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 co-clustering of the lineages from the Grand Princess cruise ship and those from several Northern California counties with community-transmitted cases in Washington State suggests an established lineage of SARS-CoV-2 in the USA. Notably, the WA1 lineage has been recently identified in COVID-19 cases in Illinois, Minnesota, Connecticut, and Utah. The early date and basal phylogenetic position of the WA1 lineage makes it likely that the direction of dissemination was from Washington State to other states; however that conclusion could change if further genomic sampling in the US revealed substantial levels of virus genetic diversity. SARS-CoV-2 mutates more slowly than many other human RNA viruses, on the order of 1 to 2 SNV mutations a month across its ~29 kB genome (20) , as it contains a nonstructural gene with proofreading activity (21). Despite this, the WA1 lineage of SARS-CoV-2 is readily identifiable with 3 key SNVs, C8782T, C18060T, and T28144C (Figure 3 ) which, at this stage in the epidemic, are distinct from other SARS-CoV-2 lineages.