Revisiting the Dangers of the Coronavirus in the Ophthalmology Practice
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Genome Organization of Canada Goose Coronavirus, a Novel
www.nature.com/scientificreports OPEN Genome Organization of Canada Goose Coronavirus, A Novel Species Identifed in a Mass Die-of of Received: 14 January 2019 Accepted: 25 March 2019 Canada Geese Published: xx xx xxxx Amber Papineau1,2, Yohannes Berhane1, Todd N. Wylie3,4, Kristine M. Wylie3,4, Samuel Sharpe5 & Oliver Lung 1,2 The complete genome of a novel coronavirus was sequenced directly from the cloacal swab of a Canada goose that perished in a die-of of Canada and Snow geese in Cambridge Bay, Nunavut, Canada. Comparative genomics and phylogenetic analysis indicate it is a new species of Gammacoronavirus, as it falls below the threshold of 90% amino acid similarity in the protein domains used to demarcate Coronaviridae. Additional features that distinguish the genome of Canada goose coronavirus include 6 novel ORFs, a partial duplication of the 4 gene and a presumptive change in the proteolytic processing of polyproteins 1a and 1ab. Viruses belonging to the Coronaviridae family have a single stranded positive sense RNA genome of 26–31 kb. Members of this family include both human pathogens, such as severe acute respiratory syn- drome virus (SARS-CoV)1, and animal pathogens, such as porcine epidemic diarrhea virus2. Currently, the International Committee on the Taxonomy of Viruses (ICTV) recognizes four genera in the Coronaviridae family: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. While the reser- voirs of the Alphacoronavirus and Betacoronavirus genera are believed to be bats, the Gammacoronavirus and Deltacoronavirus genera have been shown to spread primarily through birds3. Te frst three species of the Deltacoronavirus genus were discovered in 20094 and recent work has vastly expanded the Deltacoronavirus genus, adding seven additional species3. -
Broad Receptor Engagement of an Emerging Global Coronavirus May Potentiate Its Diverse Cross-Species Transmissibility
Broad receptor engagement of an emerging global coronavirus may potentiate its diverse cross-species transmissibility Wentao Lia,1, Ruben J. G. Hulswita,1, Scott P. Kenneyb,1, Ivy Widjajaa, Kwonil Jungb, Moyasar A. Alhamob, Brenda van Dierena, Frank J. M. van Kuppevelda, Linda J. Saifb,2, and Berend-Jan Boscha,2 aVirology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; and bDepartment of Veterinary Preventive Medicine, Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691 Contributed by Linda J. Saif, April 12, 2018 (sent for review February 15, 2018; reviewed by Tom Gallagher and Stefan Pöhlmann) Porcine deltacoronavirus (PDCoV), identified in 2012, is a common greatly increase the potential for successful adaptation to a new enteropathogen of swine with worldwide distribution. The source host (6, 12). A pivotal criterion of cross-species transmission and evolutionary history of this virus is, however, unknown. concerns the ability of a virus to engage a receptor within the PDCoV belongs to the Deltacoronavirus genus that comprises pre- novel host, which for CoVs, is determined by the receptor dominantly avian CoV. Phylogenetic analysis suggests that PDCoV specificity of the viral spike (S) entry protein. originated relatively recently from a host-switching event be- The porcine deltacoronavirus (PDCoV) is a recently discov- tween birds and mammals. Insight into receptor engagement by ered CoV of unknown origin. PDCoV (species name coronavirus PDCoV may shed light into such an exceptional phenomenon. Here HKU15) was identified in Hong Kong in pigs in the late 2000s we report that PDCoV employs host aminopeptidase N (APN) as an (13) and has since been detected in swine populations in various entry receptor and interacts with APN via domain B of its spike (S) countries worldwide (14–24). -
Downloaded from the Genbank Database As of July 2020
viruses Article Modular Evolution of Coronavirus Genomes Yulia Vakulenko 1,2 , Andrei Deviatkin 3 , Jan Felix Drexler 1,4,5 and Alexander Lukashev 1,3,* 1 Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; [email protected] (Y.V.); [email protected] (J.F.D.) 2 Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia 3 Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; [email protected] 4 Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany 5 German Centre for Infection Research (DZIF), Associated Partner Site Charité, 10117 Berlin, Germany * Correspondence: [email protected] Abstract: The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and the extent of genetic divergence between partners, are scarce. Common methods of recombination detection based on phylogenetic incongruences (e.g., a phylogenetic com- patibility matrix) may fail in cases where too many events diminish the phylogenetic signal. Thus, an approach comparing genetic distances in distinct genome regions (pairwise distance deviation matrix) was set up. In alpha, beta, and delta-coronaviruses, a low incidence of recombination between closely related viruses was evident in all genome regions, but it was more extensive between the spike gene and other genome regions. -
Exposure of Humans Or Animals to Sars-Cov-2 from Wild, Livestock, Companion and Aquatic Animals Qualitative Exposure Assessment
ISSN 0254-6019 Exposure of humans or animals to SARS-CoV-2 from wild, livestock, companion and aquatic animals Qualitative exposure assessment FAO ANIMAL PRODUCTION AND HEALTH / PAPER 181 FAO ANIMAL PRODUCTION AND HEALTH / PAPER 181 Exposure of humans or animals to SARS-CoV-2 from wild, livestock, companion and aquatic animals Qualitative exposure assessment Authors Ihab El Masry, Sophie von Dobschuetz, Ludovic Plee, Fairouz Larfaoui, Zhen Yang, Junxia Song, Wantanee Kalpravidh, Keith Sumption Food and Agriculture Organization for the United Nations (FAO), Rome, Italy Dirk Pfeiffer City University of Hong Kong, Hong Kong SAR, China Sharon Calvin Canadian Food Inspection Agency (CFIA), Science Branch, Animal Health Risk Assessment Unit, Ottawa, Canada Helen Roberts Department for Environment, Food and Rural Affairs (Defra), Equines, Pets and New and Emerging Diseases, Exotic Disease Control Team, London, United Kingdom of Great Britain and Northern Ireland Alessio Lorusso Istituto Zooprofilattico dell’Abruzzo e Molise, Teramo, Italy Casey Barton-Behravesh Centers for Disease Control and Prevention (CDC), One Health Office, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, United States of America Zengren Zheng China Animal Health and Epidemiology Centre (CAHEC), China Animal Health Risk Analysis Commission, Qingdao City, China Food and Agriculture Organization of the United Nations Rome, 2020 Required citation: El Masry, I., von Dobschuetz, S., Plee, L., Larfaoui, F., Yang, Z., Song, J., Pfeiffer, D., Calvin, S., Roberts, H., Lorusso, A., Barton-Behravesh, C., Zheng, Z., Kalpravidh, W. & Sumption, K. 2020. Exposure of humans or animals to SARS-CoV-2 from wild, livestock, companion and aquatic animals: Qualitative exposure assessment. FAO animal production and health, Paper 181. -
The Characterization of Chifitms in Avian Coronavirus Infection in Vivo, Ex Vivo and in Vitro
G C A T T A C G G C A T genes Article The Characterization of chIFITMs in Avian Coronavirus Infection In Vivo, Ex Vivo and In Vitro Angela Steyn 1,*, Sarah Keep 1, Erica Bickerton 1 and Mark Fife 1,2 1 The Pirbright Institute, Pirbright, Woking GU24 0NF, UK; [email protected] (S.K.); [email protected] (E.B); mfi[email protected] (M.F.) 2 AVIAGEN UK, Ltd. Newbridge, Midlothian EH28 8SZ, Scotland, UK * Correspondence: [email protected]; Tel.: +44-(0)148-323-4762 Received: 20 July 2020; Accepted: 7 August 2020; Published: 10 August 2020 Abstract: The coronaviruses are a large family of enveloped RNA viruses that commonly cause gastrointestinal or respiratory illnesses in the infected host. Avian coronavirus infectious bronchitis virus (IBV) is a highly contagious respiratory pathogen of chickens that can affect the kidneys and reproductive systems resulting in bird mortality and decreased reproductivity. The interferon-inducible transmembrane (IFITM) proteins are activated in response to viral infections and represent a class of cellular restriction factors that restrict the replication of many viral pathogens. Here, we characterize the relative mRNA expression of the chicken IFITM genes in response to IBV infection, in vivo, ex vivo and in vitro using the pathogenic M41-CK strain, the nephropathogenic QX strain and the nonpathogenic Beaudette strain. In vivo we demonstrate a significant upregulation of chIFITM1, 2, 3 and 5 in M41-CK- and QX-infected trachea two days post-infection. In vitro infection with Beaudette, M41-CK and QX results in a significant upregulation of chIFITM1, 2 and 3 at 24 h post-infection. -
The COVID-19 Pandemic: a Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control
Journal of Clinical Medicine Review The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control Yosra A. Helmy 1,2,* , Mohamed Fawzy 3,*, Ahmed Elaswad 4, Ahmed Sobieh 5, Scott P. Kenney 1 and Awad A. Shehata 6,7 1 Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA; [email protected] 2 Department of Animal Hygiene, Zoonoses and Animal Ethology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt 3 Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt 4 Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt; [email protected] 5 Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA; [email protected] 6 Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, Sadat City University, Sadat 32897, Egypt; [email protected] 7 Research and Development Section, PerNaturam GmbH, 56290 Gödenroth, Germany * Correspondence: [email protected] (Y.A.H.); [email protected] (M.F.) Received: 18 March 2020; Accepted: 21 April 2020; Published: 24 April 2020 Abstract: A pneumonia outbreak with unknown etiology was reported in Wuhan, Hubei province, China, in December 2019, associated with the Huanan Seafood Wholesale Market. The causative agent of the outbreak was identified by the WHO as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), producing the disease named coronavirus disease-2019 (COVID-19). The virus is closely related (96.3%) to bat coronavirus RaTG13, based on phylogenetic analysis. -
Broad Host Range of SARS-Cov-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates
Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates Joana Damasa,1, Graham M. Hughesb,1, Kathleen C. Keoughc,d,1, Corrie A. Paintere,1, Nicole S. Perskyf,1, Marco Corboa, Michael Hillerg,h,i, Klaus-Peter Koepflij, Andreas R. Pfenningk, Huabin Zhaol,m, Diane P. Genereuxn, Ross Swoffordn, Katherine S. Pollardd,o,p, Oliver A. Ryderq,r, Martin T. Nweeias,t,u, Kerstin Lindblad-Tohn,v, Emma C. Teelingb, Elinor K. Karlssonn,w,x, and Harris A. Lewina,y,z,2 aThe Genome Center, University of California, Davis, CA 95616; bSchool of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland; cGraduate Program in Pharmaceutical Sciences and Pharmacogenomics, Quantitative Biosciences Consortium, University of California, San Francisco, CA 94117; dGladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158; eCancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142; fGenetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142; gMax Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; hMax Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany; iCenter for Systems Biology Dresden, 01307 Dresden, Germany; jCenter for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630; kDepartment of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213; lDepartment of Ecology, -
And Betacoronaviruses in Rodents from Yunnan, China Xing-Yi Ge1,4, Wei-Hong Yang2, Ji-Hua Zhou2, Bei Li1, Wei Zhang1, Zheng-Li Shi1* and Yun-Zhi Zhang2,3*
Ge et al. Virology Journal (2017) 14:98 DOI 10.1186/s12985-017-0766-9 RESEARCH Open Access Detection of alpha- and betacoronaviruses in rodents from Yunnan, China Xing-Yi Ge1,4, Wei-Hong Yang2, Ji-Hua Zhou2, Bei Li1, Wei Zhang1, Zheng-Li Shi1* and Yun-Zhi Zhang2,3* Abstract Background: Rodents represent the most diverse mammals on the planet and are important reservoirs of human pathogens. Coronaviruses infect various animals, but to date, relatively few coronaviruses have been identified in rodents worldwide. The evolution and ecology of coronaviruses in rodent have not been fully investigated. Results: In this study, we collected 177 intestinal samples from thress species of rodents in Jianchuan County, Yunnan Province, China. Alphacoronavirus and betacoronavirus were detected in 23 rodent samples from three species, namely Apodemus chevrieri (21/98), Eothenomys fidelis (1/62), and Apodemus ilex (1/17). We further characterized the full-length genome of an alphacoronavirus from the A. chevrieri rat and named it as AcCoV-JC34. The AcCoV-JC34 genome was 27,649 nucleotides long and showed a structure similar to the HKU2 bat coronavirus. Comparing the normal transcription regulatory sequence (TRS), 3 variant TRS sequences upstream the spike (S), ORF3, and ORF8 genes were found in the genome of AcCoV-JC34. In the conserved replicase domains, AcCoV-JC34 was most closely related to Rattus norvegicus coronavirus LNRV but diverged from other alphacoronaviruses, indicating that AcCoV-JC34 and LNRV may represent a novel alphacoronavirus species. However, the S and nucleocapsid proteins showed low similarity to those of LRNV, with 66.5 and 77.4% identities, respectively. -
A Novel Human Coronavirus: Middle East Respiratory Syndrome Human Coronavirus
SCIENCE CHINA Life Sciences SPECIAL TOPIC: Haunted with and hunting for viruses August 2013 Vol.56 No.8: 683–687 • REVIEW • doi: 10.1007/s11427-013-4519-8 A novel human coronavirus: Middle East respiratory syndrome human coronavirus GENG HeYuan & TAN WenJie* Biotech Center for Viral Disease Emergency, Key Laboratory of Medical Virology and Viral Diseases Prevention and Control, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China Received May 25, 2013; accepted June 15, 2013 In 2012, a novel coronavirus, initially named as human coronavirus EMC (HCoV-EMC) but recently renamed as Middle East respiratory syndrome human coronavirus (MERS-CoV), was identified in patients who suffered severe acute respiratory infec- tion and subsequent renal failure that resulted in death. Ongoing epidemiological investigations together with retrospective studies have found 61 laboratory-confirmed cases of infection with this novel coronavirus, including 34 deaths to date. This novel coronavirus is culturable and two complete genome sequences are now available. Furthermore, molecular detection and indirect immunofluorescence assay have been developed. The present paper summarises the limited recent advances of this novel human coronavirus, including its discovery, genomic characterisation and detection. HCoV-EMC, MERS-CoV, genomic characterisation, molecular detection Citation: Geng H Y, Tan W J. A novel human coronavirus: Middle East respiratory syndrome human coronavirus. Sci China Life Sci, 2013, 56: 683–687, doi: 10.1007/s11427-013-4519-8 Coronaviruses, a genus in the family Coronaviridae (order BCoV), mice (mouse hepatitis virus, MHV), dog (canine Nidovirales), are a large family of viruses that can cause coronavirus, CCoV), cat (feline infectious peritonitis virus, respiratory, enteric, hepatic, nephric and neurological dis- FIPV) and bat (bat coronavirus HKU4, BatCoV-HKU4). -
Betacoronavirus Genomes: How Genomic Information Has Been Used to Deal with Past Outbreaks and the COVID-19 Pandemic
International Journal of Molecular Sciences Review Betacoronavirus Genomes: How Genomic Information Has Been Used to Deal with Past Outbreaks and the COVID-19 Pandemic Alejandro Llanes 1 , Carlos M. Restrepo 1 , Zuleima Caballero 1 , Sreekumari Rajeev 2 , Melissa A. Kennedy 3 and Ricardo Lleonart 1,* 1 Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City 0801, Panama; [email protected] (A.L.); [email protected] (C.M.R.); [email protected] (Z.C.) 2 College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA; [email protected] 3 College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA; [email protected] * Correspondence: [email protected]; Tel.: +507-517-0740 Received: 29 May 2020; Accepted: 23 June 2020; Published: 26 June 2020 Abstract: In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of coronaviruses in the aftermath of the 2002–2003 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019–2020 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2. -
Coronavirus: Detailed Taxonomy
Coronavirus: Detailed taxonomy Coronaviruses are in the realm: Riboviria; phylum: Incertae sedis; and order: Nidovirales. The Coronaviridae family gets its name, in part, because the virus surface is surrounded by a ring of projections that appear like a solar corona when viewed through an electron microscope. Taxonomically, the main Coronaviridae subfamily – Orthocoronavirinae – is subdivided into alpha (formerly referred to as type 1 or phylogroup 1), beta (formerly referred to as type 2 or phylogroup 2), delta, and gamma coronavirus genera. Using molecular clock analysis, investigators have estimated the most common ancestor of all coronaviruses appeared in about 8,100 BC, and those of alphacoronavirus, betacoronavirus, gammacoronavirus, and deltacoronavirus appeared in approximately 2,400 BC, 3,300 BC, 2,800 BC, and 3,000 BC, respectively. These investigators posit that bats and birds are ideal hosts for the coronavirus gene source, bats for alphacoronavirus and betacoronavirus, and birds for gammacoronavirus and deltacoronavirus. Coronaviruses are usually associated with enteric or respiratory diseases in their hosts, although hepatic, neurologic, and other organ systems may be affected with certain coronaviruses. Genomic and amino acid sequence phylogenetic trees do not offer clear lines of demarcation among corona virus genus, lineage (subgroup), host, and organ system affected by disease, so information is provided below in rough descending order of the phylogenetic length of the reported genome. Subgroup/ Genus Lineage Abbreviation -
And Gammacoronaviruses (Γ-Cov) in Wild Birds in the United States
viruses Article Epidemiology of Deltacoronaviruses (δ-CoV) and Gammacoronaviruses (γ-CoV) in Wild Birds in the United States Francine C. Paim 1, Andrew S. Bowman 2 , Lauren Miller 3, Brandi J. Feehan 4, Douglas Marthaler 4 , Linda J. Saif 1,* and Anastasia N. Vlasova 1,* 1 Food Animal Health Research Program, The Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA; [email protected] 2 Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, 1920 Coffey Rd, Columbus, OH 43210, USA; [email protected] 3 College of Public Health, The Ohio State University, 250 Cunz Hall, 1841 Neil Ave, Columbus, OH 43210, USA; [email protected] 4 Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA; [email protected] (B.J.F.); [email protected] (D.M.) * Correspondence: [email protected] (L.J.S.); [email protected] (A.N.V.) Received: 5 September 2019; Accepted: 20 September 2019; Published: 26 September 2019 Abstract: Porcine deltacoronavirus (δ-CoV) is the object of extensive research in several countries including the United States. In contrast, the epidemiology of δ-CoVs in wild birds in the US is largely unknown. Our aim was to comparatively assess the prevalence of δ- and γ-CoVs in wild migratory terrestrial and aquatic birds in Arkansas, Illinois, Indiana, Maryland, Mississippi, Missouri, Ohio, Tennessee and Wisconsin. A total of 1236 cloacal/fecal swabs collected during the period 2015–2018 were tested for γ- and δ-CoVs using genus-specific reverse transcription-PCR assays.