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Graber TE, Mercier É, Bhatnagar K, Fuzzen M, D'Aoust PM, Hoang HD, Tian X, Towhid ST, Plaza-Diaz J, Eid W, Alain T, Butler A, Goodridge L, Servos M, Delatolla R. Near real-time determination of B.1.1.7 in proportion to total SARS-CoV-2 viral load in wastewater using an allele-specific primer extension PCR strategy. Water Res 2021; 205:117681. [PMID: 34619611 PMCID: PMC8459324 DOI: 10.1016/j.watres.2021.117681] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 05/02/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed millions of lives to date. Antigenic drift has resulted in viral variants with putatively greater transmissibility, virulence, or both. Early and near real-time detection of these variants of concern (VOC) and the ability to accurately follow their incidence and prevalence in communities is wanting. Wastewater-based epidemiology (WBE), which uses nucleic acid amplification tests to detect viral fragments, is a reliable proxy of COVID-19 incidence and prevalence, and thus offers the potential to monitor VOC viral load in a given population. Here, we describe and validate a primer extension PCR strategy targeting a signature mutation in the N gene of SARS-CoV-2. This allows quantification of B.1.1.7 versus non-B.1.1.7 allele frequency in wastewater without the need to employ quantitative RT-PCR standard curves. We show that the wastewater B.1.1.7 profile correlates with its clinical counterpart and benefits from a near real-time and facile data collection and reporting pipeline. This assay can be quickly implemented within a current SARS-CoV-2 WBE framework with minimal cost; allowing early and contemporaneous estimates of B.1.1.7 community transmission prior to, or in lieu of, clinical screening and identification. Our study demonstrates that this strategy can provide public health units with an additional and much needed tool to rapidly triangulate VOC incidence/prevalence with high sensitivity and lineage specificity.
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Affiliation(s)
- Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada
| | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kamya Bhatnagar
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Huy-Dung Hoang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Xin Tian
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Syeda Tasneem Towhid
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Julio Plaza-Diaz
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Ainslie Butler
- Simcoe Muskoka District Health Unit, Barrie, Ontario, L4M 6K9, Canada
| | - Lawrence Goodridge
- Department of Food Science, Canadian Research Institute for Food Safety, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mark Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada.
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