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

• DOI: 10.1126/science.abb9263
• Publication Date: 2020-06-08T19:05:24Z
• Authors: Xianding Deng; Wei Gu; Scot Federman; Louis du Plessis; Oliver G. Pybus; Nuno R. Faria; Candace Wang; Guixia Yu; Brian Bushnell; Chao-Yang Pan; Hugo Guevara; Alicia Sotomayor-...; Kelsey Zorn; Allan Gopez; Venice Servellita; Elaine Hsu; Steve Miller; Trevor Bedford; Alexander L. Gren...; 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
• Keywords: 2019-20 coronavirus outbreak; Betacoronavirus; Pandemic; Sars virus; Coronavirus Infections

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology SARS-CoV-2 Northern from late January to mid-March 2020, using samples 36 patients spanning nine counties and Grand Princess cruise ship. Phylogenetic analyses revealed cryptic introduction at least seven different lineages into California, including epidemic WA1 strains associated Washington state, lack a predominant lineage limited transmission among communities. Lineages outbreak clusters two were defined single base substitution viral genome. These findings support contact tracing, social distancing, travel restrictions contain other states.