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

Two out of the 29 individuals examined in this study (UC12 and UC29) had COVID-19 infections associated with international travel or exposure to travelers. UC12 was a resident of San Mateo County with a travel history to Switzerland. The genome from UC12 fell within a large lineage containing many sequences from European residents or travelers from Europe and therefore it is likely the infection was acquired there. The sequence from individual UC29 (MT027062 is from the same patient) was a returning traveler from China and has an identical COVID-19 sequence to a household contact (MT027063). Their viral genomes were more closely related to ancestral lineages from China. Interestingly, three further genomes (UC24, UC26 and UC27) also grouped within a viral lineage with widespread circulation in Europe. Individual UC27 was diagnosed after returning from a New York trip, raising the possibility of interstate transmission. Individual UC26 also reported domestic travel, while local resident UC24 had no known travel history, illustrating the existence of undetected virus transmission in the community.