Preprint Open Access
Pekar, Jonathan E.; Magee, Andrew; Parker, Edyth; Moshiri, Niema; Izhikevich, Katherine; Havens, Jennifer L.; Gangavarapu, Karthik; Malpica Serrano, Lorena M.; Crits-Christoph, Alexander; Matteson, Nathaniel L.; Zeller, Mark; Levy, Joshua I.; Wang, Jade C.; Hughes, Scott; Lee, Jungmin; Park, Heedo; Park, Man-Seong; Ching Zi Yan, Katherine; Tzer Pin Lin, Raymond; Mat Isa, Mohd Noor; Muhammad Noor, Yusuf; Vasylyeva, Tetyana I.; Garry, Robert F.; Holmes, Edward C.; Rambaut, Andrew; Suchard, Marc A.; Andersen, Kristian G.; Worobey, Michael; Wertheim, Joel O.
Understanding the circumstances that lead to pandemics is critical to their prevention. Here, we analyze the pattern and origin of genomic diversity of SARS-CoV-2 early in the COVID-19 pandemic. We show that the SARS-CoV-2 genomic diversity prior to February 2020 comprised only two distinct viral lineages—denoted A and B—with no transitional haplotypes. Novel phylodynamic rooting methods, coupled with epidemic simulations, indicate that these two lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses and occurred in late-November/early-December 2019 and no earlier than the beginning of November 2019, while the introduction of lineage A likely occurred within weeks of the first event. These findings define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. Hence, as with SARS-CoV-1 in 2002 and 2003, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.