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

Author:

Deng Xianding12ORCID,Gu Wei12ORCID,Federman Scot12ORCID,du Plessis Louis3ORCID,Pybus Oliver G.34ORCID,Faria Nuno R.35ORCID,Wang Candace12,Yu Guixia12ORCID,Bushnell Brian6ORCID,Pan Chao-Yang7,Guevara Hugo7,Sotomayor-Gonzalez Alicia12ORCID,Zorn Kelsey8ORCID,Gopez Allan1,Servellita Venice1,Hsu Elaine1,Miller Steve1ORCID,Bedford Trevor910ORCID,Greninger Alexander L.911ORCID,Roychoudhury Pavitra911ORCID,Starita Lea M.1012ORCID,Famulare Michael13ORCID,Chu Helen Y.1014,Shendure Jay101115ORCID,Jerome Keith R.911ORCID,Anderson Catie16,Gangavarapu Karthik16,Zeller Mark16,Spencer Emily16,Andersen Kristian G.16ORCID,MacCannell Duncan17ORCID,Paden Clinton R.17ORCID,Li Yan17,Zhang Jing17,Tong Suxiang17ORCID,Armstrong Gregory17,Morrow Scott18ORCID,Willis Matthew19,Matyas Bela T.20,Mase Sundari21,Kasirye Olivia22ORCID,Park Maggie23ORCID,Masinde Godfred24,Chan Curtis24,Yu Alexander T.7ORCID,Chai Shua J.717ORCID,Villarino Elsa25,Bonin Brandon25,Wadford Debra A.7ORCID,Chiu Charles Y.1226ORCID

Affiliation:

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 Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.

Abstract

Epidemic in Northern California Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks is valuable for tracing the sources and perhaps for drawing lessons about preventing future outbreaks. Genomic analysis by Deng et al. revealed that Northern California experienced a complex series of introductions of the virus, deriving not only from state-to-state transmission but also from international travel by air and ship. The study highlights the importance of being able to rapidly test and trace contacts of positive cases to enable swift control. Science , this issue p. 582

Funder

National Institutes of Health

National Institute of Allergy and Infectious Diseases

Medical Research Council

Wellcome Trust Centre for Mitochondrial Research

Charles and Helen Schwab Foundation

Burroughs-Wellcome CAMS Award

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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