Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
Xianding DengWei GuScot FedermanLouis du PlessisOliver George PybusNuno Rodrigues FariaCandace WangGuixia YuBrian BushnellChao-Yang PanHugo GuevaraAlicia Sotomayor GonzalezKelsey C ZornAllan GopezVenice ServellitaElaine HsuSteve MillerTrevor Felix BedfordAlexander L GreningerPavitra RoychoudhuryJoshua T SchifferMichael FamulareHelen Y ChuJay ShendureKeith R JeromeCatie AndersonKarthik GangavarapuMark ZellerEmily SpencerKristian G AndersenDuncan R MacCannellClinton R PadenYan LiJing ZhangSuxiang TongGregory ArmstrongScott MorrowMatthew WillisBela T MatyasSundari MaseOlivia KasiryeMaggie ParkGodfred MasindeCurtis ChanAlexander Tin Han YuShua J ChaiElsa VillarinoBrandon BoninDebra A WadfordCharles Y ChiuPublished in: Science (New York, N.Y.) (2020)
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.