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Zelyas N, Pabbaraju K, Croxen MA, Lynch T, McCullough E, Murphy SA, Shokoples S, Wong A, Kanji JN, Tipples G. Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing. Sci Rep 2023; 13:17478. [PMID: 37838804 PMCID: PMC10576821 DOI: 10.1038/s41598-023-44796-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023] Open
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.
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Affiliation(s)
- Nathan Zelyas
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada.
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
| | - Kanti Pabbaraju
- Alberta Precision Laboratories, Public Health Laboratory, Calgary, AB, Canada
| | - Matthew A Croxen
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Tarah Lynch
- Alberta Precision Laboratories, Public Health Laboratory, Calgary, AB, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Emily McCullough
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
| | - Stephanie A Murphy
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Edmonton, AB, Canada
| | - Sandy Shokoples
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
| | - Anita Wong
- Alberta Precision Laboratories, Public Health Laboratory, Calgary, AB, Canada
| | - Jamil N Kanji
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Alberta Precision Laboratories, Public Health Laboratory, Calgary, AB, Canada
- Division of Infectious Diseases, Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Graham Tipples
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
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Hook PW, Timp W. Beyond assembly: the increasing flexibility of single-molecule sequencing technology. Nat Rev Genet 2023; 24:627-641. [PMID: 37161088 PMCID: PMC10169143 DOI: 10.1038/s41576-023-00600-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, including filling gaps in the human reference genome, measuring the epigenome and characterizing splicing variants in the transcriptome. With recent technological developments, these single-molecule technologies have moved beyond genome assembly and are being used in a variety of ways, including to selectively sequence specific loci with long reads, measure chromatin state and protein-DNA binding in order to investigate the dynamics of gene regulation, and rapidly determine copy number variation. These increasingly flexible uses of single-molecule technologies highlight a young and fast-moving part of the field that is leading to a more accessible era of nucleic acid sequencing.
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Affiliation(s)
- Paul W Hook
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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