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, View ORCID ProfileKelsey Zorn, Allan Gopez, Venice Servellita, Elaine Hsu, Steve Miller, Trevor Bedford, Alexander Greninger, View ORCID ProfilePavitra 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, View ORCID ProfileCharles Y Chiu
doi: https://doi.org/10.1101/2020.03.27.2004492
Abstract
The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.
