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

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.

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.