Efficient Tracing of the SARS-CoV-2 Omicron Variants in Santa Barbara County Using a Rapid Quantitative Reverse Transcription PCR Assay

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.

Development of primer-probe sets to rapidly distinguish single nucleotide polymorphisms in SARS-CoV-2 lineages

“…Despite this limitation, we showed that all probes were specific for their cognate sequences and to independently confirm the SNP calling, regions harbouring respective mutation in the S -gene were amplified and Sanger sequenced. Other studies have used either Sanger sequencing or WGS for confirmation ( Erster et al., 2021 ; Aralis et al., 2022 ; Moisan et al., 2023 ; Spiess et al., 2023 ; Zare Ashrafi et al., 2023 ). A large proportion of samples, particularly from Clinical Site 2, could not be confirmed as PCR failed to generate amplicons for sequencing.…”

Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing

“…Most studies in the published literature describing rRT-PCR assays that identify Omicron lineages are only capable of differentiating the original Omicron lineage (B.1.1.529, equivalent to BA.1) from other VOCs or BA.1 from BA.2 15 , 44 – 49 . Few studies have been published which describe rRT-PCR assays that detect and distinguish between BA.1, BA.2, BA.4, and BA.5.…”