An integrated genomic surveillance platform reveals multiple introductions and accelerating localization of SARS-CoV-2 into California, USA and worldwide countries

The Children's Hospital, Los Angeles (CHLA) COVID-19 Analysis Research Database (CARD) (https://covid19.cpmbiodev.net/) is a comprehensive genomic resource of SARS-CoV-2 viral genomes and associated meta-data of over 80,000 (as of August 13, 2020) isolates collected from global sequencing laboratories and the Center for Personalized Medicine (CPM) at CHLA. A Virus Genome Tracker accepts virus genome sequence and places the new viral isolate within the global or USA phylogenetic contexts based upon variant and haplotype comparisons to trace the transmission for genomic surveillance.
By haplotype analysis of 4,200 California isolates, 6,356 USA isolates, and over 80,000 global isolates, we identified a pattern of strongly localized outbreaks at the city-, state-, and country-levels, and temporal transmissions. Phylogenetic analyses revealed the cryptic introduction of multiple SARS-CoV-2 lineages into California and Los Angeles, deriving from state-to-state transmission, and from international travel by air and ship. The majority of sequences Orange County isolates formed distinct outbreak clusters whose haplotypes were different from isolates of the neighboring Los Angeles. From the 50,000 global isolates, 22,171 (45.8%) isolates carried country-private haplotypes. The percentage were 28.2-29.6% in January to March, and rapidly increased to 46.4% and 59.6% in April and May, co-occurring with global travel restrictions.