Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California

Elsa Villarino; Xianding Deng; Carol A Kemper; Michelle A Jorden; Brandon Bonin; Sarah L Rudman; George S Han; Guixia Yu; Candace Wang; Scot Federman; Brian Bushnell; CZB COVIDTracker Consortium; Debra A Wadford; Wen Lin; Ying Tao; Clinton R Paden; Julu Bhatnagar; Tara MacCannell; Suxiang Tong; Joshua Batson; Charles Y Chiu

doi:10.1093/infdis/jiab199

Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California

J Infect Dis. 2021 Jul 15;224(2):207-217. doi: 10.1093/infdis/jiab199.

Authors

Elsa Villarino¹, Xianding Deng^{2

3}, Carol A Kemper⁴, Michelle A Jorden⁵, Brandon Bonin¹, Sarah L Rudman¹, George S Han¹, Guixia Yu^{2

3}, Candace Wang^{2

3}, Scot Federman^{2

3}, Brian Bushnell⁶; CZB COVIDTracker Consortium; Debra A Wadford⁷, Wen Lin¹, Ying Tao⁸, Clinton R Paden⁸, Julu Bhatnagar⁸, Tara MacCannell¹, Suxiang Tong⁸, Joshua Batson^{9

10}, Charles Y Chiu^{2

3

11

12}

Affiliations

¹ County of Santa Clara Public Health Department, San Jose, California, USA.
² Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.
³ UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
⁴ El Camino Hospital, Mountain View and Los Gatos, California, USA.
⁵ Office of the Medical Examiner-Coroner, County of Santa Clara, San Jose, California, USA.
⁶ Lawrence Berkeley National Laboratory, Berkeley, California, USA.
⁷ Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, USA.
⁸ Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
⁹ Chan Zuckerberg Biohub, San Francisco, California, USA.
¹⁰ The Public Health Company, Goleta, California, USA.
¹¹ Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, California, USA.
¹² Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.

Abstract

We combined viral genome sequencing with contact tracing to investigate introduction and evolution of severe acute respiratory syndrome coronavirus 2 lineages in Santa Clara County, California, from 27 January to 21 March 2020. From 558 persons with coronavirus disease 2019, 101 genomes from 143 available clinical samples comprised 17 lineages, including SCC1 (n = 41), WA1 (n = 9; including the first 2 reported deaths in the United States, with postmortem diagnosis), D614G (n = 4), ancestral Wuhan Hu-1 (n = 21), and 13 others (n = 26). Public health intervention may have curtailed the persistence of lineages that appeared transiently during February and March. By August, only D614G lineages introduced after 21 March were circulating in Santa Clara County.

Keywords: COVID-19; D614G lineage; SARS-CoV-2; epidemiology; public health surveillance; viral evolution; viral whole-genome sequencing.

Publication types

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

MeSH terms

Adult
Aged
COVID-19 / epidemiology*
COVID-19 / prevention & control
COVID-19 / transmission*
California / epidemiology
Contact Tracing
Female
Genetic Variation
Genome, Viral / genetics
Genotype
Humans
Male
Middle Aged
Phylogeny
Risk Factors
SARS-CoV-2 / classification
SARS-CoV-2 / genetics*
Travel
Young Adult

Abstract

Publication types

MeSH terms

Grants and funding