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

Author(s):Show less -

Deng, Xianding ^{[1, 2]} ; Gu, Wei ^{[1, 2]} ; Federman, Scot ^{[1, 2]} ; Du Plessis, Louis ^[3] ; Pybus, Oliver G. ^{[3, 4]} ; Faria, Nuno R. ^{[3, 5]} ; Wang, Candace ^{[1, 2]} ; Yu, Guixia ^{[1, 2]} ; Bushnell, Brian ^[6] ; Pan, Chao-Yang ^[7] ; Guevara, Hugo ^[7] ; Sotomayor-Gonzalez, Alicia ^{[1, 2]} ; Zorn, Kelsey ^[8] ; Gopez, Allan ^[1] ; Servellita, Venice ^[1] ; Hsu, Elaine ^[1] ; Miller, Steve ^[1] ; Bedford, Trevor ^{[9, 10]} ; Greninger, Alexander L. ^{[9, 11]} ; Roychoudhury, Pavitra ^{[9, 11]} ; Starita, Lea M. ^{[12, 10]} ; Famulare, Michael ^[13] ; Chu, Helen Y. ^{[14, 10]} ; Shendure, Jay ^{[15, 11, 10]} ; Jerome, Keith R. ^{[9, 11]} ; Anderson, Catie ^[16] ; Gangavarapu, Karthik ^[16] ; Zeller, Mark ^[16] ; Spencer, Emily ^[16] ; Andersen, Kristian G. ^[16] ; MacCannell, Duncan ^[17] ; Paden, Clinton R. ^[17] ; Li, Yan ^[17] ; Zhang, Jing ^[17] ; Tong, Suxiang ^[17] ; Armstrong, Gregory ^[17] ; Morrow, Scott ^[18] ; Willis, Matthew ^[19] ; Matyas, Bela T. ^[12] ; Mase, Sundari ^[20] ; Kasirye, Olivia ^[21] ; Park, Maggie ^[22] ; Masinde, Godfred ^[23] ; Chan, Curtis ^[23] ; Yu, Alexander T. ^[7] ; Chai, Shua J. ^{[17, 7]} ; Villarino, Elsa ^[24] ; Bonin, Brandon ^[24] ; Wadford, Debra A. ^[7] ; Chiu, Charles Y. ^{[1, 2, 25]}

Affiliation:Show less -

^[1] Univ Calif San Francisco, Dept Lab Med, San Francisco, CA 94143 - USA

^[2] Univ Calif San Francisco, Abbott Viral Diagnost & Discovery Ctr, San Francisco, CA 94143 - USA

^[3] Univ Oxford, Dept Zool, Oxford - England

^[4] Royal Vet Coll, Dept Pathobiol & Populat Sci, London - England

^[5] Imperial Coll London, J IDEA, MRC Ctr Global Infect Dis Anal, London - England

^[6] Lawrence Berkeley Natl Lab, Berkeley, CA - USA

^[7] Calif Dept Publ Hlth, Richmond, CA - USA

^[8] Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA - USA

^[9] Fred Hutchinson Canc Res Ctr, 1124 Columbia St, Seattle, WA 98104 - USA

^[10] Brotman Baty Inst Precis Med, Seattle, WA - USA

^[11] Univ Washington, Dept Lab Med, Seattle, WA 98195 - USA

^[12] Univ Washington, Dept Genome Sci, Seattle, WA 98195 - USA

^[13] Inst Dis Modelling, Bellevue, WA - USA

^[14] Univ Washington, Dept Med, Seattle, WA - USA

^[15] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 - USA

^[16] Scripps Res Inst, Dept Immunol & Microbiol, La Jolla, CA 92037 - USA

^[17] US Ctr Dis Control & Prevent, Atlanta, GA - USA

^[18] San Mateo Cty Dept Publ Hlth, San Mateo, CA - USA

^[19] Marin Cty Div Publ Hlth, San Rafael, CA - USA

^[20] Sonoma Cty Dept Publ Hlth, Santa Rosa, CA - USA

^[21] Sacramento Cty Div Publ Hlth, Sacramento, CA - USA

^[22] San Joaquin Cty Dept Publ Hlth, Stockton, CA - USA

^[23] San Francisco Cty Dept Publ Hlth, San Francisco, CA - USA

^[24] Cty Santa Clara, Dept Publ Hlth, Santa Clara, CA - USA

^[25] Univ Calif San Francisco, Dept Med, Div Infect Dis, San Francisco, CA 94143 - USA

• Document type: Journal article
• Source: Science; v. 369, n. 6503, p. 582+, JUL 31 2020.
• Web of Science Citations: 4

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 tomid-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. (AU)

• FAPESP's process: 18/14389-0 - Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE)
• Grantee: Ester Cerdeira Sabino
• Support Opportunities: Research Projects - Thematic Grants