14 states, March 1-30, 2020. MMWR Morb Mortal Wkly Rep. 2020 Apr 17;69(15):458-464.

Garibaldi BT, et al. Patient Trajectories Among Persons Hospitalized for COVID-19 : A Cohort Study. Ann Intern Med. 2020 Sep 22. doi: 10.7326/M20-3905.

Garvin MR, et al. A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm. Elife. 2020 Jul 7;9:e59177. doi: 10.7554/eLife.59177.

Gattinoni L, et al. COVID-19 does not lead to a “typical” Acute Respiratory Distress Syndrome. Am J Respir Crit Care Med. 2020 Mar 30. doi: 10.1164/rccm.202003-0817LE.

Gattinoni L, et al. COVID-19 pneumonia: ARDS or not? Crit Care. 2020 Apr 16;24(1):154.

Gautret P, et al. Hydroxychloroquine and azithromycin as a treatment of COVID-19: Preliminary results of an open-label non-randomized clinical trial. Int J Antimicrob Agents, in press. doi: 10.1016/j.ijantmicag.2020.105949. medRxiv 2020.03.16.20037135.

Last updated 4 October 2020

Gautret P, et al. Clinical and microbiological effect of a combination of hydroxychloroquine and azithromycin in 80 COVID-19 patients with at least a six-day follow up: an observational study. Unpublished. https://www.mediterranee-infection.com/wp-content/uploads/2020/03/COVID- IHU-2-1.pdf.

Geleris J, et al. Observational study of hydroxychloroquine in hospitalized patients with COVID- 19. N Engl J Med. 2020 May 7. doi: 10.1056/NEJMoa2012410.

Gendelman O, et al. Continuous hydroxychloroquine or colchicine therapy does not prevent infection with SARS-CoV-2: Insights from a large healthcare database analysis. Autoimmun Rev. 2020 May 4:102566.

Gentry CA, et al. Long-term hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study. Lancet Rheumatol. 2020 Sep 21. https://doi.org/10.1016/ S2665-9913(20)30305-2.

Gervasoni C, et al. Clinical features and outcomes of HIV patients with coronavirus disease 2019. Clin Infect Dis. 2020 May 14;ciaa579.

Gharbharan A, et al. Convalescent plasma for COVID-19. A randomized clinical trial. medRxiv. https://doi.org/10.1101/2020.07.01.20139857.

Ghinai I, et al. Community transmission of SARS-CoV-2 at two family gatherings—Chicago, Illinois, February-March 2020. MMWR Morb Mortal Wkly Rep. 2020 Apr 8. https://www.cdc.gov/mmwr/volumes/69/wr/mm6915e1.htm?s_cid=mm6915e1_w.

Giamarellos-Bourboulis EJ, et al. Complex immun dysregulation in COVID-19 patients with severe respiratory failure. Cell Host Microbe. 2020 Apr 17. pii: S1931-3128(20)30236-5. doi: 10.1016/j.chom.2020.04.009.

Gibani MM, et al. Assessing a novel, lab-free, point-of-care test for SARS-CoV-2 (CovidNudge): A diagnostic accuracy study. Lancet Microbe. 2020 Sep 17. https://doi.org/10.1016/ S2666- 5247(20)30121-X.

Giudice V, et al. Combination of Ruxolitinib and Eculizumab for Treatment of Severe SARS-CoV- 2-Related Acute Respiratory Distress Syndrome: A Controlled Study. Front Pharmacol. 2020 Jun 5;11:857. doi: 10.3389/fphar.2020.00857.

Gladstone DE, et al. Regulatory T Cells for Treating Patients With COVID-19 and Acute Respiratory Distress Syndrome: Two Case Reports. Ann Intern Med. 2020 Jul 6;L20-0681. doi: 10.7326/L20-0681.

Last updated 4 October 2020

Godfred-Cato S, et al. COVID-19-Associated Multisystem Inflammatory Syndrome in Children - United States, March-July 2020. MMWR Morb Mortal Wkly Rep. 2020 Aug 14;69(32):1074- 1080.

Gold JAW, et al. Characteristics and Clinical Outcomes of Adult Patients Hospitalized with COVID-19 - Georgia, March 2020. MMWR Morb Mortal Wkly Rep. 2020 May 8:69(18):545-550.

Goldman JD, et al. Remdesivir for 5 or 10 days in patients with severe COVID-19. N Engl J Med. 2020 May 27. doi: 10.1056/NEJMoa2015301.

Goldman JD, et al. Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. medRxiv. 2020 Sep 25;2020.09.22.20192443. doi: 10.1101/2020.09.22.20192443.

Goldsmith CS, et al. Electron microscopy of SARS-CoV-2: a challenging task. Lancet. 2020 May 19. https:doi.org/10.1016/S0140-6736(20)31188-0.

Goldstein E, et al. On the effect of age on the transmission of SARS-CoV-2 in households, schools and the community. medRxiv. 2020 Jul 24;2020.07.19.20157362. doi: 10.1101/2020.07.19.20157362.

Gonçalves A, et al. Timing of antiviral treatment initiation is critical to reduce SARS-CoV-2 viral load. medRxiv. https://doi.org/10.1101/2020.04.04.20047886.

Gonzalez-Reiche AS, et al. Introductions and early spread of SARS-CoV-2 in the New York City area. Science. 2020 May 29:eabc1917. doi: 10.1126/scioence.abc1917.

Gordon CJ, et al. Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency. J Biol Chem. 2020 Apr 15. https://www.jbc.org/cgi/doi/10.1074/jbc.RA120.013679.

Goshua G, et al. Endotheliopathy in COVID-19-associated coagulopathyu: Evidence from a single-centre, cross-sectional study. Lancet Haematol. 2020 Jun 30. https://doi.org/10.1016/S2352-3026(20)30215-5.

Gottlieb S, et al. National Coronavirus Response: A road map to reopening. 28 Mar 2020. American Enterprise Institute. https://www.aei.org/research-products/report/national- coronavirus-response-a-road-map-to-reopening/.

Goyal A, et al. Wrong person, place and time: Viral load and contact network structure predict SARS-CoV-2 transmission and super-spreading events. medRxiv. https://doi.org/10.1101/2020.08.07.20169920.

Goyal P, et al. Clinical characteristics of COVID-19 in New York City. N Engl J Med. 2020 Apr 17. doi: 10.1056/NEJMc2010419. Last updated 4 October 2020

Grasselli G, et al. Baseline characteristics and outcomes of 1591 patients infected with SARS- CoV-2 admitted to ICUs of the Lombardy Region, Italy. JAMA. 6 Apr 2020. Doi:10.1001/jama.2020.5394.

Grasselli G, et al. Risk factors associated with mortality among patients with COVID-19 in intensive care units in Lombardy, Italy. JAMA Intern Med. 2020 Jul 15. doi: 10.1001/jamainternmed.2020.3539.

Grasselli G, et al. Pathophysiology of COVID-19-associated acute respiratory distress syndrome: a multicentre prospective observational study. 2020 Aug 27. https://doi.org/10.1016/ S2213- 2600(20)30370-2.

Green DA, et al. Clinical performance of SARS-CoV-2 molecular testing. medRxiv. https://doi.org/10.1101.2020.05.06.20093575.

Grein J, et al. Compassionate use of remdesivir for patients with severe COVID-19. N Engl J Med. 2020 Apr 10. doi: 10.1056/NEJMoa2007016.

Gremese E, et al. Sarilumab use in severe SARS-CoV-2 pneumonia. eClinicalMedicine. 2020 Oct 2. https://doi.org/10.1016/j.eclinm.2020.100553.

Grifoni A, et al. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals. Cell. 2020 May 7. https://doi.org/10.1016/j.cell.2020.05.015.

Gritti G, et al. Use of siltuximab in patients with COVID-19 pneumonia requiring ventilatory support. medRxiv. https://doi.org/10.1101/2020.04.01.20048561.

Gruber C, et al. Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C). Cell. 2020 Sep 10. https://doi.org/10.1016/j.cell.2020.09.034.

Grzelak L, et al. A comparison of four serological assays for detecting anti-SARS-CoV-2 antibodies in human serum samples from different populations. Sci Transl Med. 2020 Aug 17;eabc3103. doi: 10.1126/scitranslmed.abc3103.

Gu J, et al. COVID-19: Gastrointestinal manifestations and potential fecal-oral transmission. Gastroenterology. 2020 Mar 3. pii: S0016-5085(20)30281-X. doi: 10.1053/j.gastro.2020.02.054.

Guallar MP, et al. Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity. Int J Infect Dis. 2020 Jun 14;97:290-292.

Last updated 4 October 2020

Guan WJ, et al. Clinical Characteristics of Coronavirus Disease 2019 in China. 2020 Feb 28. doi: 10.1056/NEJMoa2002032.

Guan WJ, et al. Comorbidity and its impact on 1,590 patients with COVID-19 in China: a nationwide analysis. MedRxiv 2020.02.25.20027664.

Guaraldi G, et al. Tocilizumab in patients with severe COVID-19: a retrospective cohort study. Lancet Rheumatol. 2020 Jun 24. https://doi.org/10.1016/S2665-9913(20)30173-9.

Gudbjartsson DF, et al. Spread of SARS-CoV-2 in the Icelandic population. N Engl J Med. 2020 Apr 14. doi: 10.1056/NEJM0a2006100.

Gudbjartsson DF, et al. Humoral immune response to SARS-CoV-2 in Iceland. N Engl J Med. 2020 Sep 1. doi: 10.1056/NEJMoa2026116.

Guervilly C, et al. Circulating Endothelial Cells as a Marker of Endothelial Injury in Severe COVID -19. J Infect Dis. 2020 Aug 19;jiaa528. doi: 10.1093/infdis/jiaa528.

Guo L, et al. Profiling early humoral response to diagnose novel coronavirus disease (COVID-19). Clin Infect Dis. 2020 Mar 21. pii: ciaa310. doi: 10.1093/cid/ciaa310.

Guo T, et al. Cardiovascular implications of fatal outcomes of patients with coronavirus disease 2019 (COVID-19). JAMA Cardiol. 2020 Mar 27. doi: 10.1001/jamacardio.2020.1017.

Guo ZD. Et al. Aerosol and surface distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards, Wuhan, China, 2020. Emerg Infect Dis. 2020 Apr 10;26(7). doi: 10.3201/eid2607.200885.

Gupta A, et al. Extrapulmonary manifestations of COVID-19. Nat Med. 2020 Jul 10. doi: 10.1038/s41591-020-0968-3.

Gupta AK, et al. Current perspectives on coronavirus 2019 (COVID-19) and cardiovascular disease: A white paper by the JAHA editors. J Am Heart Assoc. 2020 Apr 29:e017013.

Gupta S, et al. Factors associated with death in critically illo patients with coronavirus disease 2019 in the US. JAMA Intern Med. 2020 Jul 15. doi: 10.1001/jamainternmed.2020.3596.

Gussow AB, et al. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Proc Natl Acad Sci USA. 2020 May 18. www.pnas.org/cgi.doi/10.1073/pnas.2008176117.

Guzik TJ, et al. COVID-19 and the cardiovascular system: Implications for risk assessment, diagnosis, and treatment options. Cardiovasc Res. 2020 Apr 30. doi: 10.1093/cvr/cvaa106.

Last updated 4 October 2020

Habel JR, et al. Suboptimal SARS-CoV-2-specific CD8+ T cell response associated with the prominent HLA-A*02:01 phenotype. Proc Natl Acad Sci USA. 2020 Sept 9. www.pnas.org/cgi/doi/10.1073/pnas.2015486117.

Haberman R, et al. COVID-19 in immune-mediated inflammatory diseases – Case series from New York. N Engl J Med. 2020 Apr 29. doi: 10.1056/NEJMc2009567.

Hadjadj J, et al. Impaired type I interferon activity and inflammatory responses in severe COVID- 19 patients. Science. 2020 Aug 7;369(6504):718-724. doi: 10.1126/science.abc6027.

Hagman K, et al. SARS-CoV-2 RNA in serum as predictor of severe outcome in COVID-19: a retrospective cohort study. Clin Infect Dis. 2020 Aug 28;ciaa1285. doi: 10.1093/cid/ciaa1285.

Hains DS, et al. Asymptomatic seroconversion of immunoglobulins to SARS-CoV-2 in a pediatric dialysis unit. JAMA. 2020 May 14. doi: 10.1001/jama.2020.8438.

Halfmann PJ, et al. Transmission of SARS-CoV-2 in domestic cats. N Engl J Med. 2020 May 13. doi: 10.1056/NEJMc2013400.

Hall MW, et al. Immune modulation in COVID-19: Strategic considerations for personalized therapeutic interventions. Clin Infect Dis. 2020 Jul 1:ciaa904. doi: 10.1093/cid/ciaa904.

Halstead SB, L Katzelnick. COVID 19 Vaccines: Should we fear ADE? J Infect Dis. 2020 Aug 12;jiaa518. doi: 10.1093/infdis/jiaa518.

Hamer M, et al. Overweight, obesity, and risk of hospitalization for COVID-19: A community- based cohort study of adults in the United Kingdom. Proc Natl Acad Sci USA. 2020 Aug 11;202011086. doi: 10.1073/pnas.2011086117.

Hamiel U, et al. SARS-CoV-2 rates in BCG-vaccinated and unvaccinated young adults. JAMA. 2020 May 13. doi: 10.1001/jama.2020.8189.

Hamner L, et al. High SARS-CoV-2 attack rate following exposure at a choir practice—Skagit County, Washington, March 2020. MMWR Morb Mortal Wkly Rep. 2020 May 12. https://www.cdc.gov/mmwr/volumes/69/wr/mm691936.htm?s_cid=mm6919e6_w.

Han C, et al. Digestive symptoms in COVID-19 patients with mild disease severity: Clinical presentation, stool viral RNA testing, and outcomes. Am J Gastroenterol 2020 Apr 15. doi: 10.14309/ajg. 0000000000000664.

Han E, et al. Lessons learnt from easing COVID-19 restrictions: an analysis of countries and regions in Asia Pacific and Europe. Lancet. 2020 Sep 24;S0140-6736(20)32007-9.

Last updated 4 October 2020

Han H, et al. SARS-CoV-2 RNA more readily detected in induced sputum than in throat swabs of convalescent COVID-19 patients. Lancet Infect Dis. 2020 Mar 12. pii: S1473-3099(20)30174-2. doi: 10.1016/S1473-3099(20)30174-2.

Han MS, et al. Clinical Characteristics and Viral RNA Detection in Children With Coronavirus Disease 2019 in the Republic of Korea. JAMA Pediatr. 2020 Aug 28. doi: 10.1001/jamapediatrics.2020.3988.

Hanff TC, et al. Thrombosis in COVID-19. Am J Hematol. 2020 Aug 28. doi: 10.1002/ajh.25982.

Hanson KE, et al. Infectious Diseases Society of America Guidelines on the Diagnosis of COVID- 19. 2020 Jun 16;ciaa760. doi: 10.1093/cid/ciaa760 and 10.1093/cid/cid1343. www.idsociety.org/COVID19guidelines/dx.

Hao X, et al. Reconstruction of the full transmission dynamics of COVID-19 in Wuhan. Nature. 2020 Jul 16. doi: 10.1038/s41586-020-2554-8.

Hanley B, et al. Histopathological findings and viral tropism in UK patients with severe fatal COVID-19: a post-mortem study. Lancet Microbe. 2020 Aug 20. doi: 10.1016/S2666- 5247(20)30115-4.

Harrison SL, et al. Comorbidities associated with mortality in 31,461 adults with COVID-19 in the United States: A federated electronic medical record analysis. PLoS Med. 2020 Sep 10;17(9):e1003321. doi: 10.1371/journal.pmed.1003321.

Harzallah I, et al. Lupus anticoagulant is frequent in patients with COVID-19. J Thromb Haemost. 2020 Apr 23. doi: 10.1111/jth.14867.

Hassan AO, et al. A SARS-CoV-2 infection model in mice demonstrates protection by neutralizing antibodies. Cell. 2020 June 3. https://doi.org/10.1016/j.cell.2020.06.011.

Hassan AO, et al. A single-dose intranasal ChAd vaccine protects upper and lower respiratory tracts against SARS-CoV-2. Cell. 2020 Aug 14. https://doi.org/10.1016/j.cell.2020.08.026.

Hastie CE, et al. Vitamin D and COVID-19 infection and mortality in UK Biobank. Eur J Nutr. 2020 Aug 26. doi: 10.1007/s00394-020-02372-4.

Havers FP, et al. Seroprevalence of antibodies to SARS-CoV-2 in 10 sites in the United States, March 23-May 12, 2020. JAMA Intern Med. 2020 Jul 21. doi: 10.1001/jamainternmed.2020.4130.

Hayek SS, et al. In-hospital cardiac arrest in critically ill patients with covid-19: multicenter cohort study. BMJ. 2020 Sep 30;371:m3513. doi: 10.1136/bmj.m3513. Last updated 4 October 2020

He X, et al. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat Med. 2020 May;26(5):672-675.

Heald-Sargent T, et al. Age-Related Differences in Nasopharyngeal Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Levels in PatientsWith Mild to Moderate Coronavirus Disease 2019 (COVID-19). JAMA Pediatr. 2020 Jul 30. doi: 10.1001.jamapediatrics.2020.3651.

Helms J, et al. High risk of thrombosis in patients with severe SARS-CoV-2 infection: A multicenter prospective cohort study. Intensive Care Med. 2020 May 4. https://doi.org/10.1007/s00134-020-06062-x.

Hendrix MJ, et al. Absence of apparent transmission of SARS-CoV-2 from two stylists after exposure at a hair salon with a universal face covering policy—Springfield, Missouri, May 2020. MMWR Morb Mortal Wkly Rep. 2020 Jul 17;69(28):930-932.

Henry BM, et al. Hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): a meta-analysis. Clin Chem Lab Med. 2020 Apr 10:j/cclm.ahead-of-print/cclm-2020-0369/cclm-2020-0369.xml

Herman A, et al. Evaluation of chilblains as a manifestation of the COVID-19 pandemic. JAMA Dermatol. 2020 Jun 25. doi: 10.1001/jamadermatol.2020.2368.

Herold T, et al. Elevated levels of IL-6 and CRP predict the need for mechanical ventilation in COVID-19. J Allergy Clin Immunol. 2020 May 18;S0091-6749(20_30685-0.

Hewitt J, et al. The effect of frailty on survival in patients with COVID-19 (COPE): A multicentre, European, observational cohort study. Lancet Public Health. 2020 Jun 30; https://doi.org/10.1016/S2468-2667(20)30146-8.

Hijnen D, et al. SARS-CoV-2 transmission from presymptomatic meeting attendee, Germany. Emerg Infect Dis. 2020 May 11;26(8). doi: 10.3201/eid2608.201235.

Hirsch JS, et al. Acute kidney injury in patients hospitalized with COVID-19. Kidney Int. 2020 May 13;S0085-2538(20)30532-9.

Hoehl S, et al. Assessment of SARS-CoV-2 Transmission on an International Flight and Among a Tourist Group. JAMA Netw Open. 2020 Aug 3;3(8):e2018044. doi: 10.1001/jamanetworkopen.2020.18044.

Hoffmann M, et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 2020 Mar 4. pii: S0092-8674(20)30229-4. doi: 10.1016/j.cell.2020.02.052. Last updated 4 October 2020

Hogan CA, et al. Sample Pooling as a Strategy to Detect Community Transmission of SARS-CoV- 2. JAMA. 2020 Apr 6;323(19):1967-1969. doi: 10.1001/jama.2020.5445.

Hogan CA, et al. High Frequency of SARS-CoV-2 RNAemia and Association With Severe Disease. Clin Infect Dis. 2020 Sep 23;ciaa1054. doi: 10.1093/cid/ciaa1054.

Holshue ML, et al. First Case of 2019 Novel Coronavirus in the United States. N Engl J Med. 2020 Mar 5;382(10):929-936. doi: 10.1056/NEJMoa2001191.

Horby PW, et al. Dexamethasone in hospitalized patients with COVID-19—Preliminary report. N Engl J Med. 2020 Jul 17. doi: 10.1056/NEJMoa2021436.

Horby PW, et al. Effect of hydroxychloroquine in hospitalized patients with COVID-19: Preliminary results from a multi-centre, randomized, controlled trial. medRxiv. https://doi.org/10.1101/2020.07.15.20151852.

Horve PF, et al. Identification of SARS-CoV-2 RNA in healthcare heating, ventilation, and air conditioning units. medRxiv. https://doi.org/10.1101.2020.06.26.20141085.

Hosier H, et al. First case of placental infection with SARS-CoV-2. medRxiv. https://doi.org/10.1101/2020.04.30.20083907.

Hossain R, et al. CT scans obtained for nonpulmonary indications: Associated resipratory findings of COVID-19. Radiology. 2020 May 11:201743. doi: 10.1148/radio.2020201743.

Hou YJ, et al. SARS-CoV-2 reverse genetics reveals a variable infection gradient in the respiratory tract. Cell. 2020 May 20. doi: 10.1016/j.cell.2020.05.042.

Howard J, et al. Face masks against COVID-19: An evidence-based review. Preprints. doi:10.20944/preprints202004.0203.ve.

Hsiang S, et al. The effect of large-scale anti-contagion policies on the COVID-19 pandemic. Nature. 2020 Jun 8. doi: 10.1038/s41586-020-2404-8.

Hu J, et al. The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera. bioRxiv. https:doi.org/10.1101/2020.06.20.161323.

Hu L. et al. Risk factors associated with clinical outcomes in 323 COVID-19 hospitalized patients in Wuhan, China. Clin Infect Dis. 2020 May 3. doi: 10.1093/cid/ciaa539.

Hu M, et al. The risk of COVID-19 transmission in train passengers: an epidemiological and modelling study. Clin Infect Dis. 2020 Jul 29;ciaa1057. doi: 10.1093/cid/ciaa1057.

Last updated 4 October 2020

Hu Z, et al. Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing, China. Sci China Life Sci. 2020 Mar 4. doi: 10.1007/s11427- 020-1661-4.

Huang AT, et al. A systematic review of antibody mediated immunity to coronaviruses: Antibody kinetics, correlates of protection, and association of antibody responses with severity of disease. medRxiv. https://doi.org/10.1101/2020.04.14.20065771.

Huang C, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020 Feb 15;395(10223):497-506.

Huang CG, et al. Culture-based virus isolation to evaluate potential infectivity of clinical specimens tested for COVID-19. J Clin Microbiol. 2020 Jun 9:JCM.01068-20. doi: 10.1128/JCM.01068-20.

Huang JT, et al. Chronological changes of viral shedding in adult inpatients with COVID-19 in Wuhan, China. Clin Infect Dis. 2020 May 23:ciaa 631. doi: 10.1093/cid/ciaa631.

Huang Y, et al. SARS-CoV-2 viral load in clinical samples of critically ill patients. Am J Respir Crit Care Med. 2020 Apr 15. doi: 10.1164/rccm.202003-0572LE.

Hue S, et al. Uncontrolled Innate and Impaired Adaptive Immune Responses in Patients with COVID-19 ARDS. Am J Respir Crit Care Med. 2020 Aug 31. doi: 10.1164/rccm.202005-1885OC.

Huet T, et al. Anakinra for severe forms of COVID-19: a cohort study. Lancet Rheumatol. 2020 May 29. https://doi.org/10.1016/S2665-9913(20)30164-8.

Huff HV, A Singh. Asymptomatic transmission during the COVID-19 pandemic and implications for public health strategies. Clin Infect Dis. 2020 May 28;ciaa654. doi: 10.1093/cid/ciaa654.

Hughes MM, et al. Update: Characteristics of Health Care Personnel with COVID-19 - United States, February 12-July 16, 2020. MMWR Morb Mortal Wkly Rep. 2020 Sep 25;69(38):1364- 1368.

Hui H, et al. Clinical and radiographic features of cardiac injury in patients with 2019 novel coronavirus pneumonia. medRxiv 2020.02.24.20027052.

Hulme OJ, et al. Reply to Gautret et al. 2020: A Bayesian reanalysis of the effects of hydroxychloroquine and azithromycin on viral carriage in patients with COVID-19. medRxiv. https://doi.org/10.1101/2020.03.31.20048777.

Hung IF, et al. SARS-CoV-2 shedding and seroconversion among passengers quarantined after disembarking a cruise ship: A case series. Lancet Infect Dis. 2020 Jun 12;S1473-3099(20)30364- 9. Last updated 4 October 2020

Hung IFN, et al. Triple combination of interferon beta-1b, lopinavir–ritonavir, and ribavirin in the treatment of patients admitted to hospital with COVID-19: an open-label, randomised, phase 2 trial. Lancet. 2020 May 8. https://doi.org/10.1016/S0140-6736(20)31042-4.

Iacobucci G. Sixty seconds on. . . anosmia. BMJ. 24 Mar 2020; 368. doi: https://doi.org/10.1136/bmj.m1202.

Iadecola C, et al. Effects of COVID-19 on the Nervous System. Cell. 2020 Aug 19;S0092- 8674(20)31070-9. doi: 10.1016/j.cell.2020.08.028.

Ibarrondo FJ, et al. Rapid decay of anti-SARS-CoV-2 antibodies in persons with mild COVID-19. N Engl J Med. 2020 Jul 21. doi: 10.1056/NEJMc2025179. See also Erratum: 2020 Jul 23. doi: 10.1056/NEJMx200017.

Ioannou GN, et al. Risk Factors for Hospitalization, Mechanical Ventilation, or Death Among 10 131 US Veterans With SARS-CoV-2 Infection. JAMA Netw Open. 2020 Sep 1;3(9):e2022310. doi: 10.1001/jamanetworkopen.2020.22310.

Islam N, et al. Physical distancing interventions and incidence of coronavirus disease 2019: natural experiment in 149 countries. BMJ. 2020 Jul 15;370:m2743. doi: 10.1136/gmj/m2743.

Ivashchenko AA, et al. Avifavir for treatment of patients with moderate COVID-19: Interim results of a phase II/III multicenter randomized clinical trial. medRxiv. https://doi.org/10.1101/2020.07.26.20154724.

Iversen K, et al. Risk of COVID-19 in health-care workers in Denmark: an observational cohort study. Lancet Infect Dis. 2020 Aug 3;S1473-3099(20)30589-2. doi: 10.1016/S1473- 3099(20)30589-2.

Iwen PC, et al. Safety Considerations in the Laboratory Testing of Specimens Suspected or Known to Contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Am J Clin Pathol. 2020 Mar 19. pii: aqaa047. doi: 10.1093/ajcp/aqaa047.

Iyer AS, et al. Dynamics and significance of the antibody response to SARS-CoV-2 infection. medRxiv. https://doi.org/10.1101.2020.07.18.20155374.

Jabri A, et al. Incidence of stress cardiomyopathy during the coronavirus disease 2019 pandemic. JAMA Netw Open. 2020 Jul 1;3(7):e2014780.

Jackson LA, et al. An mRNA vaccine against SARS-CoV-2—Preliminary report. N Engl J Med. 2020 Jul 14. doi: 10.1056/NEJMoa2022483.

Last updated 4 October 2020

Jackson BR, et al. Predictors at admission of mechanical ventilation and death in an observational cohort of adults hospitalized with COVID-19. Clin Infect Dis. 2020 Sep 24;ciaa1459. doi: 10.1093/cid/ciaa1459.

Jacot D, et al. Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses. medRxiv. https:doi.org/10.1101/2020.07.15.20154518.

Jamal AJ, et al. Sensitivity of nasopharyngeal swabs and saliva for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). medRxiv. https://doi.org/10.1101/2020.05.01.20081026.

James A, et al. High COVID-19 attack rate among attendees at events at a church—Arkansas, March 2020. MMWR Morb Mortal Wkly Rep. 2020 May 22;69(20):632-635.

Jamilloux Y, et al. Should We Stimulate or Suppress Immune Responses in COVID-19? Cytokine and Anti-Cytokine Interventions. Autoimmun Rev. 2020 May 4;102567.

Janz DR, et al. Critically Ill Adults with COVID-19 in New Orleans and Care with an Evidence- based Protocol. Chest. 2020 Sep 14;S0012-3692(20)34493-7. doi: 10.1016/j.chest.2020.08.2114.

Jarrom D, et al. Effectiveness of tests to detect the presence of SARS-CoV-2 virus, and antibodies to SARS-CoV-2, to inform COVID-19 diagnosis: a rapid systematic review. BMJ Evid Based Med. 2020 Oct 1;bmjebm-2020-111511.

Jaunmuktane Z, et al. Microvascular injury and hypoxic damage: Emerging neuropathological signatures in COVID-19. Acta Neuropathol. 2020 Jul 8;1-4. doi: 10.1007/s00401-020-02190-2.

Java A, et al. The complement system in COVID-19: Friend and Foe? JCI Insight. 2020 Jun 18;140711. doi: 10.1172/jci.insight.140711.

Jefferson T, et al. Viral cultures for COVID-19 infectivity assessment – a systematic review. medRxiv. 2020 Sep 29; 2020.08.04.20167932. doi: 10.1101/2020.08.04.20167932.

Jeremias A, et al. Prevalence of SARS-CoV-2 Infection Among Health Care Workers in a Tertiary Community Hospital. JAMA Intern Med. 2020 Aug 11;e204214. doi: 10.1001/jamainternmed.2020.4214.

Jeronimo CMP, et al. Methylprednisolone as Adjunctive Therapy for Patients Hospitalized With COVID-19 (Metcovid): A Randomised, Double-Blind, Phase IIb, Placebo-Controlled Trial. Clin Infect Dis. 2020 Aug 12;ciaa1177. doi: 10.1093/cid/ciaa1177.

Last updated 4 October 2020

Jewell NP, et al. Caution warranted: Using the Institute for Health Metrics and Evaluation model for predicting the course of the COVID-19 pandemic. Ann Intern Med. 2020 Apr 14. doi: 10.7326/M20-1565.

Jiang RD, et al. Pathogenesis of SARS-CoV-2 in transgenic mice expressing human angiotensin- converting enzyme 2. Cell. 2020 May 14. doi: 10.1016/j.cell.2020.05.027.

Jimenez JL. COVID-19 data dives: Why arguments against SARS-CoV-2 aerosol transmission don’t hold water. Medscape. 2020 Jul 30. https://www.medscape.com/viewarticle/934837.

Jin Y, et al. Diagnostic value and dynamic variance of serum antibody in coronavirus disease 2019. Int J Infect Dis. 2020 Apr 3. pii: S1201-9712(20)30198-3. doi: 10.1016/j.ijid.2020.03.065.

Jing QL, et al. Household secondary attack rate of COVID-19 and associated determinants in Guangzhou, China: A retrospective cohort study. Lancet Infect Dis. 2020 Jun 17;S1473- 3099(20)30471-0. doi: 10.1016/S1473-3099(20)30471-0.

Jones NR, et al. Two metres or one: what is the evidence for physical distancing in covid-19? BMJ. 2020 Aug 25;370:m3223. doi: 10.1136/bmj.m3223.

Jones RM. Relative contributions of transmission routes for COVID-19 among healthcare personnel providing patient care. J Occup Environ Hyg. 2020 Jul 9;1-8. doi: 10.1080/15459624.2020.1784427.

Jones TC, et al. An analysis of SARS-CoV-2 viral load by patient age. German Research Network Zoonotic Infectious Diseases preprint. https://zoonosen.charite.de/fileadmin/user_upload/microsites/m_cc05/virologie- ccm/dateien_upload/Weitere_Dateien/analysis-of-SARS-CoV-2-viral-load-by-patient-age.pdf.

Jones VG, et al. COVID-19 and Kawasaki Disease: Novel virus and novel case. Hosp Pedatr. doi: 10.1542/hpeds.2020-0123.

Jouan Y, et al. Phenotypical and functional alteration of unconventional T cells in severe COVID- 19 patients. J Exp Med. 2020 Dec 7;217(12):e20200872. doi: 10.1084/jem.20200872.

Joung J, et al. Detection of SARS-CoV-2 with SHERLOCK one-pot testing. N Engl J Med. 2020 Sep 16. doi: 10.1056/NEJMc2026172.

Joyner MJ, et al. Safety Update: COVID-19 convalescent plasma in 20,000 hospitalized patients. Mayo Clin Proc. 2020;95. https://mayoclinicproceedings.org/pb/assets/raw/Health%20Advance/journals/jmcp/jmcp_ft9 5_6_8.pdf.

Last updated 4 October 2020

Joyner MJ, et al. Effect of convalescent plasma on mortality among hospitalized patients with COVID-19: Initial three-month experience. medRxiv. https://doi.org/10.1101/2020.08.12.20169359.

Joyner MJ, et al. Evidence favouring the efficacy of convalescent plasma for COVID-19 therapy. medRxiv. https://doi.org/10.1101/2020.07.29.20162917.

Joynt GM, WK Wu. Understanding COVID-19: what does viral RNA load really mean? Lancet Infect Dis. 2020 Mar 27. pii: S1473-3099(20)30237-1. doi: 10.1016/S1473-3099(20)30237-1.

Ju B, et al. Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature. 2020 May 26. doi: 10.1038/s41586-020-2380-z.

Kampf G, et al. Persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents. J Hosp Infect. 2020 Mar;104(3):246-251. doi: 10.1016/j.jhin.2020.01.022.

Kang M, et al. Probable Evidence of Fecal Aerosol Transmission of SARS-CoV-2 in a High-Rise Building. Ann Intern Med. 2020 Sep 1. doi: 10.7326/M20-0928.

Kaptein SJF, et al. Antiviral treatment of SARS-CoV-2-infected hamsters reveals a weak effect of favipiravir and a complete lack of effect for hydroxychloroquine. bioRxiv. https:doi.org/10.1101/2020.06.19.159053.

Karagiannidis C, et al. Case characteristics, resource use, and outcomes of 10 021 patients with COVID-19 admitted to 920 German hospitals: an observational study. Lancet Respir Med. 2020 Jul 28;S2213-2600(20)30316-7.

Kabarriti R, et al. Association of Race and Ethnicity With Comorbidities and Survival Among Patients With COVID-19 at an Urban Medical Center in New York. JAMA Netw Open. 2020 Sep 1;3(9):e2019795. doi: 10.1001/jamanetworkopen.2020.19795.

Kates OS, et al. COVID-19 in solid organ transplant: A multi-center cohort study. 2020 Aug 7;ciaa1097. doi: 10.1093/cid/ciaa1097.

Keech C, et al. Phase 1-2 Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine. N Engl J Med. 2020 Sep 2. doi: 10.1056/NEJMoa2026920.

Kesici S, et al. Get riid of the bad first: Therapeutic plasma exchange with convalescent plasma for severe COVID-19. Proc Natl Acad Sci USA. 2020 May 12. doi: 10.1073/pnas.2006691117.

Kewan T, et al. Tocilizumab for treatment of patients with severe COVID-19: A retrospective cohort study. EclinicalMedicine. 2020 Jun 18. https://doi.org/10.1016/j.eclinm.2020.100418.

Last updated 4 October 2020

Khera R, et al. Association of angiotensin-converting enzyme inhibitors and angiotensin receptor blockers with the risk of hospitalization and death in hypertensive patients with coronavirus disease-19. medRxiv. https://doi.org/10.1101/2020.05.17.20104943.

Khider L, et al. Curative anticoagulation prevents endothelial lesion in COVID-19 patients. J Thromb Haemost. 2020 Jun 18. doi: 10.1111/jth.14968.

Khurshid Z, et al. Saliva as a non-invasive sample for the detection of SARS-CoV-2: a systematic review. MedRxiv. https://doi.org/10.1101/2020.05.09.20096354.

Kim AHJ, et al. A rush to judgment? Rapid reporting and dissemination of results and its consequences regarding the use of hydroxychloroquine for COVID-19. Ann Intern Med. 30 Mar 2020. doi: 10.7326/M20-1223.

Kim D, et al. Rates of co-infection between SARS-CoV-2 and other respiratory pathogens. JAMA. 2020 Apr 15. doi: 10.1001/jama.2020.6266.

Kim H, et al. Diagnostic performance of CT and reverse transcriptase-polymerase chain reaction for coronavirus disease 2019: A meta-analysis. Radiology. 2020 Sep;296(3):E145-E155. doi: 10.1148/radiol.2020201343.

Kim HN, et al. Assessment of Disparities in COVID-19 Testing and Infection Across Language Groups in Seattle, Washington. JAMA Netw Open. 2020 Sep 1;3(9):e2021213. doi: 10.1001/jamanetworkopen.2020.21213.

Kimball A, et al. Asymptomatic and presymptomatic SARS-CoV-2 infections in residents of a long-term care skilled nursing facility—King County, Washington, March 2020. MMWR Morb Mortal Wkly Rep. 27 Mar 2020; 69:1-5. https://www.cdc.gov/mmwr/volumes/69/wr/mm6913e1.htm?s_cid=mm6913e1_w.

Kimberlin DW, S Stagno. Can SARS-CoV-2 infection be acquired in utero? More definitive evidence is needed. JAMA 26 Mar 2020. doi:10.1001/jama.2020/4868.

Kimmig LM, et al. IL6 inhibition in critically ill COVID-19 patients is associated with increased secondary infections. medRxiv. https://doi.org/10.1101/2020.05.15.20103531.

Kirkcaldy RD, et al. COVID-19 and postinfection immunity: Limited evidence, many remaining questions. JAMA. 2020 May 11. doi: 10.1001/jama.2020.7869.

Kirov S. Associatio between BCG policy is significantly confounded by age and is unlikely to alter infection or mortality rates. medRxiv. https://doi.org/10.1101/2020.04.06.20055616.

Kirtsman M, et al. Probable Congenital SARS-CoV-2 Infection in a Neonate Born to a Woman With Active SARS-CoV-2 Infection. CMAJ. 2020 May 14;cmaj.200821. Last updated 4 October 2020

Kissler S, et al. Social distancing strategies for curbing the COVID-19 epidemic. Mar 2020. DASH preprint server. http://nrs.harvard.edu/urn-3:HUL.InstRepos:42638988.

Kissler SM, et al. Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science. 2020 Apr 14. 10.1126/science.abb5793.

Klein D, et al. Working paper—Model-based estimates of COVID-19 burden in King and Snohomish counties through April 7, 2020. 10 Mar 2020.

Klein SL, et al. Sex, age, and hospitalization drive antibody responses in a COVID-19 convalescent plasma donor population. J Clin Invest. 2020 Aug 7. https://doi.org/10.1172/JCI142004.

Klok FA, et al. Incidence of thrombotic complications in critically ill ICU patients with COVID-19. Thromb Res. 2020 Apr 10. pii: S0049-3848(20)30120-1. doi: 10.1016/j.thromres.2020.04.013.

Klompas M, et al. University masking in hospitals in the COVID-19 era. N Engl J Med. 2020 May 21;382(21):e63. doi: 10.1056/NEJMp2006372.

Klopfenstein T, et al. Tocilizumab therapy reduced intensive care unit admissions and/or mortality in COVID-19 patients. Med Mal Infect. 2020 May 6. doi: 10.1016/j.medmal.2020.05.001.

Knight SR, et al. Risk stratification of patients admitted to hospital with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score. BMJ. 2020 Sep 9;370:m3339. doi: 10.1136/bmj.m3339.

Kojima N, et al, Self-collected oral fluid and nasal swabs demonstrate comparable sensitivity to clinician collected nasopharyngeal swabs for COVID-19 detection. medRxiv. doi: https://doi.org/10.1101/2020.04.11.20062372.

Konig MF, et al. Baseline use of hydroxychloroquine in systemic lupus erythematosus does not preclude SARS-CoV-2 infection and severe COVID-19. Ann Rheum Dis. 2020 May 7. doi: 10.1136/annrheumdis-2020-217690.

Konno Y, et al. SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is increased by a naturally occurring elongation variant. Cell Rep. 2020 Sept 1. https://doi.org/10.1016/j.celrep.2020.108185.

Korber B, et al. Tracking changes in SARS-CoV-2 spike: Evidence that D614G increases infectivity of the COVID-19 virus. Cell. 2020 Jul 2. https://doi.org/10.1016/j.cell.2020.06.043.

Kouzy R, et al. Characteristics of the multiplicity of randomized clinical trials for Coronavirus disease 2019 launched during the pandemic. JAMA Netw Open. 2020 Jul 1:3(7):e2015100. Last updated 4 October 2020

Kox M, et al. Cytokine Levels in Critically Ill Patients With COVID-19 and Other Conditions. JAMA. 2020 Sep 3. doi: 10.1001/jama.2020.17052.

Krammer F. SARS-CoV-2 vaccines in development. Nature. 2020 Sep 23. doi: 10.1038/s41586- 020-2798-3.

Kretzschmar M, et al. Time is of the essence: Impact of delays on effectiveness of contact tracing for COVID-19. medRxiv. https://doi.org/10.1101/2020.05.09.20096289.

Kucharski AJ, et al. Early dynamics of transmission and control of COVID-19: a mathematical modelling study. Lancet Infect Dis. 2020 Mar 11. pii: S1473-3099(20)30144-4. doi: 10.1016/S1473-3099(20)30144-4.

Kucharski AJ, et al. Effectiveness of Isolation, Testing, Contact Tracing, and Physical Distancing on Reducing Transmission of SARS-CoV-2 in Different Settings: A Mathematical Modelling Study. Lancet Infect Dis. 2020 Jun 15;S1473-3099(20)30457-6.

Kucirka LM, et al. Variation in false-negative rate of reverse transcriptase polymerase chain reaction-based SARS-CoV-2 tests by time since exposure. Ann Intern Med. 2020 May 13;M20- 1495. doi: 10.7326/M20-1495.

Kuderer NM, et al. Clinical impact of COVID-19 on patients with cancer (CCC19): a cohort study. Lancet. 2020 May 28. https://doi.org/10.1016/S0140-6736(20)31187-9.

Kujawski SA, et al. Clinical and virologic characteriistics of the first 12 patients with coronavirus disease 2019 (COVID-19) in the United States. Nat Med. https://doi.org/10.1038/s41591-020- 0877-5.

Kurstjens S, et al. Rapid identification of SARS-CoV-2-infected patients at the emergency department using routine testing. Clin Chem Lab Med. 2020 Jun 29;58(9):1587-1593. doi: 10.1515/cclm-2020-0593.

Ladhani SN, et al. Investigation of SARS-CoV-2 outbreaks in six care homes in London, April 2020. EClinicalMedicine. 2020 Sept 9. https://doi.org/10.1016/j.eclinm.2020.100533.

Lai X, et al. Coronavirus 2019 (COVID-19) infection among health care workers and implications for prevention measures in a tertiary hospital in Wuhan, China. JAMA Netw Open. 2020 May 1;3(5):e209666.

Laing AG, et al. A consensus COVID-19 immune signature combines immuno-protection with discrete sepsis-like traits associated with poor prognosis. medRxiv. https://doi.org/10.1101/2020.06.08.200125112.

Last updated 4 October 2020

Lam KW, et al. Continued in-hospital ACE inhibitor and ARB use in hypertensive COVID-19 patients is associated with positive clinical outcomes. J Infect Dis. 2020 Jul 23:jiaa447. doi: 10.1093/oinfdis/jiaa447.

Lam TT, et al. Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature. 26 Mar 2020. https://doi.org/10.1038/s41586-020-2169-0(2020).

Lamers MM, et al. SARS-CoV_2 productively infects human gut enterocytes. Science. 2020 May 1. doi: 10.1126/science.abc1669.

Lamontagne F, et al. A living WHO guideline on drugs for COVID-19. BMJ. 2020 Sep 4;370:m3379. doi: 10.1136/bmj.m3379.

Lan L, et al. Positive RT-PCR Test Results in Patients Recovered From COVID-19. JAMA. 2020 Feb 27. doi: 10.1001/jama.2020.2783.

Lang M, et al. Hypoxaemia related to COVID-19: Vascular and perfusion abnormalities on dual- energy CT. Lancet Infect Dis. 2020 Apr 30. https://doi.org/10.1016/S1473-3099(20)30367-4.

Lansbury L, et al. Co-infections in people with COVID-19: A systematic review and meta- analysis. J Infect. 2020 May 27;S0163-4453(20)30323-6. doi: 10.1016/j.jinf.2020.05.046.

Larremore DB, et al. Test sensitivity is secondary to frequency and turnaround time for COVID- 19 surveillance. medRxiv. https://doi.org/10.1101.2020.06.22.20136309.

La Scola B, et al. Viral RNA Load as Determined by Cell Culture as a Management Tool for Discharge of SARS-CoV-2 Patients From Infectious Disease Wards. Eur J Clin Microbiol Infect Dis. 2020 Jun;39(6):1059-1061.

Lassauniére R, et al. Evaluation of nine commercial SARS-CoV-2 immunoassays. medRxiv. https://doi.org/10.1101/2020.04.09.20056325.

Laterre PF, et al. Association of interleukin 7 immunotherapy with lymphocyte counts among patients with severe coronavirus disease 2019 (COVID-19). JAMA Netw Open. 2020 Jul 1;3(7):e2016485.

Latinne A, et al. Origin and cross-species transmission of bat coronaviruses in China. bioRxiv. https://doi.org/10.1101.2020.05.31.116061.

Lauer SA, et al. The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Ann Intern Med. 2020 Mar 10. doi: 10.7326/M20-0504.

Last updated 4 October 2020

Lawicki S, et al. TEG max clot strength is consistently elevated and may be predictive of COVID- 19 status at the time of ICU admission. medRxiv. https://doi.org/10.1101/2020.04.30.20076703.

Lax SF, et al. Pulmonary arterial thrombosis in COVID-19 with fatal outcome: Results from a prospective, single-center, clinicopathologic case series. Ann Intern Med. 2020 May 14:M20=2566. doi: 10.7326/M20-2566.

Laxminarayan R, et al. Epidemiology and transmission dynamics of COVID-19 in two Indian states. Science. 2020 Sep 30. doi: 10.1126/science.abd7672.

Le Bert N, et al. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature. 2020 Jul 15. doi: 10.1038/s41586-020-2550-z.

Lechien JR, et al. Olfactory and gustatory dysfunctions as a clinical presentation of mild-to- moderate forms of the coronavirus disease (COVID-19): a multicenter European study. Eur Arch Oto-Rhino Laryngol. 2020 Apr 6. doi: 10.1007/s00405-020-05965-1.

Lednicky JA, et al. Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients. medRxiv. https://doi.org/10.1101/2020.08.03.20167395.

Lee JS, et al. Immunophenotyping of COVID-19 and Influenza Highlights the Role of Type I Interferons in Development of Severe COVID-19. Sci Immunol. 2020 Jul 10;eabd1554. doi: 10.1126/sciimmunol.abd1554.

Lee PY, et al. Distinct clinical and immunological features of SARS-Cov-2-induced multisystem inflammatory syndrome in children. J Clin Invest. 2020 Jul 23;141113. doi: 10.1172/JCI141113.

Lee S, et al. Clinical Course and Molecular Viral Shedding Among Asymptomatic and Symptomatic Patients With SARS-CoV-2 Infection in a Community Treatment Center in the Republic of Korea. JAMA Intern Med. 2020 Aug 6. doi: 10.1001/jamainternmed.2020.3862.

Lee WS, et al. Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies. Nat Microbiol. 2020 Sep 9. doi: 10.1038/s41564-020-00789-5.

Leeb RT, et al. COVID-19 Trends Among School-Aged Children - United States, March 1- September 19, 2020. MMWR Morb Mortal Wkly Rep. 2020 Oct 2;69(39):1410-1415. doi: 10.15585/mmwr.mm6939e2.

Lei S, et al. Clinical characteristics and outcomes of patients undergoing surgeries during the incubation period of COVID-19 infection. EclinicalMedicine. 2020. https://doi.org/10.1016/j.eclinm.2020.100331. Last updated 4 October 2020

Lemieux JE, et al. Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. medRxiv. https://doi.org/10.1101/2020.08.23.20178236.

Lescure FX, et al. Clinical and virological data of the first cases of COVID-19 in Europe: a case series. Lancet Infect Dis. 2020 Mar 27. pii: S1473-3099(20)30200-0. doi: 10.1016/S1473- 3099(20)30200-0.

Leung NHL, et al. Respiratory virus shedding in exhaled breath and efficacy of face masks. Nat Med. 3 Apr 2020. https://doi.org/10.1038/s41591-020-0843-2.

Levin M. Childhood multisystem inflammatory syndrome—A new challenge in the pandemic. N Engl J Med. 2020 Jun 29. doi: 10.1056/NEJMe2023158.

Levinson M, et al. Reopening primary schools during the pandemic. 2020 July 29. doi: 10.1056/NEJMms2024920.

Levinson R, et al. Anosmia and dysgeusia in patients with mild SARS-CoV-2 infection. medRxiv. https://doi.org/10.1101/2020.04.11.20055483.

Lewnard JA, et al. Incidence, clinical outcomes, and transmission dynamics of hospitalized 2019 coronavirus disease 2019 in California and Washington: a prospective cohort study. BMJ. 2020 May 22;369:m1923.

Li L, et al. Effect of convalescent plasma therapy on time to clinical improvement in patients with severe and life-threatening COVID-19: A randomized clinical trial. JAMA. 2020 Jun3. doi: 10.1001/jama.2020.10044.

Li R, et al. Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2). Science. 2020 Mar 16. pii: eabb3221. doi: 10.1126/science.abb3221.

Li R, et al. The demand for inpatient and ICU beds for COVID-19 in the US: Lessons from Chinese cities. medRxiv 2020.03.09.20033241.

Li Q, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus-Infected pneumonia. N Engl J Med. 2020 Jan 29. doi: 10.1056/NEJMoa2001316.

Li Q, et al. A simple laboratory parameter facilitates early identification of COVID-19 patients. MedRxiv 2020.02.13.20022830.Dis. 2020 Apr 17. pii: ciaa450. doi: 10.1093/cid/ciaa450.

Li Q, et al. The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Cell. 2020 Jul 17;S0092-8674(20)30877-1. doi: 10.1016/j.cell.2020.07.012.

Last updated 4 October 2020

Li W, et al. The characteristics of household transmission of COVID-19. Clin Infect Dis. 2020 Apr 17. pii: ciaa450. doi: 10.1093/cid/ciaa450.

Li X, et al. Emergence of SARS-CoV-2 through recombination and strong purifying selection. Sci Adv. 2020 May 29. doi: 10.1126/sciadv.abb9153.

Li Y, et al. Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant. medRxiv. https://doi.org/10.1101/2020.04/16.20067728.

Li Z, et al. The incubation period of severe acute respiratory syndrome coronavirus 2: A systematic review. medRxiv. https://doi.org/10.1101/2020.08.01.20164335.

Liang M, et al. Efficacy of face mask in preventing respiratory virus transmission: A systematic review and meta-analysis. Travel Med Infect Dis. 2020 May 27;101751. doi: 10.1016/j.tmaid.2020.101751.

Liao J, et al. Epidemiological and clinical characteristics of COVID-19 in adolescents and young adults. The Innovation. 2020 Apr 2. doi: 10.1016/j.xinn.2020.04.001.

Libby P, T Lüscher. COVID-19 is, in the end, an endothelial disease. Eur Heart J. 2020 Sep 1;41(32):3038-3044.

Licciardi F, et al. SARS-CoV-2-induced Kawasaki-like hyperinflammatory syndrome: A novel COVID phenotype in children. Pediatrics. 2020 May 21;e20201711.

Lieberman JA, et al. Comparison of commercially available and laboratory developed assays for in vitro detection of SARS-CoV-2 in clinical laboratories. J Clin Microbiol. 2020 Apr 27. doi: 10.1128/JCM.00821-20.

Lighter J, et al. Obesity in patients younger than 60 years is a risk factor for COVID-19. Clin Infect Dis. 2020 Apr 9. pii: ciaa415. doi: 10.1093/cid/ciaa415.

Lillicrap D. Disseminated intravascular coagulation in patients with 2019-nCoV pneumonia. J Thromb Haemost. 2020;00:1-2. https://doi.org.10.1111/jth/14781.

Lin C, et al. Comparison of throat swabs and sputum specimens for viral nucleic acid detection in 52 cases of novel coronavirus (SARS-Cov-2) infected pneumonia (COVID-19). medRxiv 2020.02.21.20026187.

Lin D, et al. Co-infections if SARS-CoV-2 with multiple common respiratory pathogens in infected patients. Sci China Life Sci. 2020 Mar 5. doi: 10.1007/s11427-020-1668-5.

Lins M, et al. Assessment of small pulmonary blood vessels in COVID-19 patients using HRCT. medRxiv. https://doi.org/10.1101.2020.05.22.20108084. Last updated 4 October 2020

Liu J, et al. Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro. Cell Discovery. https://doi.org/10.1038/s41421-020-0156-0.

Liu J, et al. Overlapping and discrete aspects of the pathology and pathogenesis of the emerging human pathogenic coronaviruses SARS-CoV, MERS-CoV, and 2019-CoV. J Med Virol. 2020 May; 92(5):491-494.

Liu J, et al. Large SARS-CoV-2 Outbreak Caused by Asymptomatic Traveler, China. Emerg Infect Dis. 2020 Sep;26(9). doi: 10.3201/eid2609.201798.

Liu M, et al. Use of personal protective equipment against coronavirus disease 2019 by healthcare professionals in Wuhan, China: cross sectional study. BMJ. 2020 Jun 10;369:m2195. doi: 10.1136/bmj.m2195.

Liu P, et al. Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? PloS Pathog. 2020 May 14;16(5):e1008421.

Liu PP, et al. The science underlying COVID-19: Implications for the cardiovascular system. Circulation. 2020 Apr 15. doi: 10.1161/CIRCULATIONAHA.120.047549.

Liu STH, et al. Convalescent plasma treatment of severe COVID-19: A matched control study. medRxiv. https://doi.org/10.1101/2020.05.20.20102236.

Liu Y, et al. Viral dynamics in mild and severe cases of COVID-19. Lancet Infect Dis. 2020 Mar 19. Pii: S1473-3099(20)30227-9. doi: 10.1016/S1473-3099(20)30232-3.

Liu Y, et al. Neutrophil-to-lymphocyte ratio as an independent risk factor for mortality in hospitalized patients with COVID-19. J Infect. 2020 Apr 3. doi: https://doi.org/10.1016/jinf.2020.04.002.

Liu Y, et al. Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals. Nature. 2020 Apr 27. doi: 10.1038/s41586-020-2271-3.

Liu Y, et al. Thymosin alpha 1 (Tα1) reduces the mortality of severe COVID-19 by restoration of lymphocytopenia and reversion of exhausted T cells. Clin Infect Dis. 2020 May 22:ciaa630. doi: 10.1093/cid/ciaa630.

Llitjos JF, et al. High incidence of venous thromembolic events in anticoagulated severe COVID- 19 patients. J Thromb Haemost. 2020 Apr 22. doi: 10.1111/jth.14689.

Lo MW, et al. COVID-19: Complement, coagulation, and collateral damage. J Immunol. 2020 Jul 22;ji2000644. doi: 10.4049/jimmunol.2000644.

Last updated 4 October 2020

Lodigiani C, et al. Venous and arterial thromboembolic complications in COVID-19 patients admitted to an academic hospital in Milan, Italy. Thromb Res. 2020 Apr 23;191:9-14.

Loeffelholz MJ, YW Tang. Laboratory diagnosis of emerging coronavirus infections—The state of the art. Emerg Microbes Infect. 2020 Mar 20:1-26. doi: 10.1080/22221751.2020.1745095.

Logunov DY, et al. Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia. Lancet. 2020 Sep 4. https://doi.org/10.1016/S0140-6736(20)31866-3.

Logunov DY, et al. Safety and efficacy of the Russian COVID-19 vaccine: More information needed. Authors reply. Lancet. 2020 Sep 18. https://doi.org/10.1016/ S0140-6736(20)31970-X.

Lohse S, et al. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people. Lancet Infect Dis. 2020 Apr 28;S1473-3099(20)30362-5.

Lokugamage KG, et al. Type I interferon susceptibility distinguishes SARS-CoV-2 from SARS-CoV. bioRxiv. https://doi.org/10.1101/2020.03.07/982264.

London AJ, J Kimmelman. Against pandemic research exceptionalism. Science. 2020 May 1:368(6490):476-477.

Long C, et al. Diagnosis of the coronavirus disease (COVID-19): rRT-PCR or CT? Eur J Radiol. 2020 Mar 25;126:108961.

Long DR, et al. Occurrence and timing of subsequent SARS-CoV-2 RT-PCR positivity among initially negative patients. Clin Infect Dis. 2020 Jun 7:ciaa722. doi: 10.1093/cid/ciaa773.

Long QX, et al. Antibody responses to SARS-CoV-2 in patients with COVID-19. Nat Med. 2020 Apr 29. doi: 10.1038/s41591-020-0897.

Long QX, et al. Clinical and immunological assessment to SARS-CoV-2 in patients with COVID-19 Nat Med. 2020 Jun 18. doi: 10;1038/s41591-020-0965-6.

Lopez AS, et al. Transmission dynamics of COVID-19 outbreaks associated with child care facilities—Salt Lake City, Utah, April-July 2020. MMWR Morb Mortal Wkly Rep. 2020 Sept. 11. https://www.cdc.gov/mmwr/volumes/69/wr/mm6937e3.

Lorenzo-Redondo R, et al. A unique clade of SARS-CoV-2 viruses is associated with lower viral loads in patient upper airways. medRxiv. https://doi.org/10.1101/2020.05.19.20107144.

Lou B, et al. Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset. medRxiv. https://doi.org/10.1101/2020.03.23.20051707.

Last updated 4 October 2020

Lu J, et al. COVID-19 outbreak associated with air conditioning in restaurant, Guangzhou, China, 2020. Emerg Infect Dis. 2020 Jul;26(7):1628-1631.

Lu R, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020 Feb 22;395(10224):565-574.

Lu X, et al. SARS-CoV-2 infection in children. N Engl J Med. 2020 Mar 18. doi: 10.1056/NEJMc2005073.

Lucas C, et al. Longitudinal analyses reveal immunological misfiring in severe COVID-19. Nature. 2020 Jul 27. doi: 10.1038/s41586-020-2588-y.

Luers JC, et al. Olfactory and gustatory dysfunction in coronavirus disease 19 (COVID-19). Clin Infect Dis. 2020 May 1. doi: 10.1093/cid/ciaa525.

Luo P, et al. Tocilizumab treatment in COVID-19: a single center experience. J Med Virol. 2020 Apr 6. doi: 10.1002/jmv.25801.

Lurie N, et al. Developing COVID-19 vaccines at pandemic speed. N Engl J Med. 2020 Mar 30. doi: 10.1056/NEJMp2005630.

Lynch JB, et al. Infectious Diseases Society of America guidelines on infection prevention for health care personnel caring for patients with suspected or known COVID-19. 2000 Apr 27. http://www.idsociety.org/COVID19/guidelines/ip.

Lyu W, GL Wehby. Community Use Of Face Masks And COVID-19: Evidence From A Natural Experiment Of State Mandates In The US. Health Aff (Millwood). 2020 Aug;39(8):1419-1425.

Ma J, et al. COVID-19 patients in earlier stages exhaled millions of SARS-CoV-2 per hour. Clin Infect Dis. 2020 Aug 28;ciaa1283. doi: 10.1093/cid/ciaa1283.

Ma Y, et al. Effects of temperature variation and humidity on the mortality of COVID-19 in Wuhan. medRxiv 2020.03.15.20036426.

Madewell ZJ, et al. Household transmission of SARS-CoV-2: A systematic review and meta- analysis of secondary attack rate. medRxiv. https://doi.org/10.1101/2020.07.29.20164590.

Magagnoli J, et al. Outcomes of hydroxychloroquine usage in United States veterans hospitalized with COVID-19. medRxiv. doi: https://doi.org/10.1101/2020.04.16.20065920.

Magleby R, et al. Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients With Coronavirus Disease 2019. Clin Infect Dis. 2020 Jun 30;ciaa851. doi: 10.1093/cid/ciaa851.

Last updated 4 October 2020

Magro C, et al. Complement associated microvascular injury and thrombosis in the pathogenesis of severe COVID-19 infection: A report of five cases. Transl Res. 2020 Apr 15. pii: S1931-5244(20)30070-0.

Mahévas M, et al. No evidence of clinical efficacy of hydroxychloroquine in patients hospitalised for COVID-19 infection and requiring oxygen: Results of a study using routinely collected data to emulate a target trial. medRxiv. https://doi.org/10.1101/2020.04.10.20060699.

Malcourant C, et al. Natural killer cell immunotypes related to COVID-19 disease severity. Sci Immunol. 2020 Aug 21;5(50):eabd6832. doi: 10.1126/sciimmunol.abd6832.

Malgie J, et al. Decreased mortality in COVID-19 patients treated with Tocilizumab: a rapid systematic review and meta-analysis of observational studies. Clin Infect Dis. 2020 Sep 23;ciaa1445. doi: 10.1093/cid/ciaa1445.

Mancia G, et al. Renin-angiotensin-aldosteroine system blockers and the risk of COVID-19. N Engl J Med. 2020 May 1. doi: 10.1056/NEJMoa2006923.

Mandic-Rajcevic S, et al. Contact tracint and isolation of asymptomatic spreaders to successfully control the COVID-19 epidemic among healthcare workers in Milan (Italy). medRxiv. https://doi.org/10.1101.2020.05.03.20082818.

Mangalmurti NS, et al. COVID-ARDS clarified: A vascular endotype? Am J Respir Crit Care Med. 2020 Jul 6. doi: 10.1164/rccm.202006-2598LE.

Manne BK, et al. Platelet gene expression and function in COVID-19 patients. Blood. 2020 Jun 23;blood.2020007214. doi: 10.1182/blood.2020007214.

Manson JJ, et al. COVID-19-associated hyperinflammation and escalation of patient care: a retrospective longitudinal cohort study. Lancet Rheumatol. 2020 Aug 21. https://doi.org/10.1016/ S2665-9913(20)30275-7.

Mansour M, et al. Prevalence of SARS-CoV-2 antibodies among healthcare workers at a tertiary acadeemic hospital in New York City. medRxiv. https://doi.org/10.1101/2020.05.27.20090811.

Mao B, et al. Assessing risk factors for SARS-CoV-2 infection in patients presenting with symptoms in Shanghai, China: A multicentre, observational cohort study. Lancet Digital Health. 2020 May 14. https://doi.org/10.1016/S2589-7500(20)30111-4.

Mao L, et al. Neurologic manifestations of hospitalized patients with coronavirus disease 2019 in Wuhan, China. JAMA. 2020 Apr 10. doi:10.1001/jamaneurol.2020.1127.

Last updated 4 October 2020

Mao R, et al. Manifestations and prognosis of gastrointestinal and liver involvement in patients with COVID-19: a systematic review and meta-analysis. Lancet Gastroenterol Hepatol. 2020 May 12. https://doi.org/10.1016/S2468-1253(20)30132-1.

Marini JJ and L Gattinoni. Management of COVID-19 respiratory distress. JAMA. 2020 Apr 24. doi: 10.1001/jama.2020.6825.

Marovich M, et al. Monoclonal Antibodies for Prevention and Treatment of COVID-19. JAMA. 2020 Jun 15. doi: 10.1001/jama.2020.10245.

Mateus J, et al. Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans. Science. 2020 Aug 4;eabd3871. doi: 10.1126/science.abd3871.

Mather JF, et al. Impact of Famotidine Use on Clinical Outcomes of Hospitalized Patients With COVID-19. Am J Gastroenterol. 2020 Aug 26. doi: 10.14309/ajg.0000000000000832.

Matheson NJ, PJ Lehner. How does SARS-CoV-2 cause COVID-19? Science. 2020 Jul 31;369(6503):510-511. doi: 10.1126/science.abc6156.

Mathew D, et al. Deep immune profiling of COVID-19 patients reveals distinct immunmotypes with therapeutic implications. Science. 2020 Jul 15;eabc8511. doi: 10.1126/science.abc8511.

Mathian A, et al. Clinical course of coronavirus disease 2019 (COVD-29) in a series of 17 patients with systemic lupuls erythrmatosus under long-term treatment with hydroxychloroquine. Ann Rheum Dis. 2020 Apr 24. Do: 10.1136/annrheumdis-2020-217566.

Matthay MA, et al. Treatment for severe acute respiratory distress syndrome from COVID-19. Lancet Respir Med. 2020 Mar 20. Pii: S2213-2600(20)30127-2. doi: 10.1016/S2213- 2600(20)30127-2.

Mauri T, et al. Potential for lung recruitment and ventilation-perfusion mismatch in patients with the acute respiratory distress syndrome from coronavirus disease 2019. Crit Care Med. 2020 Apr 17. doi: 10.1097/CCM. 0000000000004386.

McAloon C, et al. Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research. BMJ Open. 2020 Aug 16;10(8):e039652. doi: 10.1136/bmjopen-2020- 039652.

McCarthy C, et al. Tocilizumab therapy in individuals with COVID-19 infection and hyperinflammatory state. Respirology. 2020 Jul 21. doi: 10.1111/resp.13912.

McCormick-Baw C, et al. Saliva as an Alternate Specimen Source for Detection of SARS-CoV-2 in Symptomatic Patients Using Cepheid Xpert Xpress SARS-CoV-2. J Clin Microbiol. 2020 May 15:JCM.01109-20. Last updated 4 October 2020

McCreary EK, DC Angus. Efficacy of Remdesivir in COVID-19. JAMA. 2020 Aug 21. doi: 10.1001/jama.2020.16337.

McCrindle BW, C Manlhiot. SARS-CoV-related inflammatory multisystem syndrome in children: Different or shared etiology and pathophysiology as Kawasaki disease? JAMA. 2020 Jun 8. doi: 10.1001/jama.2020.10370.

McCulloch DJ, et al. Comparison of unsupervised home self-collected midnasal swabs with clinician-collected nasopharyngeal swabs for detection of SARS-CoV-2 infection. JAMA Netw Open. 2020:3(7):e2016382.

McGonagle D, et al. Mechanisms of pulmonary intravascular coagulopathy in COVID-19 pneumonia. Lancet Rheumatol. 2020 May 7. https://doi.org/10.1016/S2665-0013(20)30121-1.

McGuinness G, et al. High incidence of barotrauma in patients with COVID-19 infection on invasive mechanical ventilation. Radiology. 2020 Jul 1:202352. doi: 10.1148/radiol.2020202352.

McMichael TM, et al. Epidemiology of COVID-19 in a long-term care facility in King County, Washington. N Engl J Med. 27 Mar 2020. doi: 10.1056/NEJMoa2005412.

Mehta P, et al. COVIID-19: consider cytokine storm syndromes and immunosuppression. Lancet. 2020 Mar 28:395(10229):1033-1034.

Mehta V, et al. Case fatality rate of cancer patients with COVID-19 in a New York hospital system. Cancer Discov. 2020 May 1. doi: 10.1158/2159-8290.CD-20-0516.

Meltzer DO, et al. Association of Vitamin D Status and Other Clinical Characteristics With COVID-19 Test Results. JAMA Netw Open. 2020 Sep 1;3(9):e2019722. doi: 10.1001/jamanetworkopen.2020.19722.

Menter T, et al. Post-mortem examination of COVID19 patients reveals diiffuse alveolar damage with severe capillary congestion and variegated findings of lungs and other organs suggesting vascular dysfunction. Histopathology. 2020 May 4. doi: 10.1111/his.14134.

Merad M, JC Martin. Pathological inflammation in patients with COVID-19: a key role for monocytes and macrophages. Nat Rev Immunol. 2020 May 6. https://doi.org/10.1038/s41577- 020-0331-4.

Mercado NB, et al. Single-shot Ad26 vaccine protects against SARS-CoV-2 in rhesus macaques. Nature. 2020 Jul 30. doi: 10.1038/s41586-020-2607-z.

Mercante G, et al. Prevalence of taste and smell dysfunction in Coronavirus disease 2019. JAMA Otolaryngol Head Neck Surg. 2020 Jun 18;e201155. doi: 10.1001/jamaoto.2020.1155.

Last updated 4 October 2020

Merzon E, et al. Low plasma 25(OH) vitamin D level is associated with increased risk of COVID- 19 infection: an Israeli population-based study. FEBS J. 2020 Jul 23. doi: 10.1111/febs.15495.

Mikami T, et al. Risk factors for mortality in patients with COVID-19 in New York City. J Gen Intern Med. 2020 Jun 30. doi: 10.1007/s11606-020-05983-z.

Milani GP, et al. Frequency of children vs adults carrying severe acute respiratory syndrome coronavirus 2 asymptomatically. JAMA Pediatr. 2020 Sep 14. doi:10.1001/jamapediatrics.2020.3595.

Miller A, et al. Correlation between universal BCG vaccination policy and reduced morbidity and mortality for COVID-19: an epidemiological study. medRxiv. https://doi.org/10.1101.2020.03.24.20042937.

Miller JC, et al. The risk of SARS-CoV-2 transmission in the healthcare setting and potential impact of cohorting strategies. medRxiv. https://doi.org/10.1101/2020.04.20.20073080.

Miller SL, et al. Transmission of SARS-CoV-2 by inhalation of respiratory aerosol in the Skagit Valley Chorale superspreading event. Indoor Air. 2020 Sep 15. doi: https://doi.org/10.1101/2020.06.15.20132027.

Miller TE, et al. Clinical sensitivity and interpretation of PCR and serological COVID-19 diagnostics for patients presenting to the hospital. FASEB J. 2020 Aug 28. doi: 10.1096/fj.202001700RR.

Million M, et al. Early treatment of COVID-19 patients with hydroxychloroquine and azithromycin: A retrospective analysis of 1061 cases in Marseille, France. Trav Med Infect Dis. 2020 May 1. https:doi.org/10.1016/j.tmaid.2020.101738.

Mina MJ, et al. Rethinking Covid-19 Test Sensitivity - A Strategy for Containment. N Engl J Med. 2020 Sep 30. doi: 10.1056/NEJMp2025631.

Minotti C, et al. How is immunosuppressive status affecting children and adults in SARS-CoV-2 infection? A systematic review. J Infect. 2020 Apr 23. doi: 10.1016/j.jinf.2020.04.026.

Mitja O, et al. Hydroxychloroquine for early treatment of adults with mild COVID-19: A randomized-controlled trial. Clin Infect Dis. 2020 Jul 16;ciaa1009. doi: 10.1093/cid/ciaa1009.

Moderbacher CR, et al. Antigen-specific adaptive immunity to SARS-CoV-2 in acute COVID-19 and associations with age and disease severity. Cell. 2020 Sep 11. https://doi.org/10.1016/j.cell.2020.09.038.

Moghadas SM, et al. The implications of silent transmission for the control of COVID-19 outbreaks. Proc Natl Acad Sci USA. 2020 Jul 6:202008373. doi: 10.1073/pnas.2008373117. Last updated 4 October 2020

Molina JM, et al. No evidence of rapid antiviral clearance or clinical benefit with the combination of hydroxychloroquine and azithromycin in patients with severe COVID-19 infection. Med Mal Infect. doi: https://doi.org/10.1016/j.medmal.2020.04.006.

Monreal E, et al. Immunosuppression is associated with a lower risk of moderate to severe acute respiratory distress syndrome in COVID-19. Res Square. doi: 10.21203/rs.3.rs-27095/v1.

Moore BJB and CH June. Cytokine release syndrome in severe COVID-19. Science. 2020 Apr 17. pii: eabb8925. doi: 10.1126/science.abb8925.

Moore K, et al. The CIDRAP Viewpoint: The future of the COVID-19 pandemic: lessons learned from pandemic influenza. https://www.cidrap.umn.edu/covid-19/covid-19-cidrap-viewpoint.

Morawska L, Milton DK. It is time to address airborne transmission of COVID-19. Clin Infect Dis. 2020 Jul 6;ciaa939. doi: 10.1093/cid/ciaa939.

Moriarty LF, et al. Public health responses to COVID-19 outbreaks on cruise ships—Worldwide, February-March 2020. MMWR Morb Mortal Wkly Rep. 23 Mar 2020. Doi: http://dx.doi.org/10.15585/mmwr/mm6912e3.

Morris SC. Washington State disaster risk and preparedness: A primer for health care providers. Prehosp Disast Med. 2020. doi:10.1017/S1049023X20000412.

Mortus JR, et al. Thromboelastographic results and hypercoagulability syndrome in patients with coronavirus disease 2019 who are critically ill. JAMA Netw Open. 2020 Jun 1;3(6):e2011192.

Moscola J, et al. Prevalence of SARS-CoV-2 antibodies in health care personnel in the New York City area. JAMA. 2020 Aug 6. doi: 10.1001/jama.2020.14765.

Mosites E, et al. Assessment of SARS-CoV-2 infection prevalence in homeless shelters—Four U.S. cities, March 27-April 15, 2020. MMWR Morb Mortal Wkly Rep. 2020 Apr 22. https://www.cdc.gov/mmwr/volumes/69/wr/mm6917e1.htm?s_cid=mm6917e1_w.

Mudd PA, et al. Targeted immunosuppression distinguishes COVID-19 from influenza in moderate and severe disease. medRxiv. https://doi.org/10.1101/2020.05.28.20115667.

Mulligan MJ, et al. Phase 1/2 study of COVID-19 RNA vaccine BNT162b1 in adults. Nature. 020 Aug 12. doi: 10.1038/s41586-020-2639-4.

Mullins E, et al. Coronavirus in pregnancy and delivery: Rapid review. Ultrasound Obstet Gynecol. 2020 Mar 17. doi: 10.1002/uog.22014.

Last updated 4 October 2020

Munoz-Price LS, et al. Racial Disparities in Incidence and Outcomes Among Patients With COVID-19. JAMA Netw Open. 2020 Sep 1;3(9):e2021892. doi: 10.1001/jamanetworkopen.2020.21892.

Munster VJ, et al. Respiratory disease in rhesus macaques inoculated with SARS-CoV-2. Nature. 2020 May 12. doi: 10.1038/s41586-020-2324-7.

Murray CJL, et al. Forecasting COVID-19 impact on hospital bed-days, ICU-days, ventilator-days and deaths by US state in the next 4 months. medRxiv 2020.043752. http://www.healthdata.org/research-article/forecasting-covid-19-impact-hospital-bed-days- icu-days-ventilator-days-and-deaths.

Mutambudzi M, et al, Occupation and risk of COVID-19: Prospective cohort study of 120,621 UK Biobank participants. medRxiv. https://doi.org/10.1101/2020.05.22.20109892.

Myers LC, et al. Characteristics of hospitalized adults with COVID-19 in an integrated health care system in California. JAMA. 2020 Apr 24. doi: 10.1001/jama.2020.7202.

Nadkami GN, et al. Anticoagulation, Mortality, Bleeding and Pathology Among Patients Hospitalized with COVID-19: A Single Health System Study. J Am Coll Cardiol. 2020 Aug 20. https://doi.org/10.1016/j.jacc.2020.08.041.

Nagler AR, et al. Early Results From SARS-CoV-2 PCR Testing of Healthcare Workers at an Academic Medical Center in New York City. Clin Infect Dis. 2020 Jun 28;ciaa867. doi: 10.1093/cid/ciaa867.

Nahum J, et al. Venous thrombosis among critically ill patients with coronavirus disease 2019 (COVID-19). JAMA Netw Open. 2020 May1;3(5):e2010478.

Nakamichi K, et al. Outcomes associated with SARS-CoV-2 viral clades in COVID-19. medRxiv. 2020 Sep 25;2020.09.24.20201228. doi: 10.1101/2020.09.24.20201228.

Nardell EA, RR Nathavitharana. Airborne spread of SARS-CoV-2 and a potential role for air disinfection. JAMA. 2020 Jun 1. doi: 10.1001/jama.2020.7603.

Nath A. Long-haul COVID. Neurology. 2020 Aug 11;10.1212/WNL.0000000000010640.

Negri EM, et al. Heparin therapy improving hypoxia in COVID-19 patients—a case series. medRxiv. https://doi.org/10.1101.2020.04.15.20067017.

Neher RA, et al. Potential impact of seasonal forcing on a SARS-CoV-2 pandemic. medRxiv 2020.02.13.20022806.

Last updated 4 October 2020

Nelde A, et al. SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition. Nat Immunol. 2020 Sep 30. doi: 10.1038/s41590-020-00808-x.

Ng DHL, et al. Fever Patterns, Cytokine Profiles, and Outcomes in COVID-19. Open Forum Infect Dis. 2020 Aug 24;7(9):ofaa375. doi: 10.1093/ofid/ofaa375.

Ng DL, et al. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay area. medRxiv https://doi.org/10.1101/2020.05.19.20107482.

Nguyen LH, et al. Risk of symptomatic COVID-19 among front-line health-care workers and the general community: a prospective cohort study. Lancet Public Health. https://doi.org/10.1016/ S2468-2667(20)30164-X.

Ni L, et al. Detection of SARS-CoV-2-specific humoral and cellular immunity in COVID-19 convalescent individuals. Immunity. 2020 Apr 28. https://doi.org/10.1016/j.immuni.2020.04.023.

Nicolai L, et al. Immunothrombotic Dysregulation in COVID-19 Pneumonia is Associated with Respiratory Failure and Coagulopathy. Circulation. 2020 Jul 28. doi: 10.1161/CIRCULATIONAHA.120.048488.

Nie X, et al. Epidemiological characteristics and incubation period of 7,015 confirmed cases with coronavirus disease 2019 outside Hubei province. J Infect Dis. 2020 Apr 27. doi: 20.2093/infdis/jaa211.

Nielsen BF, K Sneppen. COVID-19 superspreading suggests mitigation by social network modulation. medRxiv. 2020 Oct 1;2020.09.15.20195008. doi: 10.1101/2020.09.15.20195008

Nishiura H, et al. Closed environments facilitate secondary transmission of coronavirus disease 2019 (COVID-19). MedRxiv. https://doi.org/10.1101/2020.02.28.20029272.

Nishiura H, et al. Serial interval of novel coronavirus (COVID-19) infections. 2020 Mar 4. pii: S1201-9712(20)30119-3. doi: 10.1016/j.ijid.2020.02.060.

Nobel YR, et al. Gastrointestinal symptoms and COVID-19: Case-control study from the United States. Gastroenterology. 2020 Apr 8. https://doi.org/10.1053/j.gastro.2020.04.017.

Nopp S, et al. Risk of venous thromboembolism in patients with COVID-19: A systematic review and meta-analysis. Res Pract Thromb Haemost. 2020 Sep 25. doi: 10.1002/rth2.12439.

O’Brien TR, et al. Weak induction of interferon expression by SARS-CoV-2 supports clinical trials of interferon lambda to treat early COVID-19. Clin Infect Dis. 2020 Apr 17. pii: ciaa453. doi: 10.1093/cid/ciaa453.

Last updated 4 October 2020

O’Callaghan KP, et al. Developing a SARS-CoV-2 vaccine at warp speed. JAMA. 2020 Jul 6. doi: 10.1001/jama.2020.12190.

Odak I, et al. Reappearance of effector T cells predicts successful recovery from COVID-19. medRxiv. https://doi.org/10.1101/2020.05.11.20096263.

O’Driscoll M, et al. Age-specific mortality and immunity patterns of SARS-CoV_2 infection in 45 countries. medRxiv. https://doi.org/10.1101/2020.08.24.20180851.

Okba NMA, et al. SARS-CoV-2 specific antibody responses in COVID-19 patients. medRxiv 2020.03.18.20038059.

Oliveiros B, et al. Role of temperature and humidity in the modulation of the doubling time of COVID-19 cases. medRxiv 2020.03.05.20031872.

Onder G, et al. Case-fatality rate and characteristics of patients dying in relation to COVID-19 in Italy. JAMA. 23 Mar 2020. doi: 10.1001/jama.2020.4683.

Oran DP, EJ Topol. Prevalence of asymptomatic SARS-CoV-2 infection: A narrative review. Ann Intern Med. 2020 Jun 3. doi: 10.7326/M20-3012.

Ou J, et al. Study on the expression levels of antiboies against SARS-CoV-2 at different period of disease and its related factors in 192 cases of COVID-19 patients. medRxiv. https://doi.org/10.1101/2020.05.22.20102525.

Oude Munnink BB, et al. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat Med. 2020 Jul 16. doi: 10.1038/s41591-020-0997-y.

Oxley TJ, et al. Large-vessel stroke as a presenting feature of COVID-19 in the young. N Engl J Med. 2020 Apr 28. doi: 10.1056/NEJMc2009787.

Pain CE, et al. Novel Paediatric Presentation of COVID-19 With ARDS and Cytokine Storm Syndrome Without Respiratory Symptoms. Lancet Rheumatol. 2020 May 15;2(7):e376-e379.

Paiva KJ, et al. Validation and performance comparison of three SARS-CoV-2 antibody assays. bioRxiv. https://doi.org/10.1101.2020.05.29.124776.

Paltiel AD, et al. A Assessment of SARS-CoV-2 Screening Strategies to Permit the Safe Reopening of College Campuses in the United States. JAMA Netw Open. 2020 Jul 1;3(7):e2016818. doi: 10.1001/jamanetworkopen.2020.16818.

Pan A, et al. Association of public health interventions with the epidmiology of the COVID-19 outbreak in Wuhan, China. JAMA. 2020 Apr 10. doi:10.1001/jama.2020.6130. Last updated 4 October 2020

Pan L, et al. Clinical characteristics of COVID-19 patients with digestive symptoms in Hubei, China: a descriptive, cross-sectional, multicenter study. Am J Gastroenterol. 18 Mar 2020. http://dx.doi.org/10.14309/ajg.000000000000620.

Pan Y, et al. Viral load of SARS-CoV-2 in clinical samples. Lancet Infect Dis. 2020 Feb 24. pii: S1473-3099(20)30113-4. doi: 10.1016/S1473-3099(20)30113-4.

Panigada M, et al. Hypercoagulability of COVID-19 patients in intensive care unit. A report of thromboelastography findings and other parameters of hemostasis. J Thromb Haemost. 2020 Apr 17. doi: 10.1111/jth/14850.

Paranjpe I, et al. Association of treatment dose anticoagulation with in-hospital survival among hospitalized patients with COVID-109. J Am Coll Cadiol. 2020 May 5. https://doi.org/10.1016/j.jacc.2020.05.001.

Paranjpe I, et al. Clinical characteristics of hospitalized COVID-19 patients in New York City. medRxiv. https://woi.org/10.1101/2020.04.19.20062117.

Parasa S, et al. Prevalence of gastrointestinal symptoms and fecal viral shedding in patients with coronavirus disease 2019. A systematic review and meta-analysis. JAMA Network Open. 2020;3(6):e2011335.

Park A, A Iwasaki. Type I and type III interferons—Induction, signaling, evasion, and application to combat COVID-19. Cell Host Microbe. 2020 May 27:S1931-3129(20)30290-0.

Park SY, et al. Coronavirus disease outbreak in call center, South Korea. Emerg Infect Dis. 2020 Apr 23;26(8)1666-1670. doi: 10.3201/eid2608.201274.

Park YJ, et al. Contact Tracing during Coronavirus Disease Outbreak, South Korea, 2020. Emerg Infect Dis. 2020 Oct;26(10):2465-2468. doi: 10.3201/eid2610.201315.

Parri N, et al. Children with COVID-19 in pediatric emergency departments in Italy. N Engl J Med. 2020 May 1. doi: 10.1056/NEJMc2007617.

Passamonti F, et al. Clinical characteristics and risk factors associated with COVID-19 severity in patients with haematological malignancies in Italy: A retrospective, multicentre, cohort study. Lancet Haematol. 2020 Aug 13. https://doi.org/10.1016/S2352-3026(20)30252-0.

Patel AB, A Verma. COVID-19 and angiotensin-converting enzyme inhibitors and angiotensin receptor blockers: What is the evidence? JAMA. 24 Mar 2020. doi:10.1001/jama.2020.4812.

Last updated 4 October 2020

Patel BV, et al. Pulmonary Angiopathy in Severe COVID-19: Physiologic, Imaging and Hematologic Observations. Am J Respir Crit Care Med. 2020 Jul 15. doi: 10.1164/rccm.202004- 1412OC.

Patel MC, et al. Asymptomatic SARS-CoV-2 infection and COVID-19 mortality during an outbreak investigation in a skilled nursing facility. Clin Infect Dis. 2020 Jun 16;ciaa763. doi: 10.1093/cid/ciaa763.

Patel MM, et al. Change in Antibodies to SARS-CoV-2 Over 60 Days Among Health Care Personnel in Nashville, Tennessee. JAMA. 2020 Sep 17. doi: 10.1001/jama.2020.18796.

Patel MR, et al. Performance of Oropharyngeal Swab Testing Compared to Nasopharyngeal Swab Testing for Diagnosis of COVID-19 -United States, January-February 2020. Clin Infect Dis. 2020 Jun 16;ciaa759. doi: 10.1093/cid/ciaa759.

Paterson RW, et al. The emerging spectrum of COVID-19 neurology: Clinical, radiological and laboratory findings. Brain. 2020 Jul 8;awaa240. doi: 10.1093/brain/awaa240.

Patterson BK, et al. Disruption of the CCL5/TANTES-CCR5 pathway restores immune homeostasis and reduces plasma viral load in critical COVID-19. medRxiv. https://doi.org/10.1101/2020.05.02.20084673.

Pearce L, et al. The cytokine storm of COVID-19: a spotlight on prevention and protection. Expert Opin Ther Targets. 2020 Jun 27:1-8. doi: 10.1080/14728222.2020.1783243.

Peccia J, et al. Measurement of SARS-CoV-2 in wastewater tracks community infection dynamics. Nat Biotechnol. 2020 Sep 18. https://doi.org/10.1038/s41587-020-0684-z.

Pedersen SR, YC Ho. SARS-CoV-2: A storm is raging. J Clin Invest. 2020 Mar 27. pii: 137647. doi: 10.1172/JCI137647.

Peeples L. Avoiding pitfalls in the pursuit of a COVID-19 vaccine. Proc Natl Acad Sci USA. 2020 Mar 30. Pii: 202005456. doi: 10.1073/pnas.2005456117.

Penarrubia L, et al. Multiple Assays in a Real-Time RT-PCR SARS-CoV-2 Panel Can Mitigate the Risk of Loss of Sensitivity by New Genomic Variants During the COVID-19 Outbreak. Int J Infect Dis. 2020 Jun 11;S1201-9712(20)30463-X.

Peng L, et al. 2019 novel coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples. medRxiv 2020.02.21.20026179.

Peng QY, et al. Findings of lung ultrasonography of novel corona virus pneumonia during the 2019-2020 epidemic. Intensive Care Med. 2020 Mar 12. doi: 10.1007/s00134-020-05996-6.

Last updated 4 October 2020

Percivalle E, et al. Prevalence of SARS-CoV-2 Specific Neutralising Antibodies in Blood Donors From the Lodi Red Zone in Lombardy, Italy, as at 06 April 2020. Euro Surveill. 2020 Jun;25(24). doi: 10.2807/1560-7917.ES.2020.25.24.2001031.

Perez-Bermejo JA, et al. SARS-CoV-2 infection of human iPSC-derived cardiac cells predicts novel cytopathic features in hearts of COVID-19 patients. bioRxiv. https://doi.org/10.1101/2020.08.25.265561.

Perez-Guzman PN, et al. Clinical characteristics and predictors of outcomes of hospitalized patients with COVID-19 in a multi-ethnic London NHS Trust: a retrospective cohort study. Clin Infect Dis. 2020 Aug 7;ciaa1091. doi: 10.1093/cid/ciaa1091.

Perez-Toledo M, et al. Serology confirms SARS-CoV-2 infection in PCR-negative children presenting with paediatric inflammatory multi-system syndrome. medRxiv. https://doi.org/10.1101/2020.06.05.20123117.

Perinel S, et al. Towards optimization of hydroxychloroquine dosing in intensive care unit COVID-19 patients. Clin Infect Dis. 2020 Apr 7. pii: ciaa394. doi: 10.1093/cid/ciaa394.

Perkins TA, et al. Estimating unobserved SARS-CoV-2 infections in the United States. Proc Natl Acad Sci USA. 2020 Aug 21;202005476. doi: 10.1073/pnas.2005476117.

Perrault J, et al. Waning of SARS-CoV-2 RBD antibodies in logitudinal convalescent plasma samples within four months after symptom onset. Blood, in press. bioRxiv. 2020 Jul 17. doi: https://doi.org/10.1101/2020.07.16.206847.

Petrilli CM, et al. Factors associated with hospital admission and critical illness among 5279 people with coronavirus disease 2019 in New York City: Prospective cohort study. BMJ. 2020;369:m1966. http://dx.doi.org/10.1136/bmj.m1966.

Pettengill MA, AJ McAdam. Can We Test Our Way Out of the COVID-19 Pandemic? J Clin Microbiol. 2020 Aug 25;JCM.02225-20. doi: 10.1128/JCM.02225-20.

Phua J, et al. Intensive care management of coronavirus disease 2019 (COVID-19): challenges and recommendations. Lancet Respir Med. 6 Apr 2020. https://doi.org/10.1016/S2213- 2600(20)30161-2.

Pierce CA, et al. Immune responses to SARS-CoV-2 infection in hospitalized pediatric and adult patients. Sci Transl Med. 2020 Sep 21;eabd5487. doi: 10.1126/scitranslmed.abd5487.

Pinninti S, et al. Comparing Nasopharyngeal and Mid-Turbinate Nasal Swab Testing for the Identification of SARS-CoV-2. Clin Infect Dis. 2020 Jun 29;ciaa882. doi: 10.1093/cid/ciaa882.

Last updated 4 October 2020

Piras A, et al, Inappropriate nasopharyngeal sampling for SARS-CoV-2 detection is a relevant cause of false-negative reports. Otolaryngol Head Neck Surg. 2020 May 26:194599820931793.

Plucinski MM, et al. COVID-19 in Americans aboard the Diamond Princess cruise ship. Clin Infect Dis. 2020 Aug 12;ciaa1180. doi: 10.1093/cid/ciaa1180.

Polak SB, et al. A systematic review of pathological findings in COVID-19: A pathophysiological timeline and possible mechanisms of disease progression. Mod Pathol. 2020 Jun 22;1-11. doi: 10.1038/s41379-020-0603-3.

Poline J, et al. Systematic SARS-CoV-2 screening at hospital admission in children: a French prospective multicenter study. 2020 Jul 25;ciaa1044. doi: 10.1093/cid/ciaa1044.

Pollan M, et al. Prevalence of SARS-CoV-2 in Spain (ENE-COVID): A Nationwide, Population- Based Seroepidemiological Study. Lancet. 2020 Jul 3;S0140-6736(20)31483-5. doi: 10.1016/S0140-6736(20)31483-5.

Ponti G, et al. Biomarkers associated with COVID-19 disease progression. Crit Rev Clin Lab Sci. 2020 Jun 5;1-11.

Poor HD, et al. COVID-19 critical illness pathophysiology driven by diffuse pulmonary thrombi and pulmonary endothelial dysfunction responsive to thrombolysis. Clin Transl Med. 2020 May 13;10.1002/ctm2.44. doi: 10.1002/ctm2.44.

Prather KA, et al. Reducing transmission of SARS-CoV-2. Science. 2020 May 27. doi: 10.1126/science.abc6197.

Prebensen C, et al. SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19. Clin Infect Dis. 2020 Sep 5;ciaa1338. doi: 10.1093/cid/ciaa1338.

Premkumar L, et al. The Receptor Binding Domain of the Viral Spike Protein Is an Immunodominant and Highly Specific Target of Antibodies in SARS-CoV-2 Patients. Sci Immunol. 2020 Jun 11;5(48):eabc8413. doi: 10.1126/sciimmunol.abc.8413.

Price CC, et al. Tocilizumab treatment for cytokine release syndrome in hospitalized COVID-19 patients: Survival and clinical outcomes. Chest. 2020 Jun 15;S0012-3692(20)31670-6. doi: 10.1016/j.chest.2020.06.006.

Price S, et al. Respiratory management in severe acute respiratory syndrome coronavirus 2 infection. Eur Heart J. 2020 Apr 16. doi: 10.1177/2048872620924613.

Price-Haywood EG, et al. Hospitalization and mortality among black patients and white patients with COVID-19. N Engl J med. 2020 May 27. doi: 10.1056/NEJMsa2011686. Last updated 4 October 2020

Prieto-Alhambra D, et al. Hospitalization and 30-day fatality in 121263 COVID-19 outpatient cases. medRxiv. https://doi.org/10.1101/2020.05.04.20090050.

Puelles VG, et al. Multiorgan and renal tropism of SARS-CoV-2. N Engl J Med. 2020 May 13. doi: 10.1056/NEJMc2011400.

Pujadas, E, et al. SARS-CoV-2 viral load predicts COVID-19 mortality. Lancet Respir Med. 2020 Aug 6. https://doi.org/10.1016/S2213-2600(20)30354-5..

Puntmann VO, et al. Outcomes of Cardiovascular Magnetic Resonance Imaging in Patients Recently Recovered From Coronavirus Disease 2019 (COVID-19). JAMA Cardiol. 2020 Jul 27. doi: 10.1001/jamacardio.2020.3557.

Qian G, et al. A COVID-19 transmission within a family cluster by presymptomatic infectors in China. Clin Infect Dis. 2020 Mar 23. Pii: ciaa316. Doi: 10.1093/cid/ciaa316.

Qian H, et al. Indoor transmission of SARS-CoV-2. medRxiv. https://doi.org/10.1101/2020.04.04.20053058.

Qian J, et al. Age-dependent gender differences of COVID-10 in mainland China: comparative study. Clin Infect Dis. 2020 May 30:ciaa683. doi: 10.1093/cid/ciaa683.

Qian Q, et al. Direct evidence of active SARS-CoV-2 replication in the intestine. Clin Infect Dis. 2020 Jul 8:ciaa925. doi: 10.1093/cid/ciaa925.

Qin C, et al. Dysregulation of immune response in patients with COVID-19 in Wuhan, China. Clin Infect Dis. 12 Mar 2020. https://doi.org/10.1093/cid/ciaa248.

Qiu H, et al. Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study. Lancet Infect Dis. 25 Mar 2020. https://doi.org/10.1016/S1473-3099(20)30198-5.

Ra SH, et al. Upper respiratory viral load in asymptomatic individuals and mildly symptomatic patients with SARS-CoV-2 infection. Thorax. 2020 Sep 22;thoraxjnl-2020-215042. doi: 10.1136/thoraxjnl-2020-215042.

Radbel J, et al. Use of tocilizumab for COVID-19 infection-induced cytokine release syndrome: a cautionary case report. Chest. 2020 Apr 25. doi: 10.1016/j.chest.2020.04.024.

Rajpal S, et al. Cardiovascular magnetic resonance findings in competitive athletes recovering from COVID-19 infection. JAMA Cardiol. 2020 Sept. 11. doi: 10.1001/jamacardio.2020.4916.

Last updated 4 October 2020

Rambaut A, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020 Jul 15. doi: 10.1038/s41564-020-0770-5.

Ramdas K, et al. ‘Test, re-test, re-test‘: Using inaccurate tests to greatly increase the accuracy of COVID-19 testing. Nat Med. 2020 May 12. doi: 10.1038/s41591-020-0891-7.

Ramlall V, et al. Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection. Nat Med. https://doi.org/10.1038/s41591-020-1021-2.

Randhawa AK, et al. Changes in SARS-CoV-2 positivity rate in outpatients in Seattle andWashington State, March 1-April 16, 2020. JAMA. 2020 May 8. doi: 10.1001/jama.2020.8097.

Ranoa DRE, et al. Saliva-based molecular testing for SARS-CoV-2 that bypasses RNA extraction. bioRxiv. https://doi.org/10.1101/2020.06.18.159434.

Ranucci M, et al. The procoagulant pattern of patients with COVID-19 acute respiratory distress syndrome. J Thromb Haemost. 2020 Apr 17. doi: 10.1111/jth.14854.

Rawson TM, et al. Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing. Clin Infect Dis. 2020 May 2. doi: 10.1093/cid/ciaa530.

Reifer J, et al. SARS-CoV-2 antibody responses in New York City. Diagn Microbiol Infect Dis. 2020 Jul 21;98(3):115128. doi: 10.1016/j.diagmicrobio.2020.115128.

Rello J, et al. Clinical phenotypes of SARS-CoV-2: Implications for clinicians and researchers. Eur Respir J. 2000 Apr 27. doi: 10.1183/13993003.01028-2020.

Ren B, et al. Extremely High Incidence of Lower Extremity Deep Venous Thrombosis in 48 Patients With Severe COVID-19 in Wuhan. Circulation. 2020 May 15. doi: 10.1161/CIRCULATIONAHA.120.047407.

Ren L, et al. Antibody Responses and Clinical Outcomes in Adults Hospitalized with Severe COVID-19: A Post hoc Analysis of LOTUS China Trial. Clin Infect Dis. 2020 Aug 25;ciaa1247. doi: 10.1093/cid/ciaa1247.

Rentsch CT, et al. Hydroxychloroquine for prevention of COVID-19 mortality: a population- based cohort study. medRxiv. https://doi.org/10.1101.2020.09.04.20187781.

Reynolds HJR, et al. Renin-angiotensin-aldosteroine system inhibitors and risk of COVID-19. N Engl J Med. 2020 May 1. doi: 10.1056/NEJM0a2008975.

Last updated 4 October 2020

Rhee C, et al. Incidence of Nosocomial COVID-19 in Patients Hospitalized at a Large US Academic Medical Center. JAMA Netw Open. 2020 Sep 1;3(9):e2020498. doi: 10.1001/jamanetworkopen.2020.20498.

Richardson S, et al. Presenting characteristics, comorbidities, and outcomes among 5700 patients hospitalized with COVID-19 in the New York City area. JAMA. 2020 Apr 16. doi:10.1001/jama.2020.6775.

Rickman HM, et al. Nosocomial Transmission of COVID-19: A Retrospective Study of 66 Hospital-Acquired Cases in a London Teaching Hospital. Clin Infect Dis. 2020 Jun 20;ciaa816. doi: 10.1093/cid/ciaa816.

Ridgway J, et al. Prolonged shedding of SARS-CoV-2 RNA among patients with COVID-19. Infet Control Hosp Epidemiol. 2020 Jun 24;1-8. doi: 10.1017/ice.2020.307.

Rijkers G, et al. Differences in antibody kinetics and functionality between severe and mild SARS-CoV-2 infections. medRxiv. https://doi.org/10.1101/2020.06.09.20122036.

Riollano-Cruz M, et al. Multisystem inflammatory syndrome in children (MIS-C) related to COVID-19: A New York City experience. J Med Virol. 2020 Jun 25. doi: 10.1002/jmv.26224.

Riphagen S, et al. Hyperinflammatory shock in children during COVID-19 pandemic. Lancet. 2020 May 6. https://doi.org/10.1016/S0140-6736(20)31094-1.

Ripperger TJ, et al. Detection, prevalence, and duration of humoral responses to SARS-CoV-2 under conditions of limited population exposure. medRxiv. 2020 Aug 15;2020.08.14.20174490. doi: 10.1101/2020.08.14.20174490.

Risitano AM, et al. Complement as a target in COVID-19? Nat Rev Immunol. 2020 Apr 23. https://doi.org/10.1038/s41577-020-0320-7.

Rivett L, et al. Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission. Elife. 2020 May 11;9. doi: 10.7554/eLife.58728.

Robbiani DF, et al. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature. 2020 Jun 18. doi: 10.1038/s41586-020-2456-9.

Robilotti EV, et al. Determinants of COVID-19 disease severity in patients with cancer. medRxiv. Nat Med. 2020 Jun 24. doi: 10.1038/s41591-020-0979-0.

Roche. Media and investor Release: Update on the phase III COVACTA trial of Actemra/RoActemra in hospitalised patients with severe COVID-19 associated pneumonia. https://www.roche.com/investors/updates/inv-update-2020-07-29.htm Last updated 4 October 2020

Rochwerg B, et al. Remdesivir for severe covid-19: a clinical practice guideline. BMJ. 2020 Jul 30;370:m2924. doi: 10.1136/bmj.m2924.

Rockett RJ, et al. Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nat Med. 2020 Jul 9. doi: 10.1038/s41591-020-1000-7.

Rockx B, et al. Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model. Science. 2020 Apr 17. pii: eabb7314. doi: 10.1126/science.abb7314.

Rodriguez-Bano J, et al. Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19). Clin Microbiol Infect. 2020 Aug 26;S1198-743X(20)30492-4. doi: 10.1016/j.cmi.2020.08.010.

Rogers JH, et al. Characteristics of COVID-19 in Homeless Shelters : A Community-Based Surveillance Study. Ann Intern Med. 2020 Sep 15. doi: 10.7326/M20-3799.

Rogers TF, et al. Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. Science. 2020 Jun 15;eabc7520. doi: 10.1126/science.abc7520.

Rojas M, et al. Convalescent plasma in COVID-19: Possible mechanisms of action. Autoimmun Rev. 2020 May 4:102554.

Roschewski M, et al. Inhibition of Bruton Tyrosine Kinase in patients with severe COVID-19. Sci Immunol. 2020 Jun 5;5(48):eabd0110.

Rosenberg ES, et al. Association of treatment with hydroxychloroquine or azithromycin with in- hospital mortality in patients with COVID-19 in New York State. JAMA. 2020 May 11. doi: 10.1001/jama.2020.8630.

Rosenke K, et al. Hydroxychloroquine proves ineffective in hamsters and macaques infected with SARS-CoV-2. bioRxiv. https://doi.org/10.1101/2020.06.10.145144.

Rostad CA, et al. Quantitative SARS-CoV-2 serology in children with Multisystem Inflammatory Syndrome (MIS-C). Pediatrics. 2020 Sep 2; e2020018242; doi: 10.1542/peds.2020-018242.

Rothe C, et al. Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany. N Engl J Med. 2020 Mar 5;382(10):970-971.

Rovina N, et al. Soluble urokinase plasminogen activator receptor (suPAR) as an early predictor of severe respiratory failure in patients with COVID-19 pneumonia. Crit Care. 2020 Apr 30;24(1):187. doi: 10.1186/s13054-020-02897-4.

Last updated 4 October 2020

Rowley AH. Understanding SARS-CoV-2-related Multisystem Inflammatory Syndrome in Children. Nat Rev Immunol. 2020 Jun 16;1-2. doi: 1-.1-38/s41577-020-0367-5.

Roxby AC, et al. Detection of SARS-CoV-2 among residents and staff members of an independent and assisted living community for older adults—Seattle, Washington, 2020. MMWR Morb Mortal Wkly Rep. https://www.cdc.gov/mmwr/volumes/69/wr/mm6914e2.

Roxby AC, et al. Outbreak investigation of COVID-19 among residents and staff of an independent and assisted living community for older adults in Seattle, Washington. JAMA Intern Med. 2020 May 21. doi: 10.1001/jamainternmed.2020.2233.

Rubin D, et al. Association of Social Distancing, Population Density, and Temperature with the Instantaneous Reproduction Number of SARS-CoV-2 in Counties Across the United States. JAMA Net Open. 2020:3(7):e2016099. doi: 10.1001/jamanetworkopen.2020.16099.

Rubin GD, et al. The role of chest imaging in patient management during the COVID-19 pandemic: A multinational consensus statement from the Fleischner Society. Radiology. 7 Apr 2020. https://doi.org/10.1148/radio.2020201365.

Russell CD, et al. Clinical evidence does not support corticosteroid treatment for 2019-nCoV lung injury. Lancet. 2020 Feb 15;395(10223):473-475.

Sagar M, et al. Recent endemic coronavirus infection is associated with less severe COVID-19. J Clin Invest. 2020 Sep 30;143380. doi: 10.1172/JCI143380.

Sajadi MM, et al. Temperature, humidity and latitude analysis to predict potential spread and seasonality of coronavirus disease 2019 (COVID-19). JAMA Network Open. 2020;3(6):e2011834.

Sakurai A, et al. Natural history of asymptomatic SARS-CoV-2 infection. N Engl J Med. 2020 Jun 12. doi: 10.10156/NEJMc2013020.

Salazar E, et al. Treatment of COVID-19 patients with convalescent plasma. Am J Pathol. 2020 May 21. https://doi.org/10.1016/j.ajpath.2020.05.014.

Salje H, et al. Estimating the burden of SARS-CoV-2 in France. Science. 2020 May 13. doi: 10.1126/science.abc3517.

Salvatore CM, et al. Neonatal management and outcomes during the COVID-19 pandemic: AN observation cohort study. Lancet Child Adolesc Health. 2020 Jul 23. https://doi.org/10.1016/S2352-4642(20)30241-8.

Sanders JM, et al. Pharmacologic treatments for coronavirus disease 2019 (COVID-19). A review. JAMA. 2020 Apr 13. doi:10.1001/jama.2020.6019.

Last updated 4 October 2020

Santarpia JL, et al. Aerosol and surface contamination of SARS-CoV-2 observed in quarantine and isolation care. Sci Rep. 2020 Jul 29;10(1):12732. doi: 10.1038/s41598-020-69286-3.

Santarpia JL, et al. The infectious nature of patient-generated SARS-CoV-2 aerosol. medRxiv. https://doi.org/10.1101.2020.07.13.20041632.

Sa Ribero M, et al. Interplay between SARS-CoV-2 and the type I interferon response. PLoS Pathog. 2020 Jul 29;16(7):e1008737. doi: 10.1371/journal.ppat.1008737.

Sattler A, et al. SARS-CoV-2 specific T-cell responses and correlations with COVID-19 patient predisposition. J Clin Invest. 2020 Aug 24;140965. doi: 10.1172/JCI140965.

Savvides C, R Siegel. Asymptomatic and presymptomatic transmission of SARS-CoV-2: A systematic review. medRxiv. https://doi.org/10.1101.2020.06.11.20129072.

Schaefer IM, et al. In situ detection of SARS-CoV-2 in lungs and airways of patients with COVID- 10. Mod Pathol. 2020 Jun 19;1-11. doi: 10.1038/s41379-020-0595-z.

Schaller T, et al. Postmortem examination of patients with COVID-19. JAMA. 2020 May 21. doi: 10.1001/jama.2020.8907.

Schiffer JT, et al. An Early Test-and-Treat Strategy for Severe Acute Respiratory Syndrome Coronavirus 2. Open Forum Infect Dis. 2020 Jun 12;7(7):ofaa232. doi: 10.1093/ofid/ofaa232.

Schneider EC. Failing the test—The tragic data gap undermining the U.S. pandemic response. N Engl J Med. 2020 May 15. doi: 10.1056/NEJMp2014836.

Schurink B, et al. Viral presence and immunopathology in patients with lethal COVID-19: a prospective autopsy cohort study. Lancet Microbe. 2020 Sep 25. https://doi.org/10.1016/ S2666-5247(20)30144-0.

Schwartz DA. An Analysis of 38 Pregnant Women with COVID-19, Their Newborn Infants, and Maternal-Fetal Transmission of SARS-CoV-2: Maternal Coronavirus Infections and Pregnancy Outcomes. Arch Pathol Lab Med. 2020 Mar 17. doi: 10.5858/arpa.2020-0901-SA.

Schulte-Schrepping J, et al. Severe COVID-19 is marked by a dysregulated myeloid cell compartment. Cell. 31 July 31. Cell. https://doi.org/10.1016/j.cell.2020.08.001.

Schultze A, et al. Risk of COVID-19-related death among patients with chronic obstructive pulmonary disease or asthma prescribed inhaled corticosteroids: an observational cohort study using the OpenSAFELY platform. Lancet Respir Med. 2020 Sep 24. https://doi.org/10.1016/ S2213-2600(20)30415-X.

Last updated 4 October 2020

Schwierzeck V, et al. First reported nosocomial outbrea of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a pediatric dialysis unit. Clin Infect Dis. 2020 Apr 27;ciaa491. doi: 10.1093/cid/ciaa491.

Sekine T, et al. Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19. Cell. 2020 Aug 11. https://doi.org/10.1016/j.cell.2020.08.017.

Self WH, et al. Seroprevalence of SARS-CoV-2 Among Frontline Health Care Personnel in a Multistate Hospital Network - 13 Academic Medical Centers, April-June 2020. MMWR Morb Mortal Wkly Rep. 2020 Sep 4;69(35):1221-1226. doi: 10.15585/mmwr.mm6935e2.

Seow J, et al. Longitudinal evaluation and decline of antibody responses in SARS-CoV-2 infection. medRxiv. https://doi.org/10.1101/2020.07/09.20148429.

Sepulveda J, et al. Bacteremia and blood culture utilization during COVID-19 surge in New York City. medRxiv. https://doi.org/10.1101/2020.05.05.20080044.

Sethuraman N, et al. Interpreting diagnostic tests for SARS-CoV-2. JAMA. 2020 May 6. doi: 10.1001/jama.2020.8259.

Sette A, S Crotty. Pre-existing immunity to SARS-CoV-2: the knowns and unknowns. Nat Rev Immunol. 2020 Aug;20(8):457-458. doi: 10.1038/s41577-020-0389-z.

Shah GL, et al. Favorable outcomes of COVID-19 in recipients of hematopoietic cell transplantation. J Clin Invest. 2020 Sep 8;141777. doi: 10.1172/JCI141777.

Shah SJ, et al. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A comparison of patients with and without COVID-19. medRxiv. https:doi.org/10.1101.2020.05.02.20082461.

Shane AL, et al. A Pediatric Infectious Disease Perspective of SARS-CoV-2 and COVID-19 in Children. J Pediatr Infect Dis Soc. 2020 Aug 25;piaa099. doi: 10.1093/jpids/piaa099.

Shang L, et al. On the use of corticosteroids for 2019-nCoV pneumonia. Lancet. 2020 Feb 29;395(10225):683-684.

Shakya KM, et al. Evaluating the efficacy of cloth facemasks in reducing particulate matter exposure. J Expo Sci Environ Epidemiol. 2017 May;27(3):352-357.

Shekerdemian LS, et al. Characteristics and Outcomes of Children With Coronavirus Disease 2019 (COVID-19) Infection Admitted to US and Canadian Pediatric Intensive Care Units. JAMA Pediatr. 2020 May 11. doi: 10.1001/jamapediatrics.2020.1948. Last updated 4 October 2020

Shen C, et al. Treatment of 5 critically ill patients with COVID-19 with convalescent plasma. JAMA. 27 Mar 2000. Doi: 10.1001/jama.2020.4783.

Shen Y, et al. Community Outbreak Investigation of SARS-CoV-2 Transmission Among Bus Riders in Eastern China. JAMA Intern Med. 2020 Sep 1. doi: 10.1001/jamainternmed.2020.5225.

Shet A, et al. Differential COVID-19-attributable mortality and BCG vaccine use in countries. medRxiv. https://doi.org/10.1101/2020.04.01.20049478.

Shi H, et al. Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study. Lancet Infect Dis. 2020 Feb 24. pii: S1473-3099(20)30086-4. doi: 10.1016/S1473-3099(20)30086-4.

Shi H, et al. The inhibition of IL-2/IL-2R gives rise to CD8+ T cell and lymphocyte decrease through JAK1-STAT5 in critical patients with COVID-19 pneumonia. Cell Death Dis. 2020 Jun 8. https://doi.org/10.1038/s41419-020-2636-4.

Shi J, et al. Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS- Coronavirus 2. Science. 2020 May 29;368()6494):1016-1020.

Shi S, et al. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China. JAMA Cardiol. 25 Mar 2020. doi: 10.1001/jamacardio.2020.0950.

Shields AM, et al. SARS-CoV-2 seroprevalence and asymptomatic viral carriage in healthcare workers: A cross-sectional study. Thorax. 2020 Sept. 11. doi :10.1136/thoraxjnl-2020-215414.

Shuren J, T Stenzel. COVID-19 molecular diagnostic testing—Lessons learned. N Engl J Med. 2020 Sep 9. doi: 10.1056/NEJMp2023830.

Siddiqi HK and MR Mehra. COVID-19 illness in native and immunosuppressed states: A clinical- therapeutic staging proposal. J Heart Lung Transpl. doi: 10.1016/j.healun.2020.03.012.

Siedner MJ, et al. Social distancing to slow the US COVID-19 epidemic: Longitudinal pretest- posttest comparison group study. PLoS Med. 2020 Aug 11;17(8):e1003244. doi: 10.1371/journal.pmed.1003244.

Siemieniuk RAC, et al. Drug treatments for covid-19: living systematic review and network meta-analysis. BMJ. 2020 Jul 30;370:m2980. doi: 10.1136/bmj.m2980.

Silvin A, et al. Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19. Cell. 2020 Sep 17;182(6):1401-1418.e18. doi: 10.1016/j.cell.2020.08.002.

Sinha P, et al. Is a “cytokine storm” relevant to COVID-19? JAMA Intern Med. 2020 Jun 30. doi: 10.1001/jamainternmed.2020.3313. Last updated 4 October 2020

Sinha P, et al. Prevalence of phenotypes of acute respiratory distress syndrome in critically ill patients with COVID-19: a prospective observational study. Lancet Respir Med. 2020 Aug 27. https://doi.org/10.1016/ S2213-2600(20)30366-0.

Skendros P, et al. Complement and tissue factor-enriched neutrophil extracellular traps are key drivers in COVID-19 immunothrombosis. J Clin Invest. 2020 Aug 6;141374. doi: 10.1172/JCI141374.

Skipper CP, et al. Hydroxychloroquine in Nonhospitalized Adults With Early COVID-19: A Randomized Trial. Ann Intern Med. 2020 Jul 16;M20-4207. doi: 10.7326/M20-4207.

Smolders EJ, et al. SARS-CoV-2 and HIV protease inhibitors: why lopinavir/ritonavir will not work for COVID-19 infection. Antivir Ther. 2020 Jun 26. doi: 10.3851/IMP3365.

Solomon IH, et al. Neuropathological features of COVID-19. N Engl J Med. 2020 Jun 12. doi: 10.1056/NEJMc2019373.

Somers EC, et al. Tocilizumab for treatment of mechanically ventilated patients with COVID-19. medRxiv. https://doi.org/10.1101/2020.05.29.20117358.

Somsen GA, et al. Small droplet aerosols in poorly ventilated spaces and SARS-CoV-2 transmission. Lancet Respir Med. 2020 May 27. https://doi.org/10.1016/S2213-2600(20)30245- 9.

Song E, et al. Neuroinvasion of SARS-CoV-2 in human and mouse brain. bioRxiv. https://doi.org/10.1101/2020.06.25.169946.

Song F, et al. COVID-19: Recommended sampling sites at different stage of the disease. J Med Virol. 2020 Apr 16. doi: 10.1002/jmv.25892.

Sood N, et al. Seroprevalence of SARS-CoV-2-specific antibodies among adults in Los Angeles County, California, on April 10-11, 2020. JAMA. 2020 May 10. doi: 10.1001/jama.2020.8279.

Spiezia L, et al. COVID-19-related severe hypercoagulability in patients admitted to intensive care unit for acute respiratory failure. Thromb Haemost. 2020 Apr 21. doi: 10.1055/s-0040- 1710018.

Spinato G, et al. Alterations in smell or taste in mildly symptomatic outpatients with SARS-CoV- 2 infection. 2020 Apr 20. doi: 10.1001/jama.2020.6771.

Spinner CD, et al. Effect of Remdesivir vs Standard Care on Clinical Status at 11 Days in Patients With Moderate COVID-19: A Randomized Clinical Trial. JAMA. 2020 Aug 21. doi: 10.1001/jama.2020.16349. Last updated 4 October 2020

Stadnytskyi V, et al. The airborne lifetime of small speech droplets and their potential importance in SARS-CoV-2 transmission. Proc Natl Acad Sci USA. 2020 May 12. www.pnas.org/cgi/doi/10.1073/pnas.2006874117.

Staines HM, et al. Dynamics of IgG seroconversion and pathophysiology of COVID-19 infections. medRxiv. https://doi.org/10.1101/2020.06.07.20124636.

Steinberg J, et al. COVID-19 Outbreak Among Employees at a Meat Processing Facility - South Dakota, March-April 2020. MMWR Morb Mortal Wkly Rep. 2020 Aug 7;69(31):1015-1019. doi: 10.15585/mmwr.mm6931a2.

Steinman JB, et al. Reduced development of COVID-19 in children reveals molecular checkpoints gating pathogenesis illuminating potential therapeutics. Proc Natl Acad Sci USA. 2020 Sep 3;202012358. doi: 10.1073/pnas.2012358117.

Sterling RK, et al. The FIB-4 Index Is Associated with Need for Mechanical Ventilation and 30- day Mortality in Patients Admitted with COVID-19. J Infect Dis. 2020 Aug 28;jiaa550. doi: 10.1093/infdis/jiaa550.

Sterne JAC, et al. Association Between Administration of Systemic Corticosteroids and Mortality Among Critically Ill Patients With COVID-19: A Meta-analysis. JAMA. 2020 Sep 2. doi: 10.1001/jama.2020.17023.

Stringhini S, et al. Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Geneva, Switzerland( SEROCoV-POP): a population-based study. Lancet. 2020 June 11. https://doi.org/10.1016/S0140-6736(20)31304-0.

Struyf T, et al. Signs and Symptoms to Determine if a Patient Presenting in Primary Care or Hospital Outpatient Settings Has COVID-19 Disease. Cochrane Database Syst Rev. 2020 Jul 7;7:CD013665. doi: 10.1002/14651858.CD013665.

Sudharsanan N, et al. The Contribution of the Age Distribution of Cases to COVID-19 Case Fatality Across Countries: A 9-Country Demographic Study. Ann Intern Med. 2020 Jul 22;M20- 2973. doi: 10.7326/M20-2973.

Sungnak W, et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat Med. 2020 Apr 23. https://doi.org/10.1038/s41591- 020-0868-6.

Surkova E, et al. False-positive COVID-19 results: hidden problems and costs. Lancet Respir Med. 2020 Sep 29;S2213-2600(20)30453-7.

Last updated 4 October 2020

Suthar MS, et al. Rapid generation of neutralizing antibody responses in COVID-19 patients. medRxiv. https://doi.org/10.1101/2020.05.03.20084442.

Sutton D, et al. Universal screening for SARS-CoV-2 in women admitted for delivery. N Engl J Med. 2020 Apr 16. doi: 10.1056/NEJMc2009316.

Swann OV, et al. Clinical characteristics of children and young people admitted to hospital with covid-19 in United Kingdom: prospective multicentre observational cohort study. BMJ. 2020 Aug 17. http://dx.doi.org/10.1136/bmj.m3249.

Szablewski CM, et al. SARS-CoV-2 transmission and infection among attendees of an overnight camp—Georgia, June 2020. MMWR Morb Mortal Wkly Rep. 2020 Jul 31. http://dx.doi.org/10.15585/mmwr.mm6931e1.

Szigeti R, et al. BCG protects against COVID-19? A word of caution. medRxiv. https://doi.org/10.1101.2020.04.09.20056903.

Tai DBG, et al. The disproportionate impact of COVID-19 on racial and ethnic minorities in the United States. Clin Infect Dis. 2020 Jun 20;ciaa815. doi: 10.1093/cid/ciaa815.

Takahashi T, et al. Sex differences in immune responses that underlie COVID-19 disease outcomes. Nature. 2020 Aug 26. doi: 10.1038/s41586-020-2700-3.

Tam PCK, et al. Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus 2019 (COVID-19). Clin Infect Dis. 2020 May 30;ciaa673. doi: 10.1093/cid/ciaa673.

Tan L, et al. Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study. MedRxiv 2020.03.01.20029074.

Tang N, et al. Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia. J Thromb Haemost. 18 Feb 2020;1-4. https://doi.org.10.1111/jth/14768.

Tang N, et al. Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy. J Thromb Haemost. 2020 Mar 27. doi: 10.1111/jth.14817.

Tang W, et al. Hydroxychloroquine in patients with mainly mild to moderate coronavirus disease 2019: open label, randomised controlled trial. BMJ. 2020 May 14;369:m1849.

Tang X, et al. On the origin and continuing evolution of SARS-CoV-2. Nat Sci Rev. https://doi:org/10.1093/nsr/nwaa036.

Last updated 4 October 2020

Tang YW, et al. The laboratory diagnosis of COVID-19 infection: Current issues and challenges. J Clin Microbiol. 2020 Apr 3. pii: JCM.00512-20. doi: 10.1128/JCM.00512-20.

Tao Y, et al. High incidence of asymptomatic SARS-CoV-2 infection, Chongqing, China. medRxiv 2020.03.16.20037259; doi: https://doi.org/10.1101/2020.03.16.20037259.

Tartof SY, et al. Obesity and Mortality Among Patients Diagnosed With COVID-19: Results From an Integrated Health Care Organization. Ann Intern Med. 2020 Aug 12. doi: 10.7326/M20-3742.

Tay MZ, et al. The trinity of COVID-19: immunity, inflammation and intervention. Nat Rev Immunol. 2020 Apr 28. https://doi.org/10.1038/s41577-020-0311-8.

Taylor J, et al. Serial Testing for SARS-CoV-2 and Virus Whole Genome Sequencing Inform Infection Risk at Two Skilled Nursing Facilities with COVID-19 Outbreaks - Minnesota, April-June 2020. MMWR Morb Mortal Wkly Rep. 2020 Sep 18;69(37):1288-1295.

Telford CT, et al. Preventing COVID-19 Outbreaks in Long-Term Care Facilities Through Preemptive Testing of Residents and Staff Members - Fulton County, Georgia, March-May 2020. MMWR Morb Mortal Wkly Rep. 2020 Sep 18;69(37):1296-1299.

Temime L, et al. A conceptual discussion about R0 of SARS-CoV-2 in healthcare settings. Clin Infect Dis. 2020 May 30;ciaa682. doi: 10.1093/cid/ciaa682.

Tenforde MW, et al. Symptom Duration and Risk Factors for Delayed Return to Usual Health Among Outpatients with COVID-19 in a Multistate Health Care Systems Network - United States, March-June 2020. MMWR Morb Mortal Wkly Rep. 2020 Jul 31;69(30):993-998. doi: 10.15585/mmwr.mm6930e1.

Teuwen LA, et al. COVID-19: the vasculature unleashed. Nat Rev Immunol. 2020 May 21. doi: 10.1038/s41577-020-0343-0.

Thachil J, et al. ISTH interim guidance on recognition and management of coagulopathy in COVID-19. J Thromb Haemost. 2020. https://doi.org.10.1111/jth/14810.

Theel ES, et al. The role of antibody testing for SARS-CoV-2: Is there one? J Clin Microbiol. 2020 Apr 29. doi: 10.1128/JCM.00797-20.

Thevarajan I, et al. Breadth of concomitant immune responses prior to patient recovery: a case report of non-severe COVID-19. Nat Med. 16 Mar 2020. doi: https://doi.org/10.1038/s41591- 020-0819-2.

Thieme CJ, et al. Robust T cell response towards spike, membrane, and nucleocapsid SARS-CoV- 2 proteins is not associated with recovery in critical COVID-19 patients. Cell Rep Med. 2020 Aug 29;100092. doi: 10.1016/j.xcrm.2020.100092. Last updated 4 October 2020

Thompson GR 3d, et al. Invasive Aspergillosis as an Under-recognized Superinfection in COVID- 19. Open Forum Infect Dis. 2020 Jun 19;7(7):ofaa242. doi: 10.1093/ofid/ofaa242.

Thomson K, H Nachlis. Emergency Use Authorizations During the COVID-19 Pandemic: Lessons From Hydroxychloroquine for Vaccine Authorization and Approval. JAMA. 2020 Aug 31. doi: 10.1001/jama.2020.16253.

Tian J, et al. Clinical characteristics and risk factors associated with COVID-19 disease severity in patients with cancer in Wuhan, China: a multiicentre, retrospective, cohort study. Lancet Oncol. 2020 May 29. https://doi.org/10.1016/S1470-2045(20)30309-0.

Tillett RL, et al. Genomic evidence for a case of reinfection with SARS-CoV-2. Lancet Infect Dis. 2020 Aug 27. THELANCETID-D-20-05376. https://ssrn.com/abstract-3681489.

Tindale L, et al. Transmission interval estimates suggest pre-symptomatic spread of COVID-19. medRxiv 2020.03.03.20029983.

Titanji BK, et al. Use of baracitinib in patients with moderate and severe COVID-19. Clin Infect Dis. 2020 Jun 29;ciaa879. doi: 10.1093/cid/ciaa879.

To KK, et al. Consistent detection of 2019 novel coronavirus in saliva. Clin Infect Dis. 2020 Feb 12. pii: ciaa149. doi: 10.1093/cid/ciaa149.

To KK, et al. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. Lancet Infect Dis. 23 Mar 2020. https://doi.org/10.1016/S1473.3099(20)30196-1.

To KK, et al. Seroprevalence of SARS-CoV-2 in Hong Kong and in residents evacuated from Hubei province, China: A multicohort study. Lancet Microbe. 2020 Jun 3. https://doi.org/10.1016/S2666-5247(20)30053-7.

To KK, et al. COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing. Clin Infect Dis. 2020 Aug 25;ciaa1275. doi: 10.1093/cid/ciaa1275.

To KK, et al. Serum antibody profile of a patient with COVID-19 reinfection. Clin Infect Dis. 2020 Sep 23;ciaa1368. doi: 10.1093/cid/ciaa1368.

Tobolowsky FA, et al. COVID-19 outbreak among three affiliated homeless service sites—King County, Washington, 2020. MMWR Morb Mortal Wkly Rep. 2020 Apr 22. https://www.cdc.gov/mmwr/volumes/69/wr/mm6917e2.htm?s_cid-mm6917e2_w.

Last updated 4 October 2020

Tomazini BM, et al. Effect of Dexamethasone on Days Alive and Ventilator-Free in Patients With Moderate or Severe Acute Respiratory Distress Syndrome and COVID-19: The CoDEX Randomized Clinical Trial. JAMA. 2020 Sep 2. doi: 10.1001/jama.2020.17021.

Tong ZD, et al. Potential Presymptomatic Transmission of SARS-CoV-2, Zhejiang Province, China, 2020. Emerg Infect Dis. 2020 May 17;26(5). doi: 10.3201/eid2605.200198.

Toscano G, et al. Guillain-Barré Syndrome associated with SARS-CoV-2. N Engl J Med. 2020 Apr 17. doi: 10.1056/NEJMc2009191.

Tostanoski LH, et al. Ad26 vaccine protects against SARS-CoV-2 severe clinical disease in hamsters. Nat Med. 2020 Sep 3. doi: 10.1038/s41591-020-1070-6.

Toubiana J, et al. Kawasaki-like multisystem inflammatory syndrome in children during the COVID-19 pandemic in Paris, France: Prospective observational study. BMJ. 2020 Jun 3;369:m2094. doi: 10.1136/bmj.m2094.

Townsend L, et al. Persistent fatigue following SARS-CoV-2 infection is common and independent of severity of initial infection. medRxiv. https://doi.org/10.1101/2020.07/29.20164293.

Toyoshima Y, et al. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. J Hum Genet. 2020 Jul 22:1-8. doi: 10.10138/s10038-020-0808-9.

Traugott M, et al. Performance of SARS-CoV-2 antibody assays in different stages of the infection: Comparison of commercial ELISA and rapid tests. J Infect Dis. 2020 May 30;jiaa305. https://doi.org/10.1093/infdis/jiaa305.

Treibel TA, et al. COVID-19: PCR screening of asymptomatic health-care workers at London hospital. Lancet. 2020 May 7. https://doi.org/10.1016/S0140-6736(20)1100-4.

Trinh MA, et al. Therapeutic anticoagulation is associated with decreased mortality in mechanically ventilated COVID-19 patients. medRxiv. https://doi.org/10.1101/2020.05.30.20117929.

Tschopp J, et al. First Experience of SARS-CoV-2 Infections in Solid Organ Transplant Recipients in the Swiss Transplant Cohort Study. Am J Transplant. 2020 May 15. doi: 10.1111/ajt.16062.

Tu YP, et al. Swabs collected by patients or health care workers for SARS-CoV-2 testing. N Engl J Med. 2020 Jun 3. doi: 10.1056/NEJMc2016321.

Ulrich H, et al. Dengue Fever, COVID-19 (SARS-CoV-2), and Antibody-Dependent Enhancement (ADE): A Perspective. Cytometry A. 2020 Jul;97(7):662-667. doi: 10.1002/cyto.a.24047.

Last updated 4 October 2020

Vabret N, et al. Immunology of COVID-19: Current state of the science. Immunity. 2020 May 5. https://doi.org/10.1016/j.immuni.2020.05.002.

Vaduganathan M, et al. Renin-angiotensin-aldosterone system inhibitors in patients with COVID-19. N Engl J Med. 2020 Mar 30. doi: 10.1056/NEJMs2005760.

Van Arkel ALE, et al. COVID-19 associated pulmonary aspergillosis. Am J Respir Crit Care Med. 2020 May 12. doi: 10.1164/rccm.202004-1038LE.

Van Caeseele P, et al. SARS-CoV-2 (COVID-19) serology: implications for clinical practice, laboratory medicine and public health. CMAJ. 2020 Aug 3;cmaj.201588. doi: 10.1503/cmaj.201588.

Van De Veerdonk FL, et al. Outcomes Associated With Use of a Kinin B2 Receptor Antagonist Among Patients With COVID-19. JAMA Netw Open. 2020 Aug 3;3(8):e2017708. doi: 10.1001/jamanetworkopen.2020.17708.

Van Der Made CI, et al. Presence of genetic variants among young men with severe COVID-19. JAMA. 2020 Jul 24. doi: 10.1001/jama.2020.13719.

Van Doremalen N, et al. Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS- CoV-1. N Engl J Med. 2020 Mar 17. doi: 10.1056/NEJMc2004973.

Van Doremalen N, et al. ChAdOx1 nCoV-19 vaccination prevents SARS-CoV-2 pneumonia in rhesus macaques. bioRxiv. 2020 May 13. https://doi.org/10.1101/2020.05.13.093195.

Van Dorp L, et al. No evidence for increased transmissibility from recurrent mutations in SARS- CoV-2. bioRxiv. https://doi.org/10.1101/2020.05.21.108506.

Van Kampen JJA, et al. Shedding of infectious virus in hospitalized patients with coronavirus disease-2019 (COVID-19): Duration and key determinants. medRxiv. https://doi.org/10.1101/2020.06.08.20125310.

Varatharaj A, et al. Neurological and neuropsychiatric complications of COVID-19 in 153 patients: A UK-wide surveillance study. Lancet Psychiatry. 2020 Jun 25. https://doi.org/10.1016/S2215-0366(20)30287-X.

Vardhana SA, JD Wolchok. The many faces of the anti-COVID immune response. J Exp Med. 2020. 217:e20200678.

Varga Z, et al. Endothelial cell infection and endotheliitis in COVID-19. Lancet. 2020 Apr 17. https://doi.org/10.1016/S0140-6736(20)30937-5.

Last updated 4 October 2020

Varga Z, et al. Electron microscopy of SARS-CoV-2: A challenging Task—Authors’ reply. Lancet. 2020 May 30;395(10238):e100. doi: 10.1016/S0140-6736(20)31185-5.

Vaughn VM, et al. Empiric Antibacterial Therapy and Community-onset Bacterial Co-infection in Patients Hospitalized with COVID-19: A Multi-Hospital Cohort Study. Clin Infect Dis. 2020 Aug 21;ciaa1239. doi: 10.1093/cid/ciaa1239.

Verdoni L, et al. An outbreak of severe Kawasaki-like disease at the Italian epicentre of the SARS-CoV-2 epidemic: an observational cohort study. Lancet. 2020 May 13. https://doi.org/10.1016/S0140-6736(20)31129-6.

Verity R, et al. Estimates of the severity of COVID-19 disease. medRxiv 2020.03.09.20033357.

Veyer D, et al. Highly sensitive quantification of plasma SARS-CoV-2 RNA shelds light on its potential clinical value. Clin Infect Dis. 2020 Aug 17;ciaa1196. doi: 10.1093/cid/ciaa1196.

Viner RM, et al. Susceptibility to SARS-CoV-2 Infection Among Children and Adolescents Compared With Adults. A Systematic Review and Meta-analysis. JAMA Pediatr. 2020 Sep 25. doi:10.1001/jamapediatrics.2020.4573.

Violi F, et al. Hypercoagulation and anththrombotiic treatment in Coronavirus 2019: a new challenge. Thromb Haemost. 2020 Apr 29. doi: 10.1055/s-0040-1710317.

Vivanti AJ, et al. Transplacental transmission of SARS-CoV-2 infection. Nat Commun. 2020 Jul 14;11(1):3572.

Vizcarra P, et al. Description of COVID-19 in HIV-infected individuals: a single-centre, prospective cohort. Lancet HIV. 2020 May 28. https://doi.org/10.1016/S2352-3018(20)30164-8.

Vogels CBF, et al. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 qRT-PCR assays. medRxiv. https://doi.org/10.1101/2020.03.30.20048108.

Vogels CBF, et al. Saliva Direct: Simple and sensitive molecular diagnostic test for SARS-CoV-2 surveillance. medRxiv. doi: https://doi.org/10.1101/2020.08.03.20167791.

Voicu S, et al. High prevalence of deep vein thrombosis in mechanically ventilated COVID-19 patients. J Am Coll Cardiol. 2020 May 29;S0735-1097(20)35462-0. doi: 10.1016/j.jacc.2020.05.053.

Von Vopelius-Feldt J et al. Estimated SpO2/FiO2 ratio to predict mortality in patients with suspected COVID-19 in the Emergency Department: A prospective cohort study. medRxiv. https://doi.org/10.1101/2020.05.28.20116194.

Last updated 4 October 2020

Wajnberg A, et al. Humoral immune response and PCR positivity in patients with COVID-19 the New York City region, USA: an observational study. Lancet Microbe. 2020 Sep 25. https://doi.org/10.1016/ S2666-5247(20)30120-8.

Walker J, et al. Decreasing High Risk Exposures for Healthcare-workers through Universal Masking and Universal SARS-CoV-2 Testing upon entry to a Tertiary Care Facility. Clin Infect Dis. 2020 Sept 8. https://doi.org/10.1093/cid/ciaa1358.

Waltenburg MA, et al. Update: COVID-19 among workers in meat and poultry processing facilities – United States, April-May 2020. MMWR Morb Mortal Wkly Rep. 2020 Jul 10. 69(27):887-892.

Wang C, et al. Evolving epidemiology and impact of non-pharmaceutical interventions on the outbreak of coronavirus disease 2019 in Wuhan, China. medRxiv 2020.03.03.20030593.

Wang D, et al. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. JAMA. 020 Feb 7. doi: 10.1001/jama.2020.1585.2/jci.insight.137799.

Wang F, et al. The laboratory tests and host immunity of COVID-19 patients with different severity of illness. JCI Insight. 2020 Apr 23. doi: 10.117

Wang J, et al. Tissue plasminogen activator (tPA) treatment for COVID-19 associated acute respiratory distress syndrome (ARDS): a case series. J Thromb Haemost. 2020 Apr 8. doi: 10.1111/jth.14828.

Wang J, et al. Persistent SARS-COV-2 RNA positivity in a patient for 92 days after disease onset: A case report. Medicine. 2020 Aug 21;99(34):e21865. doi: 10.1097/MD.0000000000021865.

Wang M, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020 Mar;30(3):269-271.

Wang M, et al. Temperature significant change COVID-19 transmission in 429 cities. medRxiv 2020.02.22.20025791.

Wang P, et al. SARS-CoV-2 neutralizing antibody responses are more robust in patients with severe disease. bioRxiv. https://doi.org/10.1101/2020.06.13.150250.

Wang W, et al. Detection of SARS-CoV-2 in different types of clinical specimens. JAMA. 2020 Mar 11. doi: 10.1001/jama.2020.3786.

Wang W Jr., et al. The definition and risks of Cytokine Release Syndrome-Like in 11 COVID-19- Infected Pneumonia critically ill patients: Disease Characteristics and Retrospective Analysis. medRxiv 2020.02.26.20026989. Last updated 4 October 2020

Wang X, et al. Association between 2019-nCoV transmission and N95 respirator use. J Hosp Infect. 2020 Mar 3. Pii: S0195-6701(20)30097-9. Doi: 10.1016/jhin.2020.02.021.

Wang X, et al. A case of novel coronavirus in a pregnant woman with preterm delivery. Clin Infect Dis. 2020 Feb 28. pii: ciaa200. doi: 10.1093.cid/ciaa200.

Wang X, et al. Neutralizing antibodies responses to SARS-CoV-2 in COVID-19 inpatients and convalescent patients. Clin Infect Dis. 2020 Jun 4:ciaa721. doi: 10.1093/cid/ciaa721.

Wang X, et al. Association between universal masking in a health care system and SARS-CoV-2 positivity among health care workers. JAMA. 2020 Jul 14. doi: 10.1001/jama.2020.12897.

Wang Y, et al. Clinical outcome of 55 asymptomatic cases at the time of hospital admission infected with SARS-Coronavirus-2 in Shenzhen, China. J Infect Dis. 2020 Mar 17. pii: jiaa119. doi: 10.1093/infdis/jiaa119.

Wang Y, et al. Early, low-dose and short-term application of corticosteroid treatment in patients with severe COVID-19 pneumonia: single-center experience from Wuhan, China. medRxiv 2020.03.06.20032342.

Wang Y, et al. Clinical course and outcomes of 344 intensive care patients with COVID-19. Am J Respir Crit Care Med. 2020 Apr 8. doi: 10.1164/rccm.202003-0736LE.

Wang Y,et al. Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo- controlled, multicentre trial. Lancet. 2020 Apr 29. https://doi.org/10.1016/S0140- 6736(20)31022-9.

Wang Y, et al. Characterization of an asymptomatic cohort of SARS-CoV-2 infected individuals outside of Wuhan, China. Clin Infect Dis. 2020 May 22;ciaa620. doi: 10.1093/cid/ciaa629.

Wang Y, et al. Kinetics of viral load and antibody response in relation to COVID-19 severity. J Clin Invest. 2020 Jul 7:138759. doi: 10.1172/JCI138759.

Wang Z, et al. Clinical features of 69 cases with coronavirus disease 2019 in Wuhan, China. Clin Infect Dis. 2020 Mar 16. pii: ciaa272. doi: 10.1093/cid/ciaa272.

Wang Z, et al. Analysis of hospitalized COVID-19 patients in the Mount Sinai Health System using electronic medical records (EMR) reveals important prognostic factors for improved clinical outcomes. medRxiv. https://doi.org/10.1101/2020.04.28.20075788.

Watson J, et al. Open letter to MR Mehra, SS Desai, F Ruschitzka, and AN Patel, authors of “Hydroxychloroquine or chloroquine with or without a macrolide for treatment of COVID-19: a multinational registry analysis.” https://zenodo.org/record/3864691. Last updated 4 October 2020

Wec AZ, et al. Broad neutralization of SARS-related viruses by human monoclonal antibodies. Science. 2020 Jun 15;eabc7424. doi: 10.1126/science.abc7424.

Wehrhahn MC, et al. Self-collection: an appropriate alternative during the SARS-CoV-2 pandemic. medRxiv. https://doi.org/10.1101/2020.04.09.20057901.

Wei M, et al. Novel coronavirus infection in hospitalized infants under 1 year of age in China. JAMA. 2020 Feb 14. doi: 10.1001/jama.2020.2131.

Wei WE, et al. Presymptomatic transmission of SARS-CoV-2—Singapore, January 23-March 16, 2020. MMWR Morb Mortal Wkly Rep. 1 Apr 2020. https://www.cdc.gov/mmwr/volumes/69/wr/mm691e1.

Weinberger DM, et al. Estimation of Excess Deaths Associated With the COVID-19 Pandemic in the United States, March to May 2020. JAMA Intern Med. 2020 Jul 1. doi: 10.1001/jamainternmed.2020.3391.

Weiskopf D, et al. Phenotype and kinetics of SARS-CoV-2-specific T cells in COVID-19 patients with acute respiratory distress syndrome. Sci Immunol. 2020 Jun 26. 10.1126/sciimmunol.abd2071.

Wells CR, et al. Impact of international travel and border control measures on the global spread of the novel 2019 coronavirus outbreak. Proc Natl Acad Sci USA. 2020 Mar 13. pii: 202002616. doi: 10.1073/pnas.2002616117.

Westblade LF, et al. SARS-CoV-2 viral load predicts mortality in patients with and without cancer who are hospitalized with COVID-19. Cancer Cell. 2020 Sep 11. https://doi.org/10.1016/j.ccell.2020.09.007.

Whitcroft KL, T Hummel. Olfactory dysfunction in COVID-19: Diagnosis and management. JAMA. 2020 May 20. doi: 10.1001/jama.2020.8391.

Whitman JD, et al. Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nat Biotechnol. 2020 Aug 27. https://doi.org/10.1038/s41587-020-0659-0.

Whittaker W, et al. Clinical characteristics of 58 children with a pediatric inflammatory multisystem syndrome temporarily associated with SARS-Cov-2. JAMA. 2020 Jun 8. doi: 10.1001.jama.2020.10369.

Wichmann D, et ao. Autopsy findings and venous thromboembolism in patients with COVID-19: A prospective cohort study. Ann Intern Med. 2020 May 6. doi: 10.7326/M20-2003.

Last updated 4 October 2020

Wiersinga WJ, et al. Pathophysiology, transmission, diagnosis, and treatment of coronavirus disease 2019 (COVID-19): A review. JAMA. 2020 Jul 10. doi: 10.1001/jama.2020.12839.

Wilder B, et al. Modeling between-population variation in COVID-19 dynamics in Hubei, Lombardy, and New York City. Proc Natl Acad Sci USA. 2020 Sep 24;202010651. doi: 10.1073/pnas.2010651117.

Wilk AJ, et al. A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nat Med. 2020 Jun 8. doi: 10.1038/s41591-020-0944-y.

Wilkerson RG, et al. Silent hypoxia: A harbinger of clinical deterioration in patients with COVID- 19. Am J Emerg Med. 2020 May 22;S0735-6757(20)30390-9.

Williams E, et al. Saliva as a non-invasive specimen for detection of SARS-CoV-2. J Clin Microbiol. 2020 Apr 21. doi: 10.1128/JCM.00776-20.

Williams TC, et al. Sensitivity of RT-PCR testing of upper respiratory tract samples for SARS-CoV- 2 in hospitalised patients: A retrospective cohort study. MedRxiv. https://doi.org/10.1101/2020.06.19.20135756.

Williamson BN, et al. Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV- 2. bioRxiv. doi: https://doi.org/10.1101/2020.04.15.043166.

Williamson EJ, et al. OpenSAFELY: factors associated with COVID-19 death in 17 million patients. Nature. 2020 Jul 8. doi: 10.1038/s41586-020-2521-4.

Wilson E, et al. Multiple COVID-19 Clusters on a University Campus - North Carolina, August 2020. MMWR Morb Mortal Wkly Rep. 2020 Oct 2;69(39):1416-1418. doi: 10.15585/mmwr.mm6939e3.

Winichakoon P, et al. Negative Nasopharyngeal and Oropharyngeal Swab Does Not Rule Out COVID-19. J Clin Microbiol. 2020 Feb 26. pii: JCM.00297-20. doi: 10.1128/JCM.00297-20.

Winkler ES, et al. SARS-CoV-2 infection of human ACE2-transgenic mice causes severe lung inflammation and impaired function. Nat Immunol. 2020 Aug 24. doi: 10.1038/s41590-020- 0778-2.

Woelfel R, et al. Virological assessment of hospitalized patients with COVID-1029. Nature. https://doi.org/10.1038/s41586-020-2196-x (2020).

Woldemeskel BA, et al. Healthy donor T-cell responses to common cold coronaviruses and SARS-CoV-2. J Clin Invest. 2020 Sep 23;143120. doi: 10.1172/JCI143120.

Last updated 4 October 2020

Wolff G, et al. A molecular pore spans the double membrane of the coronavirus replication organelle. Science. 2020 Aug 6. doi: 10.1126/science.abd3629.

Woloshin S, et al. False negative tests for SARS-CoV-2 infection—Challenges and implications. N Engl J Med. 2020 Jun 5. doi: 10.1056/NEJMp2015897.

Wong SCY, et al. Posterior oropharyngeal saliva for the detection of SARS-CoV-2. Clin Infect Dis. 2020 Jun 21;ciaa797. doi: 10.1093/cid/ciaa797.

Woolf SH, et al. Excess deaths from COVID-19 and other causes, March-April 2020. JAMA. 2020 Jul 1. doi: 10.1001/jama.2020.11787.

Worobey M, et al. The emergence of SARS-CoV-2 in Europe and North America. Science. 2020 Sept. 10. doi: 10.1126/science.abc8169 (2020).

Wrapp D, et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020 Mar 13;367(6483):1260-1263.

Wu C, et al. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China. JAMA Intern Med. 2020 Mar 13. doi: 10.1001/jamainternmed.2020.0994.

Wu F, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020 Mar;579(7798):265-269.

Wu F, et al. Evaluating the Association of Clinical Characteristics With Neutralizing Antibody Levels in Patients Who Have Recovered From Mild COVID-19 in Shanghai, China. JAMA Intern Med. 2020 Aug 18. doi: 10.1001/jamainternmed.2020.4616.

Wu J, et al. Detection and analysis of nucleic acid in various biological samples of COVID-19 patients. Travel Med Infect Dis. 2020 Apr 17:101673. doi: 10.1016/j.tmaid.2020.101673.

Wu J, et al. Coronavirus disease 2019 test results after clinical recovery and hospital discharge among patients in China. JAMA Network Open. 2020 May 22. 2020:3(5):e209759.

Wu J, et al. SARS-CoV-2 infection induces sustained humoral immune responses in convalescent patients following symptomatic COVID-19. medRxiv. https://doi.org/10.1101/2020.07.21.20159178.

Wu JT, et al. Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China. Nature Medicine. 19 Mar 2020. https://doi.org/10.1038/s41591-020-0822-7.

Last updated 4 October 2020

Wu P, et al. Characteristics of ocular findings of patients with Coronavirus disease 2019 (COVID- 19) in Hubei province, China. JAMA Ophthalmol. 31 Mar 2020. doi:10.1001/jamaophthalmol.2020.1291.

Wu Z, JM McGoogan. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention. JAMA. 2020 Feb 24. doi: 10.1001/jama.2020.2648.

Wyllie AL, et al. Saliva or nasopharyngeal swab specimens for detection of SARS-CoV-2. N Engl J Med. 2020 Aug 28. doi: 10.1056/NEJMc2016359.

Xi J, et al. Virus strain of a mild COVID-19 patient in Hangzhou representing a new trend in SARS-CoV-2 evolution related to furin cleavage site. MedRxiv 2020.03.10.20033944.

Xia S, et al. Effect of an Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity Outcomes: Interim Analysis of 2 Randomized Clinical Trials. JAMA. 2020 Aug 13. doi: 10.1001/jama.2020.15543.

Xia W, et al. Transmission of corona virus disease 2019 during the incubation period may lead to a quarantine loophole. medRxiv 2020.03.06.20031955; doi: https://doi.org/10.1101.2020.03.06.20031955.

Xiang F, et al. Antibody detection and dynamic characteristics in patients with COVID-19. Clin Infect Dis. 2020 Apr 19. pii: ciaa461. doi: 10.1093/cid/ciaa461.

Xiao AT, et al. Dynamic profile of RT-PCR findings from 301 COVID-19 patients in Wuhan, China: A descriptive study. J Clin Virol. 2020 Apr 11;127:104346.

Xiao AT, et al. Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients. Clin Infect Dis. 2020 Apr 19. pii: ciaa460. doi: 10.1093/cid/ciaa460.

Xiao K, et al. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature. 2020 May 7. doi: 10.1038/s41586-020-2313-x.

Xie J, et al. Association between hypoxemia and mortality in patients with COVID-19. Mayo Clin Prof. 2020 Apr 11. doi: 10.1016/j. mayocp.2020.04.006.

Xu X, et al. Effective treatment of severe COVID-19 patients with tocilizumab. Proc Natl Acad Sci USA. 2020 Apr 29. doi: 10.1073/pnas.20056.15117.

Xu XW, et al. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series. BMJ. 2020 Feb 19;368:m606.

Last updated 4 October 2020

Wu Y, et al. Prolonged presence of SARS-CoV-2 viral RNA in faecal samples. Lancet Gastroenterol Hepatol. 19 Mar 2020. Doi: https://doi.org/10.1016/S2468-1253(20)30083-2.

Xu D, et al. Relationship Between serum SARS-CoV-2 nucleic acid(RNAemia) and Organ Damage in COVID-19 Patients: A Cohort Study. Clin Infect Dis. 2020 Jul 28;ciaa1085. doi: 10.1093/cid/ciaa1085.

Xu X, et al. Seroprevalence of immunoglobulin M and G antibodies against SARS-CoV-2 in China. Nat Med. 2020 Jun 5. doi: 10.1038/s41591-020-0949-6.

Xu XK, et al. Reconstruction of Transmission Pairs for Novel Coronavirus Disease 2019 (COVID- 19) in Mainland China: Estimation of Super-spreading Events, Serial Interval, and Hazard of Infection. Clin Infect Dis. 2020 Jun 18;ciaa790. doi: 10.1093/cid/ciaa790.

Xu Y, et al. Characteristics of pediatric SARS-CoV-2 infection and potential evidence for persistent fecal viral shedding. Nat Med. 2020 Apr;26(4):502-505.

Xu Z, et al. Pathological findings of COVID-19 associated with acute repiratory distress syndrome. Lancet Respir Med. 2020 Feb 18. Pii: S221302600(20)30076-X.

Yaghi S, et al. SARS-CoV-2 and stroke in a New York healthcare system. Stroke. 2020 May 20:STROKEAHA120030335.

Yan R, et al. Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2. Science. 2020 Mar 4. pii: eabb2762. doi: 10.1126/science.abb2762.

Yang J, et al. A vaccine targeting the RBD of the S protein of SARS-CoV-2 induces protective immunity. Nature. 2020 Jul 29. doi: 10.1038/s41586-020-2599-8.

Yang K, et al. Clinical characteristics, outcomes, and risk factors for mortality in patients with cancer and COVID-19 in Hubei, China: a multicentre, retrospective, cohort study. Lancet Oncol. 2020 May 29. https://doi.org/10.1016/S1470-2045(20)30310-7.

Yang R, et al. Comparison of clinical characteristics of patients with asymptomatic vs symptomatic coronavirus disease 2019 in Wuhan, China. JAMA Network Open. 2020;3(5):e2010182.

Yang W, et al. Estimating the infection fatality rate of COVID-19 in New York City, March 1-May 16, 2020. medRxiv. https://doi.org/10.1101.2020.06.27.20141689.

Yang Y, et al. Exuberant elevation of IP-10, MCP-3 and IL-1ra during SARS-CoV-2 infection is associated with disease severity and fatal outcome. medRxiv 2020.03.02.20029975.

Last updated 4 October 2020

Yao X, et al. In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Clin Infect Dis. 2020 Mar 9. pii: ciaa237. doi: 10.1093/cid/ciaa237.

Yazdany J, AHJ Kim. Use of hydroxychloroquine and chloroquine during the COVID-19 pandemic: What every clinician should know. Ann Intern Med. 2020 Mar 31. doi: 10.7326/M20- 1334.

Ye G, et al. Environmental contamination of the SARS-CoV-2 in healthcare premises. J Infect. 2020 Apr 30. doi: 10.1016/j.jinf.2020.04.034..

Yehia BR, et al. Association of Race With Mortality Among Patients Hospitalized With Coronavirus Disease 2019 (COVID-19) at 92 US Hospitals. JAMA Netw Open. 2020 Aug 3;3(8):e2018039. doi: 10.1001/jamanetworkopen.2020.18039.

Yelin I, et al. Evaluation of COVID-19 RT-qPCR test in multi-sample pools. Clin Infect Dis. 2020 May 2;ciaa531. doi: 10.1093/cid/ciaa531.

Yin W, et al. Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS- CoV-2 by remdesiriv. Science. 2020 May 1. doi: 10.1126/science.abc1560.

Yokota I, et al. Mass screening of asymptomatic persons for SARS-CoV-2 using saliva. Clin Infect Dis. 2020 Sep 25;ciaa1388. doi: 10.1093/cid/ciaa1388.

Yonker LM, et al. Pediatric SARS-CoV-2: Clinical Presentation, Infectivity, and Immune Responses. J Pediatr. 2020 Aug 18;S0022-3476(20)31023-4. doi: 10.1016/j.jpeds.2020.08.037.

Young BE, et al. Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study. Lancet. 2020 Aug 18;S0140-6736(20)31757-8. doi: 10.1016/S0140-6736(20)31757-8.

Yu F, et al. Quantitative detection and viral load analysis of SARS-CoV-2 in infected patients. Clin Infect Dis. 2020 Mar 28. pii: ciaa345. doi: 10.1093/cid/ciaa345.

Yu J, et al. DNA vaccine protection against SARS-CoV-2 in rhesus macaques. Science. 2020 May 20:eabc6284. doi: 10.1126/science.abc6284.

Yu P, et al. A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period. J Infect Dis. 2020 Feb 18. pii: jiaa077. doi: 10.1093/infdis/jiaa077.

Yuan J, et al. PCR assays turned positive in 25 discharged COVID-19 patients. Clin Infect Dis. 2020 Apr 8. pii: ciaa398. doi: 10.1093/cid/ciaa398.

Last updated 4 October 2020

Yurkovetskiy L, et al. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Cell. 2020 Sep 9. https://doi.org/10.1016/j.cell.2020.09.032.

Zabarsky TF, et al. What are the sources of exposure in healthcare personnel with coronavirus disease 2019 infection? Am J Infect Control. 2020 Aug 12;S0196-6553(20)30769-0. doi: 10.1016/j.ajic.2020.08.004.

Zachariah P, et al. Epidemiology, clinical features, and disease severity in patients with coronavirus disease 2019 (COVID-19) in a children’s hospital in New York City, New York. JAMA Pediatr. 2020 Jun3;e2020430. doi: 10.1001/jamapediatrics.2020.2430.

Zanettini C, et al. Influenza vaccination and COVID19 mortality in the USA. medRxiv. https://doi.org/10.1101/2020.06.24.20129817.

Zeberg H, S Pääbo. The major genetic risk factor for severe COVID-19 is inherited from Neanderthals. Nature. 2020 Sep 30. doi: 10.1038/s41586-020-2818-3.

Zeng H, et al. Antibodies in infants born to mothers with COVID-19 pneumonia. JAMA. 26 Mar 2020. Doi:10.1001/jama.2020.4861.

Zeng L, et al. Neonatal early-onset infection with SARS-CoV-2 in 33 neonates born to mothers with COVID-19 in Wuhan, China. JAMA Pediatr. 2020 Mar 26. doi: 10.1001/jamapediatrics.2020.0878.

Zeng QL, et al. Effect of convalescent plasma therapy on viral shedding and survival in COVID-19 patients. J Infect Dis. 2020 Apr 29. doi: 10.1093/infdis/jaa228.

Zhang G, et al. Longitudinal change of SARS-CoV-2 antibodies in patients with COVID-19. J Infect Dis. 2020 May 2. doi: 10.1093/infdis/jiaa229.

Zhang J, et al. Evolving epidemiology and transmission dynamics of coronavirus disease 2019 outside Hubei province, China: a descriptive and modeling study. Lancet Infect Dis. 2 Apr 2020. https://doi.org/10.1016/S1473-3099(20)30230-9.

Zhang J, et al. Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China. Science. 2020 Apr 29:eabb8001. doi: 10.1126/science.abb8001.

Zhang JY, et al. Single-cell landscape of immunological responses in patients with COVID-19. Nat Immunol. 2020 Aug 12. doi: 10.1038/s41590-020-0762-x.

Zhang L, et al. D-dimer levels on admission to predict in-hospital mortality in patients with COVID-19. J Thromb Haemost. 2020 Apr 19. doi: 10.1111/jth.14859.

Last updated 4 October 2020

Zhang L, et al. The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. bioRxiv. https://doi.org/10.1101/2020.06.12.148726.

Zhang L, et al. Deep Vein Thrombosis in Hospitalized Patients With Coronavirus Disease 2019 (COVID-19) in Wuhan, China: Prevalence, Risk Factors, and Outcome. Circulation. 2020 May 10. doi: 10.1161/CIRCULATIONAHA.120.046702.

Zhang Q, et al. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science. 2020 Sep 24;eabd4570. doi: 10.1126/science.abd4570.

Zhang T, et al. Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Curr Biol. 2020 Mar 13. Pii: S0960-9822(20)30360-2. doi: 10.1016/j.cub.2020.03.022.

Zhang Y, et al. Coagulopathy and antiphospholipid antibodies in patients with COVID-19. N Engl J Med. 2020 Apr 8. doi: 10.1056/NEJMc2007575.

Zhang Y, et al. Different longitudinal patterns of nucleic acid and serology testing results based on disease severity of COVID-19 patients. Emerg Microbes Infect. doi: 10.1080/22221751.2020.1756699.

Zhang X, et al. Viral and host factors related to the clinical outcome of COVID-19. Nature. 2020 May 20. doi: 10.1038/s41586-020-2355-0.

Zhang XJ, et al. In-hospital use of statins is associated with a reduced risk of mortality among individuals with COVID-19. Cell Metab. 2020 Jun 19. https://doi.org/10.1016/j.cmet.2020.06.015.

Zhao J, et al. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019. Clin Infect Dis. 2020 Mar 20. Pii: ciaa344. doi: 10.1093/cid/ciaa344.

Zhao J, et al. Relationship between the ABO Blood Group and the COVID-19 Susceptibility. Clin Infect Dis. 2020 Aug 4;ciaa1150. doi: 10.1093/cid/ciaa1150.

Zhao R, et al. Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection. Clin Infect Dis. 2020 May 1. doi: 10.1093/cid/ciaa523.

Zhen W, et al. Comparison of four molecular in vitro diagnostic assays for the detection of SARS- CoV-2 in nasopharyngeal specimens. J Clin Microbiol. 2020 Apr 27. doi: 10.1128/JCM.00743-20.

Zheng S, et al. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China, January-March 2020: a retrospective cohort study. BMJ. 2020;369m1443.

Last updated 4 October 2020

Zheng YY, et al. COVID-19 and the cardiovascular system. Nat Rev Cardiol. 2020 Mar 5. doi: 10.1038/s41569-020-0360-5.

Zhou F, et al. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. Lancet. 2020 Mar 11. pii: S0140-6736(20)30566-3. doi: 10.1016/S0140-6736(20)30566-3.

Zhou H, et al. A novel bat coronavirus closely related to SARS-CoV=2 contains natural insertions at the S1/S2 cleavage site of the spike protein. Curr Biol. 2020 May 11:S0960-9822(20)30662-X.

Zhou P, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020 Mar;579(7798):270-273.

Zhou S, et al. CT Features of Coronavirus Disease 2019 (COVID-19) Pneumonia in 62 Patients in Wuhan, China. AJR Am J Roentgenol. 2020 Mar 5:1-8. doi: 10.2214/AJR.20.22975.

Zhou Q, et al. Interferon-α2b treatment for COVID-19. medRxiv. doi: https://doi.org/10.1101/2020.04.06.20042580.

Zhu FC, et al. Safety, tolerability, and immunogenicity of a recombinant adenovirus type-5 vectored COVID-19 vaccine: A dose-escalation, open-label, non-randomised, first-in-human trial. Lancet. 2020 May 22. https://doi.org/10.1016/S0140-6736(20)31208-3.

Zhu J, et al. CT imaging features of 4121 patients with COVID-19: A meta-analysis. J Med Virol. 2020 Apr 21. doi: 10.1002/jmv.25910.

Zhu L, et al. Association of Blood Glucose Control and Outcomes in Patients With COVID-19 and Pre-existing Type 2 Diabetes. Cell Metab. 2020 May 1:zs1550-4131(20)30238-2.

Zhu N, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020 Feb 20;382(8):727-733.

Zhu Z, et al. Arbidol monotherapy is superior to lopinavir/ritonavir in treating COVID-19. J Infect. doi: 10.1016/jinf.2020.03.060.

Ziegler CGK, et al. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets Across Tissues. Cell. 2020 Apr 27;S0092-8674(20)30500-6.

Ziehr DR, et al. Respiratory pathophysiology of mechanically ventilated patients with COVID-19: a cohort study. Am J Respir Crit Care Med. 2020 Apr 29. doi: 10.1164/rccm.202004-1163LE.

Zou L, et al. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients. N Engl J Med. 2020 Mar 19;382(12):1177-1179. Last updated 4 October 2020

Zubair AS, et al. Neuropathogenesis and neurologic manifestations of the coronaviruses in the age of coronavirus disease 2019: a review. JAMA Neurol. 2020 May 29. doi: 10.1001/jamaneurol.2020.2065.