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

Alexander Crits-Christoph; Joshua I Levy; Jonathan E Pekar; Stephen A Goldstein; Reema Singh; Zach Hensel; Karthik Gangavarapu; Matthew B Rogers; Niema Moshiri; Robert F Garry; Edward C Holmes; Marion P G Koopmans; Philippe Lemey; Saskia Popescu; Andrew Rambaut; David L Robertson; Marc A Suchard; Joel O Wertheim; Angela L Rasmussen; Kristian G Andersen; Michael Worobey; Florence Débarre

doi:10.1101/2023.09.13.557637

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

bioRxiv [Preprint]. 2023 Sep 14:2023.09.13.557637. doi: 10.1101/2023.09.13.557637.

Authors

Alexander Crits-Christoph¹, Joshua I Levy², Jonathan E Pekar³, Stephen A Goldstein⁴, Reema Singh⁵, Zach Hensel⁶, Karthik Gangavarapu⁷, Matthew B Rogers⁵, Niema Moshiri⁸, Robert F Garry⁹, Edward C Holmes¹⁰, Marion P G Koopmans¹¹, Philippe Lemey¹², Saskia Popescu¹³, Andrew Rambaut¹⁴, David L Robertson¹⁵, Marc A Suchard¹⁶, Joel O Wertheim¹⁷, Angela L Rasmussen⁵, Kristian G Andersen², Michael Worobey¹⁸, Florence Débarre¹⁹

Affiliations

¹ Independent researcher.
² Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
³ Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA.
⁴ Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA.
⁵ Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
⁶ ITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da Republica, 2780-157, Oeiras, Portugal.
⁷ Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA.
⁸ Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.
⁹ 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.
¹⁰ Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
¹¹ Department of Viroscience, and Pandemic and Disaster Preparedness Centre., Erasmus Medical Centre, Rotterdam, The Netherlands.
¹² Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
¹³ University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA.
¹⁴ Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
¹⁵ MRC-University of Glasgow Center for Virus Research, Glasgow, G61 1QH, UK.
¹⁶ Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA.
¹⁷ Department of Medicine, University of California San Diego, La Jolla, CA, USA.
¹⁸ Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
¹⁹ Institut d'Écologie et des Sciences de l'Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France.

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 Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.

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Preprint

Abstract

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