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Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with
Nathan Zelyas1,2, Kanti Pabbaraju3, Matthew A Croxen4,5,6
1Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada. nathan.zelyas@aplabs.ca.
Scientific Reports
|October 14, 2023
Summary
Rapid PCR assays accurately identified SARS-CoV-2 Omicron sublineages BA.1, BA.2, BA.4, and BA.5 in Alberta. This genomic surveillance approach enabled effective monitoring during the BA.5 wave.
Area of Science:
- Virology
- Molecular Biology
- Public Health
Background:
- Omicron (SARS-CoV-2) became globally dominant in late 2021, with distinct sublineages driving separate waves.
- Effective surveillance of emerging SARS-CoV-2 variants is crucial for public health response.
Purpose of the Study:
- To develop and implement rapid real-time PCR assays for distinguishing Omicron sublineages BA.1, BA.2, BA.4, and BA.5.
- To assess the analytical sensitivity, accuracy, and agreement with genome sequencing of these novel assays.
Main Methods:
- Design and implementation of real-time reverse transcriptase PCR assays targeting specific genetic markers (S:N501Y, S:ins214EPE, S:H69/V70, ORF7b:L11F, M:D3N).
- Combination of marker results to designate samples into specific Omicron sublineages.
- Validation against genome sequencing using 12,592 specimens.
Main Results:
- The developed PCR assays demonstrated high analytical sensitivity (132-2229 copies/mL) and in-laboratory accuracy (98.9-100%).
- A high agreement of 97.3% was observed between the PCR assays and genome sequencing.
- The assays successfully facilitated SARS-CoV-2 lineage surveillance during a BA.5-dominated period.
Conclusions:
- Real-time PCR assays targeting specific genetic markers provide a rapid and accurate method for Omicron sublineage identification.
- These assays are valuable tools for public health surveillance of SARS-CoV-2 variants.
- The integration of PCR-based detection with genome sequencing enhances genomic surveillance capabilities.
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