Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2

doi:10.3390/v14081760

. 2022 Aug 12;14(8):1760.

doi: 10.3390/v14081760.

Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2

David Pham¹, Susan Maddocks^{1

2}, Dominic E Dwyer^{1

2

3}, Vitali Sintchenko^{1

2

3}, Jen Kok^{1

2

3}, Rebecca J Rockett^{2

3}

Affiliations

¹ Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology-Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia.
² Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia.
³ Centre for Infectious Diseases & Microbiology-Public Health, Westmead Hospital, Westmead, NSW 2145, Australia.

PMID: 36016382
PMCID: PMC9416591
DOI: 10.3390/v14081760

Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2

David Pham et al. Viruses. 2022.

. 2022 Aug 12;14(8):1760.

doi: 10.3390/v14081760.

Authors

David Pham¹, Susan Maddocks^{1

2}, Dominic E Dwyer^{1

2

3}, Vitali Sintchenko^{1

2

3}, Jen Kok^{1

2

3}, Rebecca J Rockett^{2

3}

Affiliations

¹ Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology-Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia.
² Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia.
³ Centre for Infectious Diseases & Microbiology-Public Health, Westmead Hospital, Westmead, NSW 2145, Australia.

PMID: 36016382
PMCID: PMC9416591
DOI: 10.3390/v14081760

Abstract

In order to rapidly differentiate sublineages BA.1 and BA.2 of the SARS-CoV-2 variant of concern Omicron, we developed a real-time reverse-transcriptase polymerase chain reaction to target the discriminatory spike protein deletion at amino acid position 69-70 (S:del69-70). Compared to the gold standard of whole genome sequencing, the candidate assay was 100% sensitive and 99.4% specific. Sublineage typing by RT-PCR can provide a rapid, high throughput and cost-effective method to enhance surveillance as well as potentially guiding treatment and infection control decisions.

Keywords: COVID-19; Omicron; SARS-CoV-2; real-time RT-PCR; sublineage; variants of concern.

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Conflict of interest statement

The authors declare no conflict of interest.

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[1] World Health Organization WHO Coronavirus (COVID-19) Dashboard. [(accessed on 19 June 2022)]. Available online: https://covid19.who.int/

[2] World Health Organization WHO Coronavirus (COVID-19) Dashboard. [(accessed on 19 June 2022)]. Available online: https://covid19.who.int/

[3] Coronaviridae Study Group of the International Committee on Taxonomy of Viruses The species Severe acute respiratory syndrome-related coronavirus: Classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 2020;5:536–544. doi: 10.1038/s41564-020-0695-z. - DOI - PMC - PubMed

[4] Coronaviridae Study Group of the International Committee on Taxonomy of Viruses The species Severe acute respiratory syndrome-related coronavirus: Classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 2020;5:536–544. doi: 10.1038/s41564-020-0695-z. - DOI - PMC - PubMed

[5] Tang X., Wu C., Li X., Song Y., Yao X., Wu X., Duan Y., Zhang H., Wang Y., Qian Z., et al. On the origin and continuing evolution of SARS-CoV-2. Natl. Sci. Rev. 2020;7:1012–1023. doi: 10.1093/nsr/nwaa036. - DOI - PMC - PubMed

[6] Tang X., Wu C., Li X., Song Y., Yao X., Wu X., Duan Y., Zhang H., Wang Y., Qian Z., et al. On the origin and continuing evolution of SARS-CoV-2. Natl. Sci. Rev. 2020;7:1012–1023. doi: 10.1093/nsr/nwaa036. - DOI - PMC - PubMed

[7] World Health Organization Tracking SARS-CoV-2 Variants. [(accessed on 19 June 2022)]. Available online: https://www.who.int/activities/tracking-SARS-CoV-2-variants.

[8] World Health Organization Tracking SARS-CoV-2 Variants. [(accessed on 19 June 2022)]. Available online: https://www.who.int/activities/tracking-SARS-CoV-2-variants.

[9] Rambaut A., Holmes E.C., O’Toole Á., Hill V., McCrone J.T., Ruis C., Plessis L.d., Pybus O.G. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat. Microbiol. 2020;5:1403–1407. doi: 10.1038/s41564-020-0770-5. - DOI - PMC - PubMed

[10] Rambaut A., Holmes E.C., O’Toole Á., Hill V., McCrone J.T., Ruis C., Plessis L.d., Pybus O.G. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat. Microbiol. 2020;5:1403–1407. doi: 10.1038/s41564-020-0770-5. - DOI - PMC - PubMed

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Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2

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Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2

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