@article{Graber-2021-Near,
title = "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",
author = "Graber, Tyson E. and
Bhatnagar, Kamya and
Mercier, {\'E}lisabeth and
Fuzzen, Meghan and
D{'}Aoust, Patrick M. and
Hoang, Huy-Dung and
Tian, Xin and
Towhid, Syeda Tasneem and
Diaz, Julio Plaza and
Alain, Tommy and
Butler, Ainslie and
Goodridge, Lawrence and
Servos, Mark R. and
Delatolla, Robert",
journal = "",
year = "2021",
publisher = "Copernicus GmbH",
url = "https://gwf-uwaterloo.github.io/gwf-publications/G21-47001",
doi = "10.1101/2021.02.22.21252041",
abstract = "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 faithful 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 the proportional expression of B.1.1.7 versus non-B.1.1.7 alleles 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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<abstract>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 faithful 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 the proportional expression of B.1.1.7 versus non-B.1.1.7 alleles 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.</abstract>
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%0 Journal Article
%T 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
%A Graber, Tyson E.
%A Bhatnagar, Kamya
%A Mercier, Élisabeth
%A Fuzzen, Meghan
%A D’Aoust, Patrick M.
%A Hoang, Huy-Dung
%A Tian, Xin
%A Towhid, Syeda Tasneem
%A Diaz, Julio Plaza
%A Alain, Tommy
%A Butler, Ainslie
%A Goodridge, Lawrence
%A Servos, Mark R.
%A Delatolla, Robert
%D 2021
%I Copernicus GmbH
%F Graber-2021-Near
%X 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 faithful 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 the proportional expression of B.1.1.7 versus non-B.1.1.7 alleles 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.
%R 10.1101/2021.02.22.21252041
%U https://gwf-uwaterloo.github.io/gwf-publications/G21-47001
%U https://doi.org/10.1101/2021.02.22.21252041
Markdown (Informal)
[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](https://gwf-uwaterloo.github.io/gwf-publications/G21-47001) (Graber et al., GWF 2021)
ACL
- Tyson E. Graber, Kamya Bhatnagar, Élisabeth Mercier, Meghan Fuzzen, Patrick M. D’Aoust, Huy-Dung Hoang, Xin Tian, Syeda Tasneem Towhid, Julio Plaza Diaz, Tommy Alain, Ainslie Butler, Lawrence Goodridge, Mark R. Servos, and Robert Delatolla. 2021. 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.
