Using SARS-CoV-2 Sequencing Data to Identify Reinfection Cases in the Global Emerging Infections Surveillance Program, United States.

The Centers for Disease Control and Prevention defines SARS-CoV-2 reinfection as a positive COVID-19 test result >90 days after the collection date for the initial positive test or if sequencing confirms a different lineage is causing the reinfection. Reinfection dynamics have been examined by using PCR or antigen surveillance data. We identified patients in the US Military Health System who had >1 positive SARS-CoV-2 test during March 2020-July 2022 by using whole-genome sequencing data to identify reinfection cases, then compared those data with patient demographics, symptoms, and vaccination status.