Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing

Nathan Zelyas; Kanti Pabbaraju; Matthew A Croxen; Tarah Lynch; Emily McCullough; Stephanie A Murphy; Sandy Shokoples; Anita Wong; Jamil N Kanji; Graham Tipples

doi:10.1038/s41598-023-44796-y

Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing

Sci Rep. 2023 Oct 14;13(1):17478. doi: 10.1038/s41598-023-44796-y.

Authors

Nathan Zelyas^{1

2}, Kanti Pabbaraju³, Matthew A Croxen^{4

5

6}, Tarah Lynch^{3

7}, Emily McCullough⁴, Stephanie A Murphy^{4

8}, Sandy Shokoples⁴, Anita Wong³, Jamil N Kanji^{5

3

9}, Graham Tipples^{4

6

10}

Affiliations

¹ Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada. nathan.zelyas@aplabs.ca.
² Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada. nathan.zelyas@aplabs.ca.
³ Alberta Precision Laboratories, Public Health Laboratory, Calgary, AB, Canada.
⁴ Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada.
⁵ Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
⁶ Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.
⁷ Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada.
⁸ National Microbiology Laboratory, Public Health Agency of Canada, Edmonton, AB, Canada.
⁹ Division of Infectious Diseases, Department of Medicine, University of Calgary, Calgary, AB, Canada.
¹⁰ Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada.

Abstract

Omicron has become the dominant SARS-CoV-2 variant globally since December 2021, with distinct waves being associated with separate Omicron sublineages. Rapid detection of BA.1, BA.2, BA.4, and BA.5 was accomplished in the province of Alberta, Canada, through the design and implementation of real-time reverse transcriptase PCR assays targeting S:N501Y, S:ins214EPE, S:H69/V70, ORF7b:L11F, and M:D3N. Using the combination of results for each of these markers, samples could be designated as belonging to sublineages within BA.1, BA.2, BA.4, or BA.5. The analytical sensitivity of these markers ranged from 132 to 2229 copies/mL and in-laboratory accuracy was 98.9-100%. A 97.3% agreement using 12,592 specimens was demonstrated for the assays compared to genome sequencing. The use of these assays, combined with genome sequencing, facilitated the surveillance of SARS-CoV-2 lineages throughout a BA.5-dominated period.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

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

Substances

RNA-Directed DNA Polymerase

Supplementary concepts

SARS-CoV-2 variants