The Molecular Epidemiology of Multiple Zoonotic Origins of SARS-CoV-2

Science 377(6609):960-966 (2022).

Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, Park H, Park MS, Ching KZY, Lin RTP, Mat Isa MN, Noor YM, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO.

Understanding the circumstances that lead to pandemics is important for their prevention. Here, we analyze the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted A and B. Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October-8 December), while the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans prior to November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.

The Globe and Mail – COVID-19 Almost Certainly Did Not Come From a Lab Leak. Here’s How We Know
The Conversation – The COVID Lab Leak Theory is Dead. Here’s How We Know the Virus Came From a Wuhan Market
Science Perspective – Wildlife Trade is Likely the Source of SARS-CoV-2

Media Coverage (selected)
Wired UK – The Origins of COVID-19 Are More Complicated Than Once Thought
Associated Press – New Studies Bolster Theory Coronavirus Emerged From The Wild
CNN – New Studies Agree That Animals Sold at Wuhan Market Are Most Likely What Started COVID-19 Pandemic
Washington Post – Scientists Hone Argument That Coronavirus Came From Wuhan Market
National Geographic – Debate Deepens Over Wuhan Wet Market’s Role In Kickstarting The Pandemic
BBC News – Covid Origin Studies Say Evidence Points to Wuhan Market

Press Releases
Scripps Research – Pair of studies illuminates COVID-19 pandemic origins
Tulane University – Study finds Wuhan market as likely origin of COVID-19 pandemic
Arizona University – Studies link COVID-19 to wildlife sales at Chinese market, find other scenarios extremely unlikely
University of California San Diego – Coronavirus Jumped to Humans at Least Twice at Market in Wuhan, China