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

Xianding Deng(University of California, San Francisco), Wei Gu(University of California, San Francisco), Scot Federman(University of California, San Francisco), Louis du Plessis(University of Oxford), Oliver G. Pybus(Royal Veterinary College), Nuno R. Faria(University of Oxford), Candace Wang(University of California, San Francisco), Guixia Yu(University of California, San Francisco), Brian Bushnell(Lawrence Berkeley National Laboratory), Chao‐Yang Pan(California Department of Public Health), Hugo Guevara(California Department of Public Health), Alicia Sotomayor-González(University of California, San Francisco), Kelsey C. Zorn(University of California, San Francisco), Allan Gopez(University of California, San Francisco), Venice Servellita(University of California, San Francisco), Elaine Hsu(University of California, San Francisco), Steve Miller(University of California, San Francisco), Trevor Bedford(Fred Hutch Cancer Center), Alexander L. Greninger(University of Washington), Pavitra Roychoudhury(University of Washington), Lea M. Starita(University of Washington), Michael Famulare(Bellevue Hospital Center), Helen Y. Chu(University of Washington), Jay Shendure(Howard Hughes Medical Institute), Keith R. Jerome(University of Washington), Catie Anderson(Scripps Research Institute), Karthik Gangavarapu(Scripps Research Institute), Mark Zeller(Scripps Research Institute), Emily Spencer(Scripps Research Institute), Kristian G. Andersen(Scripps Research Institute), Duncan MacCannell(Centers for Disease Control and Prevention), Clinton R. Paden(Centers for Disease Control and Prevention), Yan Li(Centers for Disease Control and Prevention), Jing Zhang(Centers for Disease Control and Prevention), Suxiang Tong(Centers for Disease Control and Prevention), Gregory L. Armstrong(Centers for Disease Control and Prevention), Scott Morrow(San Mateo County Health System), Matthew Willis(Marin Health and Human Services), Bela T. Matyas(Solano Community College), Sundari Mase(Sonoma County Library), Olivia Kasirye(California Department of Public Health), Maggie Park(San Joaquin County Public Health Services), Godfred Masinde(San Francisco Department of Public Health), Curtis Chan(San Francisco Department of Public Health), Alexander T. Yu(California Department of Public Health), Shua J. Chai(Centers for Disease Control and Prevention), Elsa Villarino(Santa Clara County Behavioral Health Services), Brandon Bonin(Santa Clara County Behavioral Health Services), Debra A. Wadford(California Department of Public Health), Charles Y. Chiu(University of California, San Francisco)
Science
June 8, 2020
10.1126/science.abb9263
Cited by 308Open Access
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Abstract

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.

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