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

Zach Aralis; Stewart Comer; Henning Ansorg; Carl Palmer; Jennifer Smith; Stuart C Feinstein; Lynn N Fitzgibbons; Carolina Arias

doi:10.3390/diagnostics12112805

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

Diagnostics (Basel). 2022 Nov 15;12(11):2805. doi: 10.3390/diagnostics12112805.

Authors

Zach Aralis^{1

2}, Stewart Comer^{3

4

5}, Henning Ansorg³, Carl Palmer⁶, Jennifer Smith⁷, Stuart C Feinstein^{1

8}, Lynn N Fitzgibbons⁹, Carolina Arias^{1

2

8

10

11}

Affiliations

¹ Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
² Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA.
³ Santa Barbara County Public Health Department, Santa Barbara, CA 93106, USA.
⁴ Department of Pathology, Santa Barbara Cottage Hospital, Santa Barbara, CA 93106, USA.
⁵ Pacific Diagnostic Laboratories, Santa Barbara, CA 93106, USA.
⁶ LegacyWorks Group, Santa Barbara, CA 93106, USA.
⁷ California NanoSystems Institute, University of California, Santa Barbara, CA 93106, USA.
⁸ Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
⁹ Department of Medical Education, Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, CA 93106, USA.
¹⁰ Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA.
¹¹ Infectious Disease Initiative, Chan Zuckerberg BioHub, San Francisco, CA 93106, USA.

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.

Keywords: NGS; SARS-CoV-2; epidemiology; molecular assay; omicron; public health; qPCR.

Abstract

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