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
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Abstract	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.
AbstractList	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.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. 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.
Author	Shendure, Jay Gu, Wei Servellita, Venice du Plessis, Louis Bushnell, Brian Willis, Matthew Mase, Sundari Matyas, Bela T Andersen, Kristian G Wang, Candace Zhang, Jing Armstrong, Gregory Chu, Helen Y Federman, Scot Pan, Chao-Yang Faria, Nuno R MacCannell, Duncan Chiu, Charles Y Anderson, Catie Tong, Suxiang Famulare, Michael Hsu, Elaine Jerome, Keith R Masinde, Godfred Kasirye, Olivia Deng, Xianding Sotomayor-Gonzalez, Alicia Wadford, Debra A Zeller, Mark Guevara, Hugo Miller, Steve Gangavarapu, Karthik Paden, Clinton R Pybus, Oliver G Zorn, Kelsey Bonin, Brandon Villarino, Elsa Park, Maggie Starita, Lea M Yu, Guixia Yu, Alexander T Greninger, Alexander L Chai, Shua J Li, Yan Morrow, Scott Roychoudhury, Pavitra Bedford, Trevor Gopez, Allan Chan, Curtis Spencer, Emily
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References	32511579 - medRxiv. 2020 Mar 30:2020.03.27.20044925. doi: 10.1101/2020.03.27.20044925.
References_xml	– reference: 32511579 - medRxiv. 2020 Mar 30:2020.03.27.20044925. doi: 10.1101/2020.03.27.20044925.
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Snippet	The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000...
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SubjectTerms	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
Title	Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California
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