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Open Access Publications from the University of California

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

  • Author(s): Deng, Xianding
  • Gu, Wei
  • Federman, Scot
  • du Plessis, Louis
  • Pybus, Oliver G
  • Faria, Nuno
  • Wang, Candace
  • Yu, Guixia
  • Bushnell, Brian
  • Pan, Chao-Yang
  • Guevara, Hugo
  • Sotomayor-Gonzalez, Alicia
  • Zorn, Kelsey
  • Gopez, Allan
  • Servellita, Venice
  • Hsu, Elaine
  • Miller, Steve
  • Bedford, Trevor
  • Greninger, Alexander L
  • Roychoudhury, Pavitra
  • Starita, Lea M
  • Famulare, Michael
  • Chu, Helen Y
  • Shendure, Jay
  • Jerome, Keith R
  • Anderson, Catie
  • Gangavarapu, Karthik
  • Zeller, Mark
  • Spencer, Emily
  • Andersen, Kristian G
  • MacCannell, Duncan
  • Paden, Clinton R
  • Li, Yan
  • Zhang, Jing
  • Tong, Suxiang
  • Armstrong, Gregory
  • Morrow, Scott
  • Willis, Matthew
  • Matyas, Bela T
  • Mase, Sundari
  • Kasirye, Olivia
  • Park, Maggie
  • Masinde, Godfred
  • Chan, Curtis
  • Yu, Alexander T
  • Chai, Shua J
  • Villarino, Elsa
  • Bonin, Brandon
  • Wadford, Debra A
  • Chiu, Charles Y
  • et al.

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, with >52,000 cases in California as of May 4, 2020. Here we investigate the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning 9 counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least 7 different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington State, with lack of a predominant lineage and limited transmission between communities. Lineages associated with outbreak clusters in 2 counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain SARS-CoV-2 spread in California and other states.

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