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

Deng X, Gu W, Federman S, Du Plessis L, Pybus O, Faria N, Wang C, Yu G, Pan C, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, Miller S, Bedford T, Greninger A, Roychoudhury P, Famulare M, Chu HY, Shendure J, Starita L, Anderson C, Gangavarapu K, Zeller M, Spencer E, Andersen K, MacCannell D, Tong S, Armstrong G, Paden C, Li Y, Zhang Y, Morrow S, Willis M, Matyas B, Mase S, Kasirye O, Park M, Chan C, Yu A, Chai S, Villarino E, Bonin B, Wadford D, Chiu CY. 2020. Science 369: 582-587.


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.