Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

Science. 2020 Jul 31;369(6503):582-587. doi: 10.1126/science.abb9263. Epub 2020 Jun 8.


The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.

Publication types

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

MeSH terms

  • Betacoronavirus / genetics*
  • COVID-19
  • California / epidemiology
  • Coronavirus Infections / epidemiology*
  • Coronavirus Infections / transmission
  • Coronavirus Infections / virology*
  • Epidemiological Monitoring
  • Genome, Viral*
  • Humans
  • Pandemics
  • Phylogeny*
  • Pneumonia, Viral / epidemiology*
  • Pneumonia, Viral / transmission
  • Pneumonia, Viral / virology*
  • SARS-CoV-2
  • Sequence Alignment
  • Ships
  • Travel
  • Washington