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, Thomas P. Peacock, Saskia Popescu, Andrew Rambaut, David L. Robertson, Marc A. Suchard, Joel O. Wertheim, Angela L. RasmussenKristian G. Andersen*, Michael Worobey*, Florence Débarre*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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.
Original languageEnglish
Article number5468-5482.e11
Number of pages27
JournalCell
Volume187
Issue number19
DOIs
Publication statusPublished - 19 Sept 2024

Keywords / Materials (for Non-textual outputs)

  • metatranscriptomics
  • phylogenetics
  • phylodynamics
  • viral emergence
  • virus evolution
  • forensic genomics
  • SARS-CoV-2
  • wildlife trade

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    Crits-Christoph, A. (Creator), Levy, J. (Creator), Pekar, J. (Creator), Goldstein, S. (Creator), Singh, R. (Creator), Hensel, Z. (Creator), Gangavarapu, K. (Creator), Rogers, M. B. (Creator), Moshiri, N. (Creator), Garry, R. F. (Creator), Holmes, E. C. (Creator), Koopmans, M. P. G. (Creator), Lemey, P. (Creator), Peacock, T. P. (Creator), Popescu, S. (Creator), Rambaut, A. (Creator), Robertson, D. L. (Creator), Suchard, M. A. (Creator), Wertheim, J. O. (Creator), Rasmussen, A. L. (Creator), Worobey, M. (Creator), Andersen, K. G. (Creator) & Débarre, F. (Creator), Zenodo, 27 Jun 2024

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