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

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; Charles Y. Chiu

doi:10.1126/science.abb9263

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

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, Charles Y. Chiu

Research output: Contribution to journal › Article › peer-review

173 Scopus citations

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.

Original language	English
Pages (from-to)	582-587
Number of pages	6
Journal	Science
Volume	369
Issue number	6503
DOIs	https://doi.org/10.1126/science.abb9263
State	Published - 31 Jul 2020
Externally published	Yes

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Deng, X., Gu, W., Federman, S., du Plessis, L., Pybus, O. G., Faria, N. R., Wang, C., Yu, G., Bushnell, B., Pan, C. Y., Guevara, H., Sotomayor-Gonzalez, A., Zorn, K., Gopez, A., Servellita, V., Hsu, E., Miller, S., Bedford, T., Greninger, A. L., ... Chiu, C. Y. (2020). Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science, 369(6503), 582-587. https://doi.org/10.1126/science.abb9263

@article{530155be67af424289ce24cf8c40459b,

title = "Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California",

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.",

author = "Xianding Deng and Wei Gu and Scot Federman and \{du Plessis\}, Louis and Pybus, \{Oliver G.\} and Faria, \{Nuno R.\} and Candace Wang and Guixia Yu and Brian Bushnell and Pan, \{Chao Yang\} and Hugo Guevara and Alicia Sotomayor-Gonzalez and Kelsey Zorn and Allan Gopez and Venice Servellita and Elaine Hsu and Steve Miller and Trevor Bedford and Greninger, \{Alexander L.\} and Pavitra Roychoudhury and Starita, \{Lea M.\} and Michael Famulare and Chu, \{Helen Y.\} and Jay Shendure and Jerome, \{Keith R.\} and Catie Anderson and Karthik Gangavarapu and Mark Zeller and Emily Spencer and Andersen, \{Kristian G.\} and Duncan MacCannell and Paden, \{Clinton R.\} and Yan Li and Jing Zhang and Suxiang Tong and Gregory Armstrong and Scott Morrow and Matthew Willis and Matyas, \{Bela T.\} and Sundari Mase and Olivia Kasirye and Maggie Park and Godfred Masinde and Curtis Chan and Yu, \{Alexander T.\} and Chai, \{Shua J.\} and Elsa Villarino and Brandon Bonin and Wadford, \{Debra A.\} and Chiu, \{Charles Y.\}",

year = "2020",

month = jul,

day = "31",

doi = "10.1126/science.abb9263",

language = "English",

volume = "369",

pages = "582--587",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6503",

}

Deng, X, Gu, W, Federman, S, du Plessis, L, Pybus, OG, Faria, NR, Wang, C, Yu, G, Bushnell, B, Pan, CY, Guevara, H, Sotomayor-Gonzalez, A, Zorn, K, Gopez, A, Servellita, V, Hsu, E, Miller, S, Bedford, T, Greninger, AL, Roychoudhury, P, Starita, LM, Famulare, M, Chu, HY, Shendure, J, Jerome, KR, Anderson, C, Gangavarapu, K, Zeller, M, Spencer, E, Andersen, KG, MacCannell, D, Paden, CR, Li, Y, Zhang, J, Tong, S, Armstrong, G, Morrow, S, Willis, M, Matyas, BT, Mase, S, Kasirye, O, Park, M, Masinde, G, Chan, C, Yu, AT, Chai, SJ, Villarino, E, Bonin, B, Wadford, DA & Chiu, CY 2020, 'Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California', Science, vol. 369, no. 6503, pp. 582-587. https://doi.org/10.1126/science.abb9263

TY - JOUR

T1 - Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

AU - Deng, Xianding

AU - Gu, Wei

AU - Federman, Scot

AU - du Plessis, Louis

AU - Pybus, Oliver G.

AU - Faria, Nuno R.

AU - Wang, Candace

AU - Yu, Guixia

AU - Bushnell, Brian

AU - Pan, Chao Yang

AU - Guevara, Hugo

AU - Sotomayor-Gonzalez, Alicia

AU - Zorn, Kelsey

AU - Gopez, Allan

AU - Servellita, Venice

AU - Hsu, Elaine

AU - Miller, Steve

AU - Bedford, Trevor

AU - Greninger, Alexander L.

AU - Roychoudhury, Pavitra

AU - Starita, Lea M.

AU - Famulare, Michael

AU - Chu, Helen Y.

AU - Shendure, Jay

AU - Jerome, Keith R.

AU - Anderson, Catie

AU - Gangavarapu, Karthik

AU - Zeller, Mark

AU - Spencer, Emily

AU - Andersen, Kristian G.

AU - MacCannell, Duncan

AU - Paden, Clinton R.

AU - Li, Yan

AU - Zhang, Jing

AU - Tong, Suxiang

AU - Armstrong, Gregory

AU - Morrow, Scott

AU - Willis, Matthew

AU - Matyas, Bela T.

AU - Mase, Sundari

AU - Kasirye, Olivia

AU - Park, Maggie

AU - Masinde, Godfred

AU - Chan, Curtis

AU - Yu, Alexander T.

AU - Chai, Shua J.

AU - Villarino, Elsa

AU - Bonin, Brandon

AU - Wadford, Debra A.

AU - Chiu, Charles Y.

PY - 2020/7/31

Y1 - 2020/7/31

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85089127633

U2 - 10.1126/science.abb9263

DO - 10.1126/science.abb9263

M3 - Article

C2 - 32513865

AN - SCOPUS:85089127633

SN - 0036-8075

VL - 369

SP - 582

EP - 587

JO - Science

JF - Science

IS - 6503

ER -

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

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