Genomic Suirveillance Reveals Multiple Introductions of SARS-CoV-2 into Northern California

 


The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, with >52,000 cases in California as May 4, 2020. Here we investigate the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 pantients spanning 9 counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least 7 different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington State, with lack of predominant lineage and limited transmission  between communities. Lineages associated with outbreak clusters in 2 counties were defined by a single base substitution in the viral genome. these findings support contact tracing, social distancing, and travel restrictions to contain SARS-CoV-2 spread in California and other states.

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