Author: 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
Title: A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage Document date: 2020_3_30
ID: cbc98t7x_6
Snippet: We generated virus genomes of SARS-CoV-2 lineages in California from nasal swab samples from 29 patients, available through the University of California San Francisco (UCSF) hospital, the Santa Clara County Public Health Department, and the California Department of Public Health ( Figure 1A and Table S2 ). Presumptive positive cases were confirmed to be SARS-CoV-2 positive by testing using a CDC assay approved by the FDA EUA (Emergency Use Author.....
Document: We generated virus genomes of SARS-CoV-2 lineages in California from nasal swab samples from 29 patients, available through the University of California San Francisco (UCSF) hospital, the Santa Clara County Public Health Department, and the California Department of Public Health ( Figure 1A and Table S2 ). Presumptive positive cases were confirmed to be SARS-CoV-2 positive by testing using a CDC assay approved by the FDA EUA (Emergency Use Authorization) on February 4th, 2020 (14) . Samples to be sequenced were selected for broad representation across different counties and association with known outbreaks. The 29 infected patients spanned 9 counties in Northern California ( Figure 1B ) and included (i) 9 samples airlifted from the Grand Princess cruise ship, during its excursions from San Francisco to Mexico and Hawaii in February and March 2020, (ii) 3 samples from a Solano County cluster, including the first reported case of community transmission in the United States, and (iii) 5 patients from a Santa Clara County cluster associated with workspace transmission. Fourteen of the 29 patients did not have a source of transmission that could be readily identified by travel history or epidemiological investigation.
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