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

In the United States, SARS-CoV-2 genomic surveillance initially relied almost entirely on residual diagnostic specimens from nucleic acid amplification-based tests (NAATs). The use of NAATs waned after the end of the COVID-19 Public Health Emergency. We partnered with local- and state-level public health agencies and the Dane County Public Library System to continue genomic surveillance by obtaining SARS-CoV-2 genome sequences from freely available community rapid antigen tests (RATs). From August 15, 2023 to February 29, 2024 we received 227 tests, from which we generated 127 sequences with >10x depth of coverage for ≥90% of the genome. In a subset of tests, lower Ct values correlated with sequence success. Our results demonstrate that collecting and sequencing from RATs in partnership with community sites is a practical approach for sustaining SARS-CoV-2 genomic surveillance.