Timing the SARS-CoV-2 index case in Hubei province

Science. 2021 Apr 23;372(6540):412-417. doi: 10.1126/science.abf8003. Epub 2021 Mar 18.


Understanding when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We used a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated before the time of the most recent common ancestor of all sequenced SARS-CoV-2 genomes. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province, China. By characterizing the likely dynamics of the virus before it was discovered, we show that more than two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • COVID-19 / epidemiology*
  • COVID-19 / transmission
  • COVID-19 / virology*
  • China / epidemiology
  • Computer Simulation
  • Evolution, Molecular
  • Genetic Fitness
  • Genome, Viral*
  • Humans
  • Models, Theoretical
  • Pandemics*
  • Phylogeny
  • Retrospective Studies
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / physiology*
  • Viral Zoonoses

Associated data

  • Dryad/10.5061/dryad.4f4qrfjbm