A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

Xianding Deng; Wei Gu; Scot Federman; Louis Du Plessis; Oliver Pybus; Nuno Faria; Candace Wang; Guixia Yu; Chao-Yang Pan; Hugo Guevara; Alicia Sotomayor-Gonzalez; Kelsey Zorn; Allan Gopez; Venice Servellita; Elaine Hsu; Steve Miller; Trevor Bedford; Alexander Greninger; Pavitra Roychoudhury; Michael Famulare; Helen Y Chu; Jay Shendure; Lea Starita; Catie Anderson; Karthik Gangavarapu; Mark Zeller; Emily Spencer; Kristian Andersen; Duncan MacCannell; Suxiang Tong; Gregory Armstrong; Clinton Paden; Yan Li; Ying Zhang; Scott Morrow; Matthew Willis; Bela Matyas; Sundari Mase; Olivia Kasirye; Maggie Park; Curtis Chan; Alexander Yu; Shua Chai; Elsa Villarino; Brandon Bonin; Debra Wadford; Charles Y Chiu

The genomic epidemiology of the COVID-19 cases associated with community spread studied here do not show a predominant SARS-CoV-2 lineage circulating in Northern California. This epidemiological profile is distinct to that in Washington State, in which the vast majority of virus genomes sequenced to date belong to a single phylogenetic lineage, WA1 [Bedford, et al. 2020 ]. The WA1 lineage strains share common ancestry with an early imported lineage that seem to have established transmission in Washington State from January 2020. By contrast, in California, we conclude that multiple recent and unrelated introductions of COVID-19 into the state via different routes have occurred, giving rise to the diversity of virus lineages reported in this study, rather than cryptic transmission of a single pre-existing lineage among counties in California. We note that this does not exclude the possibility of cryptic transmission of multiple lineages in California, as the current level of sampling is not dense enough to estimate confidently the dates of the seeding events, nor the subsequent periods of cryptic transmission before a lineage was identified.