Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic

Key Points Question During the early phase of the outbreak, what were the transmission routes and genomic characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread in Los Angeles, California? Findings This case series of 192 patients found that 82% of SARS-CoV-2 isolates from Los Angeles shared closest similarity to those originating in Europe vs those from Asia (15%). Using the variation signature of the viral genomes, 2 main clusters were identified, with the top variants sharing genomic features from European SARS-CoV-2 isolates, and several subclusters of SARS-CoV-2 outbreaks represented trackable community spread in Los Angeles. Meaning These findings suggest that SARS-CoV-2 genomes in Los Angeles were predominantly related to the isolates originating from Europe, which are similar to viral strain distributions in New York, New York; a smaller subgroup of SARS-CoV-2 genomes shared similarities to those from originating from Asia, indicating multiple sources of viral introduction within the Los Angeles community.