• 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-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, and Charles Y Chiu.
• Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
• Science. 2020 Jul 31; 369 (6503): 582-587.

AbstractThe 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.Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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