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

doi:10.3390/diagnostics12112805

. 2022 Nov 15;12(11):2805.

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

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.

PMID: 36428863
PMCID: PMC9689663
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

Zach Aralis et al. Diagnostics (Basel). 2022.

. 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.

PMID: 36428863
PMCID: PMC9689663
DOI: 10.3390/diagnostics12112805

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.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**Figure 1**
Primer Positions and Method overview. Genomic coordinates of the primer binding locations in the Wu-Hu1, BA.1/BA.1.1, and BA.2 viral variant genomes for (A) the BA.1/BA.1.1 targets and (B) the BA.2 targets. (C) Schematic and estimated timeline of RT-qPCR assay.

**Figure 2**
Design timeline and metrics of the Omicron variant-specific RT-qPCR. (A) Timeline of events around the design, optimization, and implementation of the Omicron variant-specific RT-qPCR in Santa Barbara County. (B) Ct values for all samples tested. The red dashed line indicates the cutoff at a Ct of 37. (C) Ct values of a panel of samples known to be variants other than Omicron BA.1, BA.1.1, and BA.2. (D) Results of all 270 samples tested. (E) Percent concordance and (F) confusion matrix of samples with whole viral NGS and variant-specific RT-qPCR data. ND: not detected; NT: not tested.

**Figure 3**
Phylogenetic analysis based on whole-genome sequences of SARS-CoV-2 Omicron variants detected in Santa Barbara County.

**Figure 4**
Daily cases and relative variant proportions in Santa Barbara County. (A) Total new COVID-19 cases by episode date and (B) new cases in boosted, vaccinated, and unvaccinated individuals in Santa Barbara County reported by the SBCPHD [42]. (C) Relative proportion of omicron samples in Santa Barbara County, determined via variant-specific RT-qPCR and (D) whole viral NGS.

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References

1. Thomas S. Status of COVID-19 Pandemic Before the Administration of Vaccine. Methods Mol. Biol. 2022;2410:93–108. doi: 10.1007/978-1-0716-1884-4_4. - DOI - PubMed
1. Zhao Y., Huang J., Zhang L., Chen S., Gao J., Jiao H. The Global Transmission of New Coronavirus Variants. Environ. Res. 2022;206:112240. doi: 10.1016/j.envres.2021.112240. - DOI - PMC - PubMed
1. Eyre D.W., Taylor D., Purver M., Chapman D., Fowler T., Pouwels K.B., Walker A.S., Peto T.E.A. Effect of Covid-19 Vaccination on Transmission of Alpha and Delta Variants. N. Engl. J. Med. 2022;386:744–756. doi: 10.1056/NEJMoa2116597. - DOI - PMC - PubMed
1. Gobeil S.M.-C., Janowska K., McDowell S., Mansouri K., Parks R., Stalls V., Kopp M.F., Manne K., Li D., Wiehe K., et al. Effect of Natural Mutations of SARS-CoV-2 on Spike Structure, Conformation and Antigenicity. Science. 2021;373:eabi6226. doi: 10.1126/science.abi6226. - DOI - PMC - PubMed
1. Escalera A., Gonzalez-Reiche A.S., Aslam S., Mena I., Laporte M., Pearl R.L., Fossati A., Rathnasinghe R., Alshammary H., van de Guchte A., et al. Mutations in SARS-CoV-2 Variants of Concern Link to Increased Spike Cleavage and Virus Transmission. Cell Host. Microbe. 2022;30:373–387.e7. doi: 10.1016/j.chom.2022.01.006. - DOI - PMC - PubMed

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[1] Thomas S. Status of COVID-19 Pandemic Before the Administration of Vaccine. Methods Mol. Biol. 2022;2410:93–108. doi: 10.1007/978-1-0716-1884-4_4. - DOI - PubMed

[2] Thomas S. Status of COVID-19 Pandemic Before the Administration of Vaccine. Methods Mol. Biol. 2022;2410:93–108. doi: 10.1007/978-1-0716-1884-4_4. - DOI - PubMed

[3] Zhao Y., Huang J., Zhang L., Chen S., Gao J., Jiao H. The Global Transmission of New Coronavirus Variants. Environ. Res. 2022;206:112240. doi: 10.1016/j.envres.2021.112240. - DOI - PMC - PubMed

[4] Zhao Y., Huang J., Zhang L., Chen S., Gao J., Jiao H. The Global Transmission of New Coronavirus Variants. Environ. Res. 2022;206:112240. doi: 10.1016/j.envres.2021.112240. - DOI - PMC - PubMed

[5] Eyre D.W., Taylor D., Purver M., Chapman D., Fowler T., Pouwels K.B., Walker A.S., Peto T.E.A. Effect of Covid-19 Vaccination on Transmission of Alpha and Delta Variants. N. Engl. J. Med. 2022;386:744–756. doi: 10.1056/NEJMoa2116597. - DOI - PMC - PubMed

[6] Eyre D.W., Taylor D., Purver M., Chapman D., Fowler T., Pouwels K.B., Walker A.S., Peto T.E.A. Effect of Covid-19 Vaccination on Transmission of Alpha and Delta Variants. N. Engl. J. Med. 2022;386:744–756. doi: 10.1056/NEJMoa2116597. - DOI - PMC - PubMed

[7] Gobeil S.M.-C., Janowska K., McDowell S., Mansouri K., Parks R., Stalls V., Kopp M.F., Manne K., Li D., Wiehe K., et al. Effect of Natural Mutations of SARS-CoV-2 on Spike Structure, Conformation and Antigenicity. Science. 2021;373:eabi6226. doi: 10.1126/science.abi6226. - DOI - PMC - PubMed

[8] Gobeil S.M.-C., Janowska K., McDowell S., Mansouri K., Parks R., Stalls V., Kopp M.F., Manne K., Li D., Wiehe K., et al. Effect of Natural Mutations of SARS-CoV-2 on Spike Structure, Conformation and Antigenicity. Science. 2021;373:eabi6226. doi: 10.1126/science.abi6226. - DOI - PMC - PubMed

[9] Escalera A., Gonzalez-Reiche A.S., Aslam S., Mena I., Laporte M., Pearl R.L., Fossati A., Rathnasinghe R., Alshammary H., van de Guchte A., et al. Mutations in SARS-CoV-2 Variants of Concern Link to Increased Spike Cleavage and Virus Transmission. Cell Host. Microbe. 2022;30:373–387.e7. doi: 10.1016/j.chom.2022.01.006. - DOI - PMC - PubMed

[10] Escalera A., Gonzalez-Reiche A.S., Aslam S., Mena I., Laporte M., Pearl R.L., Fossati A., Rathnasinghe R., Alshammary H., van de Guchte A., et al. Mutations in SARS-CoV-2 Variants of Concern Link to Increased Spike Cleavage and Virus Transmission. Cell Host. Microbe. 2022;30:373–387.e7. doi: 10.1016/j.chom.2022.01.006. - DOI - PMC - PubMed

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

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