Abstract
The emergence of the SARS-CoV-2 Omicron variant in 2021 is associated with a global surge of cases in late 2021 and early 2022. Identifying the introduction of novel SARS-CoV-2 variants to a population is imperative to inform decisions by clinicians and public health officials. Here, we describe a quantitative reverse transcription PCR-based assay (RT-qPCR) targeting unique mutations in the Omicron BA.1/BA1.1 and BA.2 viral genomes. This assay accurately and precisely detect the presence of these Omicron variants in patient samples in less than four hours. Using this assay, we tested 270 clinical samples and detected the introduction of Omicron BA.1/BA1.1 and BA.2 in the Santa Barbara County (SBC) population in December 2021 and February 2022, respectively. Identifying Omicron variants using this RT-qPCR assay showed complete concordance with whole viral genome sequencing; both assays indicated that Omicron was the dominant variant in SB County. Our data substantiate that RT-qPCR-based virus detection assays offer a fast and inexpensive alternative to NGS for virus variant-specific detection approach, which allows streamlining the detection of Omicron variants in patient samples.