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

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…

• NS
  National Science Foundation

  Awards: U19AI135995, NSF-2028040, 2028040
• UD
  U.S. Department of Health and Human Services

  Award: 75N93021C00015
• GS
  Gilead Sciences
• WT
  Wellcome Trust

  Awards: 206298, 725422-ReservoirDOCS
• NR
  National Research Foundation
• NR
  National Research Foundation of Korea

  Award: NRF-2017M3A9E4061995
• NI
  National Institutes of Health

  Awards: OT2HL158260, R01AI153044, UL1TR002550, U01AI151812, U54HG007480, R01AI136056, U54CA260581, R01AI132244, U19AI142790, U19AI135995, 75N93021C00015, T15LM011271
• CF
  Centers for Disease Control and Prevention

  Award: 6NU50CK000517-01-07
• NI
  National Institute of Allergy and Infectious Diseases

  Awards: UL1TR002550, R01AI136056, R01AI135992, U19AI142790, U01AI151812, U54HG007480, R01AI153044, U19AI135995, 75N93021C00015
• EA
  European and Developing Countries Clinical Trials Partnership