SARS-CoV-2 genomic surveillance from community-distributed rapid antigen tests

For the first several years of the pandemic, SARS-CoV-2 genomic surveillance relied almost entirely on residual diagnostic specimens from nucleic acid amplification-based tests (NAATs). The use of NAATs waned after the end of the Stafford Act Emergency Declaration for COVID-19 in the US. To continue to monitor the spread and evolution of SARS-CoV-2, we partnered with local- and state-level public health agencies and the Dane County Public Library System to obtain SARS-CoV-2 genome sequence from freely available community rapid antigen tests (RATs). From August 15, 2023 to February 29, 2024 we received 227 tests through this system, from which we generated 127 sequences with >10x depth of coverage for ≥90% of the SARS-CoV-2 genome. Our results demonstrate that collecting and sequencing from RATs in partnership with trusted community stakeholders is a practical, useful approach for sustaining genomic surveillance for SARS-CoV-2.