Science ( IF 41.845 ) Pub Date : 2020-07-31 , DOI: 10.1126/science.abb9263 Xianding Deng,Wei Gu,Scot Federman,Louis du Plessis,Oliver G Pybus,Nuno Faria,Candace Wang,Guixia Yu,Brian Bushnell,Chao-Yang Pan,Hugo Guevara,Alicia Sotomayor-Gonzalez,Kelsey Zorn,Allan Gopez,Venice Servellita,Elaine Hsu,Steve Miller,Trevor Bedford,Alexander L Greninger,Pavitra Roychoudhury,Lea M Starita,Michael Famulare,Helen Y Chu,Jay Shendure,Keith R Jerome,Catie Anderson,Karthik Gangavarapu,Mark Zeller,Emily Spencer,Kristian G Andersen,Duncan MacCannell,Clinton R Paden,Yan Li,Jing Zhang,Suxiang Tong,Gregory Armstrong,Scott Morrow,Matthew Willis,Bela T Matyas,Sundari Mase,Olivia Kasirye,Maggie Park,Godfred Masinde,Curtis Chan,Alexander T Yu,Shua J Chai,Elsa Villarino,Brandon Bonin,Debra A Wadford,Charles Y Chiu
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.