@article{48bad317ec6d4737a0db1bf5c43a339c,
title = "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic",
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 = "forensic genomics, metatranscriptomics, phylodynamics, phylogenetics, SARS-CoV-2, viral emergence, virus evolution, wildlife trade",
author = "Alexander Crits-Christoph and Levy, \{Joshua I.\} and Pekar, \{Jonathan E.\} and Goldstein, \{Stephen A.\} and Reema Singh and Zach Hensel and Karthik Gangavarapu and Rogers, \{Matthew B.\} and Niema Moshiri and Garry, \{Robert F.\} and Holmes, \{Edward C.\} and Koopmans, \{Marion P.G.\} and Philippe Lemey and Peacock, \{Thomas P.\} and Saskia Popescu and Andrew Rambaut and Robertson, \{David L.\} and Suchard, \{Marc A.\} and Wertheim, \{Joel O.\} and Rasmussen, \{Angela L.\} and Andersen, \{Kristian G.\} and Michael Worobey and Florence D{\'e}barre",
note = "Funding Information: This project has been funded in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Department of Health and Human Services (contract no. 75N93021C00015 to M.W.). This work was partially supported through US National Institutes of Health grants U19 AI135995 (K.G.A., R.F.G., and M.A.S.), U01 AI151812 (K.G.A. and R.F.G.), R01 AI153044 (M.A.S., P.L., and A.R.), R01 AI135992 (J.O.W.), and 5T32AI007244-38 (J.I.L.); EU commission H2020 programme grant number 874735 (M.P.G.K.); Funda\textbackslash{}u00E7\textbackslash{}u00E3o para a Ci\textbackslash{}u00EAncia e a Tecnologia (FCT) through MOSTMICRO-ITQB ( UIDB/04612/2020 and UIDP/04612/2020 , Z.H.) and LS4FUTURE ( LA/P/0087/2020 , Z.H.); Wellcome Trust (Collaborators Award 206298/Z/17/Z , ARTIC network) (M.A.S., P.L., and A.R.); European Research Council (grant agreement no. 725422 \textbackslash{}u2013 ReservoirDOCS) (M.A.S., P.L., and A.R.); National Institutes of Health ( T15LM011271 ; J.E.P.); the UC San Diego Merkin Fellowship (J.E.P.); National Health and Medical Research Council, Australia ( GNT2017197 , E.C.H.); UK Medical Research Council (MRC, MC\_UU\_12014/12 , MC\_UU\_00034/5 , and MR/V01157X/1 , D.L.R.); AIR@InnoHK administered by the Innovation and Technology Commission, Hong Kong Special Administrative Region, China (E.C.H.); European Union Horizon 2020 (project MOOD, grant agreement no 874850 , P.L.); Research Foundation - Flanders ( G0D5117N and G051322N , P.L.); the Canadian Institutes of Health Research as part of the Coronavirus Variants Rapid Response Network (CoVaRR-Net; CIHR FRN\# 175622 ; A.L.R. and R.S.); and the Canada Foundation for Innovation \textbackslash{}u2013 Major Science Initiatives Fund and the Government of Saskatchewan through Innovation Saskatchewan and the Ministry of Agriculture (A.L.R., R.S., and M.B.R.). Funding Information: J.O.W. and N.M. receive funding from the Centers for Disease Control and Prevention (CDC) through contracts to J.O.W.\textbackslash{}u2019s 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. Publisher Copyright: {\textcopyright} 2024 Elsevier Inc.",
year = "2024",
month = sep,
day = "19",
doi = "10.1016/j.cell.2024.08.010",
language = "English",
volume = "187",
pages = "5468--5482.e11",
journal = "Cell",
issn = "0092-8674",
publisher = "Elsevier Science B.V., Amsterdam.",
number = "19",
}