American Society for Microbiology
SARS-CoV-2 variants of concern (VOCs) continue to pose a public health threat which necessitates a real-time monitoring strategy to complement whole genome sequencing. Thus, we investigated the efficacy of competitive probe RT-qPCR assays for six mutation sites identified in SARS-CoV-2 VOCs and, after validating the assays with synthetic RNA, performed these assays on positive saliva samples. When compared with whole genome sequence results, the SD69-70 and ORF1aD3675-3677 assays demonstrated 93.60 and 68.00% accuracy, respectively. The SNP assays (K417T, E484K, E484Q, L452R) demonstrated 99.20, 96.40, 99.60, and 96.80% accuracies, respectively. Lastly, we screened 345 positive saliva samples from 7 to 22 December 2021 using Omicron-specific mutation assays and were able to quickly identify rapid spread of Omicron in Upstate South Carolina. Our workflow demonstrates a novel approach for low-cost, real-time population screening of VOCs.
Ham, Rachel E.; Smothers, Austin R.; Che, Rui; Sell, Keegan J.; Peng, Congyue Annie; and Dean, Delphine, "Identifying SARS-CoV-2 Variants of Concern through Saliva- Based RT-qPCR by Targeting Recurrent Mutation Sites" (2022). Open Access Publishing Fund. 35.