Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.

Autor:	Crits-Christoph A; Independent researcher., Levy JI; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA., Pekar JE; Department of Biomedical Informatics, University of California, San Diego, La Jolla, San Diego, CA, USA., Goldstein SA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA., Singh R; Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada., Hensel Z; ITQB NOVA, Universidade NOVA de Lisboa, Av. da República, Oeiras, Lisbon 2780-157, Portugal., Gangavarapu K; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA., Rogers MB; Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada., Moshiri N; Department of Computer Science & Engineering, University of California, San Diego, La Jolla, San Diego, CA, USA., Garry RF; Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA., Holmes EC; School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia., Koopmans MPG; Department of Viroscience, and Pandemic and Disaster Preparedness Centre, Erasmus Medical Centre, Rotterdam, the Netherlands., Lemey P; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium., Peacock TP; The Pirbright Institute, Woking GU24 0NF, Surrey, UK; Department of Infectious Disease, Imperial College London, London W2 1P, UK., Popescu S; University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA., Rambaut A; Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK., Robertson DL; MRC-University of Glasgow Center for Virus Research, Glasgow G61 1QH, UK., Suchard MA; Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA., Wertheim JO; Department of Medicine, University of California, San Diego, La Jolla, San Diego, CA, USA., Rasmussen AL; Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada., Andersen KG; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA. Electronic address: andersen@scripps.edu., Worobey M; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA. Electronic address: worobey@arizona.edu., Débarre F; Institut d'Écologie et des Sciences de l'Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France. Electronic address: florence.debarre@sorbonne-universite.fr.
Jazyk:	angličtina
Zdroj:	Cell [Cell] 2024 Sep 19; Vol. 187 (19), pp. 5468-5482.e11.
DOI:	10.1016/j.cell.2024.08.010
Abstrakt:	Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling. Competing Interests: Declaration of interests J.O.W. and N.M. receive funding from the Centers for Disease Control and Prevention (CDC) through contracts to J.O.W.’s institution unrelated to this research. M.A.S. receives contracts from the US Food & Drug Administration, US Department of Veterans Affairs, and Janssen Research & Development, all outside the scope of this work. R.F.G. is a cofounder of Zalgen Labs, a biotechnology company developing countermeasures for emerging viruses. A.C.-C. is an employee of Cultivarium, a nonprofit organization studying environmental microbes, unrelated to the scope of this work. M.W., A.L.R., J.E.P., A.R., M.A.S., E.C.H., S.A.G., J.O.W., and K.G.A. have received consulting fees and/or provided compensated expert testimony on SARS-CoV-2 and the COVID-19 pandemic. M.P.G.K. was involved in the WHO-convened SARS-CoV-2 origins mission. (Copyright © 2024 Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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