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Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for
David Pham1, Susan Maddocks1,2, Dominic E Dwyer1,2,3
1Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology-Institute of Clinical Pathology & Medical Research, 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.
