Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
Deng X., Gu W., Federman S., du Plessis L., Pybus OG., Faria NR., Wang C., Yu G., Bushnell B., Pan C-Y., Guevara H., Sotomayor-Gonzalez A., Zorn K., Gopez A., Servellita V., Hsu E., Miller S., Bedford T., Greninger AL., Roychoudhury P., Starita LM., Famulare M., Chu HY., Shendure J., Jerome KR., Anderson C., Gangavarapu K., Zeller M., Spencer E., Andersen KG., MacCannell D., Paden CR., Li Y., Zhang J., Tong S., Armstrong G., Morrow S., Willis M., Matyas BT., Mase S., Kasirye O., Park M., Masinde G., Chan C., Yu AT., Chai SJ., Villarino E., Bonin B., Wadford DA., Chiu CY.
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.