The authors were interested in the genomic epidemiology of SARS-CoV-2 in Northern California between late January to mid-March 2020. They used samples from 36 patients across nine counties and the Grand Princess cruise ship. Phylogenetic analyses identified that at least seven different SARS-CoV-2 lineages were cryptically introduced into California, including the epidemic WA1 strains previously associated with Washington State. There was no predominant lineage, indicating limited transmission between communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution. Therefore these findings can be used to support contact tracing, social distancing and travel restrictions to contain SARS-CoV-2 spread in California and other states.
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