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

Science. 2020 Jul 31;369(6503):582-587. doi: 10.1126/science.abb9263. Epub 2020 Jun 8.

Authors

Xianding Deng^#^{1

2}, Wei Gu^#^{1

2}, Scot Federman^#^{1

2}, Louis du Plessis^#³, Oliver G Pybus^{3

4}, Nuno R Faria^{3

5}, Candace Wang^{1

2}, Guixia Yu^{1

2}, Brian Bushnell⁶, Chao-Yang Pan⁷, Hugo Guevara⁷, Alicia Sotomayor-Gonzalez^{1

2}, Kelsey Zorn⁸, Allan Gopez¹, Venice Servellita¹, Elaine Hsu¹, Steve Miller¹, Trevor Bedford^{9

10}, Alexander L Greninger^{9

11}, Pavitra Roychoudhury^{9

11}, Lea M Starita^{10

12}, Michael Famulare¹³, Helen Y Chu^{10

14}, Jay Shendure^{10

11

15}, Keith R Jerome^{9

11}, Catie Anderson¹⁶, Karthik Gangavarapu¹⁶, Mark Zeller¹⁶, Emily Spencer¹⁶, Kristian G Andersen¹⁶, Duncan MacCannell¹⁷, Clinton R Paden¹⁷, Yan Li¹⁷, Jing Zhang¹⁷, Suxiang Tong¹⁷, Gregory Armstrong¹⁷, Scott Morrow¹⁸, Matthew Willis¹⁹, Bela T Matyas²⁰, Sundari Mase²¹, Olivia Kasirye²², Maggie Park²³, Godfred Masinde²⁴, Curtis Chan²⁴, Alexander T Yu⁷, Shua J Chai^{7

17}, Elsa Villarino²⁵, Brandon Bonin²⁵, Debra A Wadford⁷, Charles Y Chiu^{26

2

27}

Affiliations

¹ Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
² UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
³ Department of Zoology, University of Oxford, Oxford, UK.
⁴ Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
⁵ MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
⁶ Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁷ California Department of Public Health, Richmond, CA, USA.
⁸ Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
⁹ Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
¹⁰ Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
¹¹ Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
¹² Department of Genome Sciences, University of Washington, Seattle, WA, USA.
¹³ Institute for Disease Modeling, Bellevue, WA, USA.
¹⁴ Department of Medicine, University of Washington, Seattle, WA, USA.
¹⁵ Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
¹⁶ Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
¹⁷ U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.
¹⁸ San Mateo County Department of Public Health, San Mateo, CA, USA.
¹⁹ Marin County Division of Public Health, San Rafael, CA, USA.
²⁰ Solano County Department of Public Health, Fairfield, CA, USA.
²¹ Sonoma County Department of Public Health, Santa Rosa, CA, USA.
²² Sacramento County Division of Public Health, Sacramento, CA, USA.
²³ San Joaquin County Department of Public Health, Stockton, CA, USA.
²⁴ San Francisco County Department of Public Health, San Francisco, CA, USA.
²⁵ County of Santa Clara, Public Health Department, Santa Clara, CA, USA.
²⁶ Department of Laboratory Medicine, University of California, San Francisco, CA, USA. [email protected].
²⁷ Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.

^# Contributed equally.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Betacoronavirus / genetics*
COVID-19
California / epidemiology
Coronavirus Infections / epidemiology*
Coronavirus Infections / transmission
Coronavirus Infections / virology*
Epidemiological Monitoring
Genome, Viral*
Humans
Pandemics
Phylogeny*
Pneumonia, Viral / epidemiology*
Pneumonia, Viral / transmission
Pneumonia, Viral / virology*
SARS-CoV-2
Sequence Alignment
Ships
Tourismus
Washington

Abstract

Publication types

MeSH terms

Grants and funding