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

Affiliations
  • 1Independent researcher.
  • 2Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA.
  • 3Department of Biomedical Informatics, University of California, San Diego, La Jolla, San Diego, CA, USA.
  • 4Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA.
  • 5Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
  • 6ITQB NOVA, Universidade NOVA de Lisboa, Av. da República, Oeiras, Lisbon 2780-157, Portugal.
  • 7Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA.
  • 8Department of Computer Science & Engineering, University of California, San Diego, La Jolla, San Diego, CA, USA.
  • 9Tulane 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.
  • 10School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
  • 11Department of Viroscience, and Pandemic and Disaster Preparedness Centre, Erasmus Medical Centre, Rotterdam, the Netherlands.
  • 12Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
  • 13The Pirbright Institute, Woking GU24 0NF, Surrey, UK; Department of Infectious Disease, Imperial College London, London W2 1P, UK.
  • 14University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA.
  • 15Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
  • 16MRC-University of Glasgow Center for Virus Research, Glasgow G61 1QH, UK.
  • 17Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA.
  • 18Department of Medicine, University of California, San Diego, La Jolla, San Diego, CA, USA.
  • 19Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA. Electronic address: andersen@scripps.edu.
  • 20Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA. Electronic address: worobey@arizona.edu.
  • 21Institut 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.

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September 20, 2024

Abstract

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.

Keywords:

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