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

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...

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Published in:Science (American Association for the Advancement of Science) Vol. 369; no. 6503; p. 582
Main Authors: Deng, Xianding, Gu, Wei, Federman, Scot, du Plessis, Louis, Pybus, Oliver G, Faria, Nuno R, 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
Format: Journal Article
Language:English
Published: United States 31.07.2020
Subjects:
Betacoronavirus - genetics
California - epidemiology
Coronavirus Infections - epidemiology
Coronavirus Infections - transmission
Coronavirus Infections - virology
COVID-19
Epidemiological Monitoring
Genome, Viral
Humans
Pandemics
Phylogeny
Pneumonia, Viral - epidemiology
Pneumonia, Viral - transmission
Pneumonia, Viral - virology
SARS-CoV-2
Sequence Alignment
Ships
Travel
Washington
Washington
California
ISSN:1095-9203, 1095-9203
Online Access:Get more information
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Summary: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.
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ISSN:1095-9203
1095-9203
DOI:10.1126/science.abb9263