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; Susan Maddocks; Dominic E Dwyer; Vitali Sintchenko; Jen Kok; Rebecca J Rockett

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

Viruses. 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.

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.

MeSH terms

COVID-19 Testing
COVID-19* / diagnosis
Humans
RNA, Viral / genetics
RNA-Directed DNA Polymerase / genetics
Reverse Transcriptase Polymerase Chain Reaction
SARS-CoV-2* / genetics

Substances

RNA, Viral
RNA-Directed DNA Polymerase

Supplementary concepts

SARS-CoV-2 variants

Grants and funding

This research received no external funding.