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

ABSTRACT: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, with >52,000 cases in California as of May 4, 2020. Here we investigate the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning 9 counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least 7 different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington State, with lack of a predominant lineage and limited transmission between communities. Lineages associated with outbreak clusters in 2 counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain SARS-CoV-2 spread in California and other states.

SUBMITTER: Deng X 

PROVIDER: S-EPMC7286545 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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

Deng Xianding X   Gu Wei W   Federman Scot S   du Plessis Louis L   Pybus Oliver G OG   Faria Nuno R NR   Wang Candace C   Yu Guixia G   Bushnell Brian B   Pan Chao-Yang CY   Guevara Hugo H   Sotomayor-Gonzalez Alicia A   Zorn Kelsey K   Gopez Allan A   Servellita Venice V   Hsu Elaine E   Miller Steve S   Bedford Trevor T   Greninger Alexander L AL   Roychoudhury Pavitra P   Starita Lea M LM   Famulare Michael M   Chu Helen Y HY   Shendure Jay J   Jerome Keith R KR   Anderson Catie C   Gangavarapu Karthik K   Zeller Mark M   Spencer Emily E   Andersen Kristian G KG   MacCannell Duncan D   Paden Clinton R CR   Li Yan Y   Zhang Jing J   Tong Suxiang S   Armstrong Gregory G   Morrow Scott S   Willis Matthew M   Matyas Bela T BT   Mase Sundari S   Kasirye Olivia O   Park Maggie M   Masinde Godfred G   Chan Curtis C   Yu Alexander T AT   Chai Shua J SJ   Villarino Elsa E   Bonin Brandon B   Wadford Debra A DA   Chiu Charles Y CY  

Science (New York, N.Y.) 20200608 6503

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 linea  ...[more]

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