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

is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.03. 27.20044925 doi: medRxiv preprint In Santa Clara County, cases with onset dates within two weeks of each other were associated with a large facility with multiple employers, large areas of shared space, and heavy pedestrian traffic. Out of five sequenced cases from this outbreak cluster (UC13 to UC17), three formed a distinct cluster by phylogenetic analysis (UC14 was an employee at the facility, while UC16 and UC17 were family members living in the same residence), indicating likely household transmission (Figures 2B and 3) . Notably, the genome from a Solano county resident (UC21) was also grouped into this cluster, suggesting possible circulation of a virus lineage between different counties. An active investigation regarding a putative epidemiologic link involving UC21 and individuals in the Santa Clara County cluster had been initiated prior to the genomic analyses and is ongoing at the time of publication. Two other workers (UC13 and UC15) also operated at the same building and had no direct contact with UC14; all three had different employers and no known social contact with each other. Consistent with this epidemiological data, the genomes (UC13-15) from the three workers in the large facility are distinct from each other (i.e. no identifiable shared SNV). Several possible scenarios could give rise to this observation, including the prospect that more than one virus lineage was introduced into the building via different events or the workers were infected as a result of community transmission.