SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 antigen self tests

Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome se-quences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.

Automated summary

The widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has resulted in a shortage of clinical samples for viral genomic surveillance. In this study, we assessed the RNA isolated from BinaxNOW swabs stored at room temperature for SARS-CoV-2 rRT-PCR and complete viral genome sequencing. Out of 103 samples, 81 (78.6%) yielded detectable RNA, and out of 57 samples, 46 (80.7%) produced complete genome sequences. Our findings demonstrate that SARS-CoV-2 RNA extracted from used Binax test swabs presents an important opportunity for enhancing SARS-CoV-2 genomic surveillance, investigating transmission clusters, and monitoring within-host evolution.