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National Surveillance of COVID-19 Infections: Variants, Vaccination Status, and Viral Spread

Aegis Sciences Corporation and Walgreens are collaborating to significantly improve access COVID-19 diagnostic testing throughout the United States. In May 2021, Aegis began performing whole genome sequencing on samples identified as positive to assist in surveillance of transmissible viral variants. This has allowed for reporting of viral lineages from over 110,000 samples, accounting for ~15% of all COVID-19 genome sequencing results in the United States found in the GISAID database.

The combination of diagnostic testing, genome sequencing, and relevant patient information allowed us to create a sizable, nationally representative database that provides valuable epidemiologic insights:

  • In May 2021, the majority of individuals testing positive were unvaccinated and infected with the Alpha variant. This began to change over time, and by July, the majority of cases were identified in unvaccinated individuals infected with the Delta variant.
  • Some of the less frequent “Other” unnamed variants appear in a relatively high percent of fully vaccinated individuals. A subset of viral mutations that were identified at a higher frequency within the “Other” category are further characterized by infection rate and vaccination status. Closely observing the trends in “Other” variants will provide an early indication of future variants of concern.

Aegis Sciences Corporation and Walgreens will continue to provide access to both testing resources and vaccines in the fight against the COVID-19 pandemic, as well as aggregation of available data to assist in public health surveillance. As we continue to fight an ever-changing illness, all available tools will be necessary to move us in a positive direction toward returning to our normal lives.

National Surveillance of COVID-19 Infections: Variants, Vaccination Status, and Viral Spread