Monitoring shared variation in genomes of SARS-CoV-2 among persons with COVID-19 with and without vaccination in Northern California

We are studying the genomes of SARS-CoV-2 in persons with COVID-19 with and without vaccination to identify and describe variants circulating within our patients, including variants of concern (such as Delta or Omicron. We also are assessing which shared genomic variations are associated with a greater risk for infection (symptomatic and asymptomatic) and severe outcomes (such as hospitalization, intensive care unit use, and death), and whether certain subpopulations, such as those with certain medical comorbidities, might be at a greater risk for infection and severe outcomes from identified variants. Through modeling, we are investigating whether and which mutations result in decreased vaccine effectiveness for prevention of infection and severe outcomes, and which may require a booster or an updated vaccine.

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