Modeling and Controlling Epidemic Outbreaks: the Role of Population Size, Model Heterogeneity and Fast Response in the Case of Measles
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MMWR Early and Were Reported to Two Respective Local Health Jurisdictions, Release on the MMWR Website (
Morbidity and Mortality Weekly Report High SARS-CoV-2 Attack Rate Following Exposure at a Choir Practice — Skagit County, Washington, March 2020 Lea Hamner, MPH1; Polly Dubbel, MPH1; Ian Capron1; Andy Ross, MPH1; Amber Jordan, MPH1; Jaxon Lee, MPH1; Joanne Lynn1; Amelia Ball1; Simranjit Narwal, MSc1; Sam Russell1; Dale Patrick1; Howard Leibrand, MD1 On May 12, 2020, this report was posted as an MMWR Early and were reported to two respective local health jurisdictions, Release on the MMWR website (https://www.cdc.gov/mmwr). without indication of a common source of exposure. On On March 17, 2020, a member of a Skagit County, March 17, the choir director sent a second e-mail stating that Washington, choir informed Skagit County Public Health 24 members reported that they had developed influenza-like (SCPH) that several members of the 122-member choir had symptoms since March 11, and at least one had received test become ill. Three persons, two from Skagit County and one results positive for SARS-CoV-2. The email emphasized the from another area, had test results positive for SARS-CoV-2, importance of social distancing and awareness of symptoms the virus that causes coronavirus disease 2019 (COVID-19). suggestive of COVID-19. These two emails led many members Another 25 persons had compatible symptoms. SCPH to self-isolate or quarantine before a delegated member of the obtained the choir’s member list and began an investigation on choir notified SCPH on March 17. March 18. Among 61 persons who attended a March 10 choir All 122 members were interviewed by telephone either practice at which one person was known to be symptomatic, during initial investigation of the cluster (March 18–20; 53 cases were identified, including 33 confirmed and 20 115 members) or a follow-up interview (April 7–10; 117); most probable cases (secondary attack rates of 53.3% among con- persons participated in both interviews. -
Population Behavioural Dynamics Can Mediate the Persistence
medRxiv preprint doi: https://doi.org/10.1101/2021.05.03.21256551; this version posted May 5, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . 1 1 Population behavioural dynamics can mediate the 2 persistence of emerging infectious diseases 1;∗ 1 1 2 3 Kathyrn R Fair , Vadim A Karatayev , Madhur Anand , Chris T Bauch 4 1 School of Environmental Sciences, University of Guelph, Guelph, ON, Canada, N1G 2W1 5 2 Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada, N2L 6 3G1 7 *[email protected] 8 Abstract 9 The critical community size (CCS) is the minimum closed population size in which a 10 pathogen can persist indefinitely. Below this threshold, stochastic extinction eventu- 11 ally causes pathogen extinction. Here we use a simulation model to explore behaviour- 12 mediated persistence: a novel mechanism by which the population response to the pathogen 13 determines the CCS. We model severe coronavirus 2 (SARS-CoV-2) transmission and 14 non-pharmaceutical interventions (NPIs) in a population where both individuals and gov- 15 ernment authorities restrict transmission more strongly when SARS-CoV-2 case numbers 16 are higher. This results in a coupled human-environment feedback between disease dy- 17 namics and population behaviour. In a parameter regime corresponding to a moderate 18 population response, this feedback allows SARS-CoV-2 to avoid extinction in the trough 19 of pandemic waves. -
Population Behavioural Dynamics Can Mediate the Persistence of Emerging Infectious Diseases
1 Supplementary information - Population behavioural dynamics can mediate the persistence of emerging infectious diseases Kathyrn R Fair1;∗, Vadim A Karatayev1, Madhur Anand1, Chris T Bauch2 1 School of Environmental Sciences, University of Guelph, Guelph, ON, Canada, N1G 2W1 2 Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada, N2L 3G1 *[email protected] 2 Supplementary methods Within the model, individuals states are updated based on the following events: 1. Exposure: fS; ·} individuals are exposed to SARS-CoV-2 with probability λ(t), shifting to fE; ·}. 2. Onset of infectious period: fE; ·} individuals become pre-symptomatic and infectious with probability (1 − π)α, shifting to fP; ·}. Alternatively, they become asymptomatic and infectious (with probability πα), shifting to fA; ·}. 3. Onset of symptoms: fP; ·} individuals become symptomatic with probability σ, shifting to fI; ·}. 4. Testing: fI;Ug individuals are tested with probability τI shifting to fI;Kg. 5. Removal: fI; ·} and fA; ·} individuals cease to be infectious with probability ρ, shifting to fR; ·}. With probability m = 0:0066 [1], individuals transitioning from the symptomatic and infec- tious state (fI; ·}) to the removed (i.e. no longer infectious) state are assigned as COVID-19 deaths. Individuals who have died due to COVID-19 do not factor into subsequent birth and non-COVID-19 death calculations. At the onset of infectiousness, newly infected individuals have a probability s = 0:2 of being assigned as super-spreaders [2]. We differentiate between super-spreaders and non-super-spreaders using subscripts (s and ns respectively), such that we have Ps, Pns, As, Ans, Is, Ins. Super-spreaders have their probability of infecting others increased by a factor of (1 − s)=s. -
Epidemiology of and Risk Factors for COVID-19 Infection Among Health Care Workers: a Multi-Centre Comparative Study
International Journal of Environmental Research and Public Health Article Epidemiology of and Risk Factors for COVID-19 Infection among Health Care Workers: A Multi-Centre Comparative Study Jia-Te Wei 1, Zhi-Dong Liu 1, Zheng-Wei Fan 2, Lin Zhao 1,* and Wu-Chun Cao 1,2,* 1 Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China; [email protected] (J.-T.W.); [email protected] (Z.-D.L.) 2 State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; [email protected] * Correspondence: [email protected] (L.Z.); [email protected] (W.-C.C.) Received: 31 August 2020; Accepted: 28 September 2020; Published: 29 September 2020 Abstract: Healthcare workers (HCWs) worldwide are putting themselves at high risks of coronavirus disease 2019 (COVID-19) by treating a large number of patients while lacking protective equipment. We aim to provide a scientific basis for preventing and controlling the COVID-19 infection among HCWs. We used data on COVID-19 cases in the city of Wuhan to compare epidemiological characteristics between HCWs and non-HCWs and explored the risk factors for infection and deterioration among HCWs based on hospital settings. The attack rate (AR) of HCWs in the hospital can reach up to 11.9% in Wuhan. The time interval from symptom onset to diagnosis in HCWs and non-HCWs dropped rapidly over time. From mid-January, the median time interval of HCW cases was significantly shorter than in non-HCW cases. -
Modeling Infectious Disease Dynamics in the Complex Landscape of Global Health Hans Heesterbeek Et Al
RESEARCH ◥ REVIEW SUMMARY linear systems in which infections evolve and spread and where key events can be governed by unpredictable pathogen biology or human EPIDEMIOLOGY behavior. In this Review, we start with an ex- amination of real-time outbreak response using the West African Ebola epidemic as an Modeling infectious disease dynamics example. Here, the challenges range from un- ◥ derreporting of cases and in the complex landscape of ON OUR WEB SITE deaths, and missing infor- Read the full article mation on the impact of at http://dx.doi. control measures to under- global health org/10.1126/ standing human responses. science.aaa4339 The possibility of future .................................................. Hans Heesterbeek,* Roy M. Anderson, Viggo Andreasen, Shweta Bansal, zoonoses tests our ability Daniela De Angelis, Chris Dye, Ken T. D. Eames, W. John Edmunds, to detect anomalous outbreaks and to esti- Simon D. W. Frost, Sebastian Funk, T. Deirdre Hollingsworth, Thomas House, mate human-to-human transmissibility against Valerie Isham, Petra Klepac, Justin Lessler, James O. Lloyd-Smith, C. Jessica E. Metcalf, a backdrop of ongoing zoonotic spillover while Denis Mollison, Lorenzo Pellis, Juliet R. C. Pulliam, Mick G. Roberts, also assessing the risk of more dangerous Cecile Viboud, Isaac Newton Institute IDD Collaboration strains evolving. Increased understanding of the dynamics of infections in food webs and BACKGROUND: Despitemanynotablesuc- lenges for prevention and control. Faced with ecosystems where host and nonhost species cesses in prevention and control, infectious this complexity, mathematical models offer interact is key. Simultaneous multispecies diseases remain an enormous threat to human valuable tools for understanding epidemio- infections are increasingly recognized as a and animal health. -
Extinction Thresholds in Host–Parasite Dynamics
Ann. Zool. Fennici 40: 115–130 ISSN 0003-455X Helsinki 30 April 2003 © Finnish Zoological and Botanical Publishing Board 2003 Extinction thresholds in host–parasite dynamics Anne Deredec & Franck Courchamp* Ecologie, Systématique & Evolution, UMR CNRS 8079, Université Paris-Sud XI, Bâtiment 362, F-91405 Orsay Cedex, France (*e-mail: [email protected]) Received 13 Jan. 2003, revised version received 5 Feb. 2003, accepted 22 Feb. 2003 Deredec, A. & Courchamp, F. 2003: Extinction thresholds in host–parasite dynamics. — Ann. Zool. Fennici 40: 115–130. In this paper, we review the main thresholds that can infl uence the population dynamics of host–parasite relationships. We start by considering the thresholds that have infl u- enced the conceptualisation of theoretical epidemiology. The most common threshold involving parasites is the host population invasion threshold, but persistence and infec- tion thresholds are also important. We recap how the existence of the invasion thresh- old is linked to the nature of the transmission term in theoretical studies. We examine some of the main thresholds that can affect host population dynamics including the Allee effect and then relate these to parasite thresholds, as a way to assess the dynamic consequences of the interplay between host and parasite thresholds on the fi nal out- come of the system. We propose that overlooking the existence of parasite and host thresholds can have important detrimental consequences in major domains of applied ecology, including in epidemiology, conservation biology and biological control. Introduction the infection would not spread and would dis- appear, and the few infected hosts would die, The interplay between parasite species and their leaving a remaining healthy and uninfected host hosts constitutes a biological process that is both population. -
Arxiv:1705.01135V2 [Q-Bio.QM] 17 Jul 2020 Author Summary
Estimating and interpreting secondary attack risk: Binomial considered harmful Yushuf Sharker1, Eben Kenah2, * 1 Division of Biometrics, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA 2 Biostatistics Division, College of Public Health, The Ohio State University, Columbus, Ohio, USA * [email protected] Abstract The household secondary attack risk (SAR), often called the secondary attack rate or secondary infection risk, is the probability of infectious contact from an infectious household member A to a given household member B, where we define infectious contact to be a contact sufficient to infect B if he or she is susceptible. Estimation of the SAR is an important part of understanding and controlling the transmission of infectious diseases. In practice, it is most often estimated using binomial models such as logistic regression, which implicitly attribute all secondary infections in a household to the primary case. In the simplest case, the number of secondary infections in a household with m susceptibles and a single primary case is modeled as a binomial(m; p) random variable where p is the SAR. Although it has long been understood that transmission within households is not binomial, it is thought that multiple generations of transmission can be safely neglected when p is small. We use probability generating functions and simulations to show that this is a mistake. The proportion of susceptible household members infected can be substantially larger than the SAR even when p is small. As a result, binomial estimates of the SAR are biased upward and their confidence intervals have poor coverage probabilities even if adjusted for clustering. -
Cohort Studies for Outbreak Investigations
VOLUME 3, ISSUE 1 Cohort Studies for Outbreak Investigations In a previous issue of FOCUS, we To be certain that an exposure caused introduced cohort studies and talked the disease, the unexposed group CONTRIBUTORS about how to decide whether a co- must be similar to the exposed group hort study is the best design for your in all respects except the exposure. Author: situation. Remember that cohort Therefore they should have similar Amy Nelson, PhD, MPH studies are useful when there is a demographic characteristics such as defined population at risk for devel- age, gender, race, and income. If you Kim Brunette, MPH oping the disease of interest (such compare an “unexposed” elementary FOCUS Workgroup* as all members of the Glee Club) and school to an “exposed” elementary when it is possible to interview all school, both schools should be lo- Reviewers: members or a representative sample cated in neighborhoods with the same FOCUS Workgroup* of the cohort. types of economic and other opportu- nities, similar socio-economic status Production Editors: In outbreak investigations, cohort (SES), similar parent involvement, Tara P. Rybka, MPH studies are usually retrospective similar school resources, and similar Lorraine Alexander, DrPH because in an outbreak an exposure has already occurred, and enough student populations. Gloria C. Mejia, DDS, MPH cases to signal an outbreak have Using groups that have other differ- Editor in chief: also occurred. The aim is to deter- ences may lead to “confounding.” If Pia D.M. MacDonald, PhD, MPH mine what exposures occurred in the you compare a low-income public past to cause these cases of dis- school to a private boarding school, ease. -
A Systematic Review of COVID-19 Epidemiology Based on Current Evidence
Journal of Clinical Medicine Review A Systematic Review of COVID-19 Epidemiology Based on Current Evidence Minah Park, Alex R. Cook *, Jue Tao Lim , Yinxiaohe Sun and Borame L. Dickens Saw Swee Hock School of Public Health, National Health Systems, National University of Singapore, Singapore 117549, Singapore; [email protected] (M.P.); [email protected] (J.T.L.); [email protected] (Y.S.); [email protected] (B.L.D.) * Correspondence: [email protected]; Tel.: +65-8569-9949 Received: 18 March 2020; Accepted: 27 March 2020; Published: 31 March 2020 Abstract: As the novel coronavirus (SARS-CoV-2) continues to spread rapidly across the globe, we aimed to identify and summarize the existing evidence on epidemiological characteristics of SARS-CoV-2 and the effectiveness of control measures to inform policymakers and leaders in formulating management guidelines, and to provide directions for future research. We conducted a systematic review of the published literature and preprints on the coronavirus disease (COVID-19) outbreak following predefined eligibility criteria. Of 317 research articles generated from our initial search on PubMed and preprint archives on 21 February 2020, 41 met our inclusion criteria and were included in the review. Current evidence suggests that it takes about 3-7 days for the epidemic to double in size. Of 21 estimates for the basic reproduction number ranging from 1.9 to 6.5, 13 were between 2.0 and 3.0. The incubation period was estimated to be 4-6 days, whereas the serial interval was estimated to be 4-8 days. Though the true case fatality risk is yet unknown, current model-based estimates ranged from 0.3% to 1.4% for outside China. -
Should We Expect Population Thresholds for Wildlife Disease?
ARTICLE IN PRESS TREE 519 Review TRENDS in Ecology and Evolution Vol.xx No.xx Monthxxxx Should we expect population thresholds for wildlife disease? James O. Lloyd-Smith1,2, Paul C. Cross1,3, Cheryl J. Briggs4, Matt Daugherty4, Wayne M. Getz1,5, John Latto4, Maria S. Sanchez1, Adam B. Smith6 and Andrea Swei4 1Department of Environmental Science, Policy and Management, University of California at Berkeley, Berkeley, CA 94720-3114, USA 2Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA 94720-3200, USA 3Northern Rocky Mountain Science Center, United States Geological Survey, 229 A.J.M. Johnson Hall, Bozeman, MT 59717, USA 4Department of Integrative Biology, University of California at Berkeley, Berkeley, CA 94720-3140, USA 5Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, 0002 South Africa 6Energy and Resources Group, University of California at Berkeley, Berkeley, CA 94720, USA Host population thresholds for the invasion or persist- expected, demographic stochasticity makes them difficult ence of infectious disease are core concepts of disease to measure under field conditions. We discuss how con- ecology and underlie disease control policies based on ventional theories underlying population thresholds culling and vaccination. However, empirical evidence for neglect many factors relevant to natural populations these thresholds in wildlife populations has been such as seasonal births or compensatory reproduction, sparse, although recent studies have begun to address raising doubts about the general applicability of standard this gap. Here, we review the theoretical bases and threshold concepts in wildlife disease systems. These empirical evidence for disease thresholds in wildlife. We findings call into question the wisdom of centering control see that, by their nature, these thresholds are rarely policies on threshold targets and open important avenues abrupt and always difficult to measure, and important for future research. -
Prevention of Hospital-Acquired Infections World Health Organization
WHO/CDS/CSR/EPH/2002.12 Prevention of hospital-acquired infections A practical guide 2nd edition World Health Organization Department of Communicable Disease, Surveillance and Response This document has been downloaded from the WHO/CSR Web site. The original cover pages and lists of participants are not included. See http://www.who.int/emc for more information. © World Health Organization This document is not a formal publication of the World Health Organization (WHO), and all rights are reserved by the Organization. The document may, however, be freely reviewed, abstracted, reproduced and translated, in part or in whole, but not for sale nor for use in conjunction with commercial purposes. The views expressed in documents by named authors are solely the responsibility of those authors. The mention of specific companies or specific manufacturers' products does no imply that they are endorsed or recommended by the World Health Organization in preference to others of a similar nature that are not mentioned. WHO/CDS/CSR/EPH/2002.12 DISTR: GENERAL ORIGINAL: ENGLISH Prevention of hospital-acquired infections A PRACTICAL GUIDE 2nd edition Editors G. Ducel, Fondation Hygie, Geneva, Switzerland J. Fabry, Université Claude-Bernard, Lyon, France L. Nicolle, University of Manitoba, Winnipeg, Canada Contributors R. Girard, Centre Hospitalier Lyon-Sud, Lyon, France M. Perraud, Hôpital Edouard Herriot, Lyon, France A. Prüss, World Health Organization, Geneva, Switzerland A. Savey, Centre Hospitalier Lyon-Sud, Lyon, France E. Tikhomirov, World Health Organization, Geneva, Switzerland M. Thuriaux, World Health Organization, Geneva, Switzerland P. Vanhems, Université Claude Bernard, Lyon, France WORLD HEALTH ORGANIZATION Acknowledgements The World Health Organization (WHO) wishes to acknowledge the significant support for this work from the United States Agency for International Development (USAID). -
Weekly Epidemiological Record Relevé Épidémiologique Hebdomadaire
2018, 93, 541–552 No 41 Weekly epidemiological record Relevé épidémiologique hebdomadaire 12 OCTOBER 2018, 93th YEAR / 12 OCTOBRE 2018, 93e ANNÉE No 41, 2018, 93, 541–552 http://www.who.int/wer Progress towards Progrès vers l’élimination Contents eliminating onchocerciasis de l’onchocercose dans 541 Progress towards in the WHO Region la Région OMS des Amériques: eliminating onchocerciasis in the WHO Region of of the Americas: advances progrès dans la cartographie the Americas: advances in mapping the Yanomami de la zone du foyer Yanomami in mapping the Yanomami focus area focus area 544 Guidance for evaluating Onchocerciasis (river blindness) is caused L’onchocercose (cécité des rivières) est provo- progress towards elimination by the parasitic worm Onchocerca volvulus, quée par Onchocerca volvulus, ver parasitaire of measles and rubella which is transmitted by Simulium species transmis par certaines espèces de Simulium black flies that breed in fast-flowing (simulies) qui se reproduisent dans les rivières Sommaire rivers and streams. In the human host, et les cours d’eau rapides. Chez l’hôte humain, adult male and female O. volvulus worms les adultes mâles et femelles d’O. volvulus s’en- 541 Progrès vers l’élimination become encapsulated in subcutaneous capsulent dans des «nodules» fibreux sous- de l’onchocercose dans fibrous “nodules”, and fertilized females cutanés et les femelles fécondées produisent la Région OMS des Amériques: progrès dans la cartographie produce embryonic microfilariae, which des microfilaires embryonnaires qui migrent de la zone du foyer Yanomami migrate to the skin, where they are vers la peau où elles sont ingérées par des 544 Orientations pour évaluer ingested by the black fly vectors during simulies vectrices lors d’un repas de sang.