The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

• Published in: Science (American Association for the Advancement of Science) Vol. 377; no. 6609; pp. 960 - 966
• Main Authors: Pekar, Jonathan E, Magee, Andrew, Parker, Edyth, Moshiri, Niema, Izhikevich, Katherine, Havens, Jennifer L, Gangavarapu, Karthik, Malpica Serrano, Lorena Mariana, 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, Lin, Raymond Tzer Pin, Mat Isa, Mohd Noor, Noor, Yusuf Muhammad, Vasylyeva, Tetyana I, Garry, Robert F, Holmes, Edward C, Rambaut, Andrew, Suchard, Marc A, Andersen, Kristian G, Worobey, Michael, Wertheim, Joel O
• Format: Journal Article
• Language: English
• Published: United States The American Association for the Advancement of Science 26.08.2022; American Association for the Advancement of Science
• Subjects: Animals; Computer Simulation; Coronaviruses; COVID-19 - epidemiology; COVID-19 - transmission; COVID-19 - virology; Epidemiology; Evolution; Genetic Variation; Genomics - methods; Humans; Molecular Epidemiology; Origins; Pandemics; Phylogeny; SARS-CoV-2 - classification; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Seafood; Severe acute respiratory syndrome coronavirus 2; Viral diseases; Viral Zoonoses - epidemiology; Viral Zoonoses - virology; Viruses; Wild animals; Zoonoses; China
• ISSN: 0036-8075; 1095-9203; 1095-9203
• DOI: 10.1126/science.abp8337

Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed 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 to 8 December), and 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 before 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.