Understanding the circumstances that lead to pandemics is important for their prevention. Phylogenetic inference of sarbecoviruses, while accounting for extensive recombination, indicates that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. Analyses of early SARS-CoV-2 genomic diversity constrain its emergence to late 2019, indicate multiple independent zoonotic transmission events, and argue against widespread circulation prior to the earliest detected cases. Environmental and metagenomic data from the Huanan Seafood Wholesale Market are consistent with early emergence there and reveal spatial association between SARS-CoV-2 positivity and wildlife stalls containing susceptible mammalian species. Together, these results integrate viral evolutionary history with early epidemic and ecological evidence to clarify the origins of SARS-CoV-2 and its close ancestors.
Jonathan Pekar is a postdoctoral researcher in the Andrew Rambaut Lab at the University of Edinburgh, jointly advised by Pardis Sabeti at the Broad Institute of MIT and Harvard. He completed his PhD at the University of California San Diego under Joel Wertheim, where he studied the origins of SARS-CoV-2 and mpox virus transmission in New York City. His current research focuses on the molecular epidemiology and phylodynamic modeling of emerging pathogens, including H5N1 influenza in U.S. dairy cattle, Mycobacterium tuberculosis complex, and RSV.