The Suitability of RNA from Positive SARS-CoV-2 Rapid Antigen Tests for Whole Virus Genome Sequencing and Variant Identification to Maintain Genomic Surveillance

The COVID-19 pandemic has transformed laboratory management, with a surge in demand for diagnostic tests prompting the adoption of new diagnostic assays and the spread of variant surveillance tools. Rapid antigen tests (RATs) were initially used only for screening and later as suitable infection assessment tools. This study explores the feasibility of sequencing the SARS-CoV-2 genome from the residue of the nasopharyngeal swab extraction buffers of rapid antigen tests (RATs) to identify different COVID-19 lineages and sub-lineages. Methods: Viral RNA was extracted from the residue of the nasopharyngeal swab extraction buffers of RATs and, after a confirmation of positivity through a reaction of RT-PCR, viral genome sequencing was performed. Results: Overall, the quality of the sequences obtained from the RNA extracted from the residue of the nasopharyngeal swab extraction buffers of RATs was adequate and allowed us to identify the SARS-CoV-2 variants’ circulation and distribution in a period when the use of molecular swabs had been drastically reduced. Conclusions: This study demonstrates the potential for genomic surveillance by sequencing SARS-CoV-2 from the residue of the nasopharyngeal swab extraction buffers of RATs, highlighting alternative possibilities for tracking variants.