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California COVID-19 Epidemic Driven by Multiple Viral Strains

SARS-CoV-2 arrived in Northern California through a complicated series of introductions internationally and between states.

As more information about SARS-CoV-2 emerges, mediators of pandemic outcomes not associated with public health measures can be better controlled for. Viral strain is a key biological variable, among others, in understanding why regions with similar policies have not always had parallel outcomes during the coronavirus disease 2019 (COVID-19) crisis.

Analysis of SARS-CoV-2 genomes from a small cohort of patients in California, published by investigators in Science, show that the virus arrived in Northern California through a complicated series of introductions internationally and between states.

Genomic surveillance was conducted through a new method called Metagenomic Sequencing with Spiked Primer Enrichment (MSSPE).

“Here we used this method and/or tiling multiplex PCR to recover viral genomes from COVID-19 patients in Northern California and perform phylogenetic analyses to better understand the genetic diversity of SARS-CoV-2 in the US and the nature of transmission of virus lineages in the community,” study authors wrote.

Insights were able to be gathered from a small group of 54 COVID-19 patients, despite California featuring at least 52,000 cases as of June. A total of 62 respiratory swabs were screened from hospitals at 8 county public health departments as well as the state department of public health and university system.

SARS-CoV-2 genomes of greater than 65% coverage were able to be recovered from 36 patients. The 36 genomes were collected from January 29 to March 20, 2020.

Authors reported that relevant cases spanned 9 counties in Northern California. There were 11 samples collected from the Grand Princess cruise ship, 3 samples from a Solano County cluster that included the first reported case of community transmission in the US with subsequent spread to 2 health care workers, 7 samples from Santa Clara County from a local outbreak cluster associated with workspace transmission, 3 samples from patients who contracted the infection from a sick contacts, 5 samples related to domestic or international travel, and 7 samples from additional cases of community transmission.

Sequencing and contextualization with other publicly accessible genomes showed that viral strains included lineages circulating in New York and Europe which are related to early lineages from China.

“Robust insights into COVID-19 transmission are achievable if virus genomic diversity is combined and jointly interpreted with detailed epidemiological case data," the authors said in a press release.

VIDEO: Adam Brufsky, MD, medical oncologist, UPMC Hillman Cancer Center, discusses the potential for several SARS-CoV-2 viral strains in the COVID-19 outbreak.