Surveillance and epidemiology of SARS-CoV-2 viral variants in the United States, May-October 2021 (Preprint)

UNSTRUCTURED Background: Genomic sequencing of SARS-CoV-2 positive specimens has been critical in detecting and tracking variants of concern. Methods: We analyzed a recent cohort of SARS-CoV-2-positive specimens collected from patients in over 5,000 testing locations across the United States. These data were combined with an online pre-screening questionnaire on symptoms, exposures and vaccination status to examine epidemiological trends related to virulence, transmissibility, and vaccine effectiveness. Results: Between May and October 2021, 177,253 patient specimens were sequenced and approximately 400 different SARS-CoV-2 lineages identified. Within this cohort, 152,373 (86.0%) were aged 16 and older, and the percent of these patients that were fully vaccinated increased from 4.5% in May to 42.3% in October. Although positivity rates of fully vaccinated patients increased, unvaccinated patients were 30.4% (95% CI 26.5-34.3%) more likely to report shortness of breath and 34.0% (95% CI 32.1-35.9%) more likely to report fever, shaking, or chills. Conclusions: Our nationally representative database of patient-reported measures and lineage data from SARS-CoV-2 specimens provides useful data to track emerging trends and lineages of concern.