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.
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.
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DOI：
10.1016/j.watres.2021.117681
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发表时间：
2021-10-15
期刊：
影响因子：
12.8
通讯作者：
Delatolla R
中科院分区：
文献类型：
--
作者：
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
由严重急性呼吸综合征冠状病毒2号(SARS-CoV-2)引起的2019年新冠肺炎大流行迄今已夺走数百万人的生命。抗原漂移导致了可能具有更大传播性、毒力或两者兼而有之的病毒变体。缺乏对这些关注变种(VOC)的早期和近乎实时的检测，以及准确跟踪其在社区中的发病率和流行率的能力。废水流行病学使用核酸扩增试验检测病毒片段，是新冠肺炎发病率和流行率的可靠指标，因此有可能监测特定人群中的挥发性有机碳病毒载量。在这里，我们描述并验证了一种针对SARS-CoV-2 N基因特征突变的引物延伸PCR策略。这使得可以量化废水中B.1.1.7和非B.1.1.7等位基因的频率，而不需要使用定量RT-PCR标准曲线。我们表明，废水B.1.1.7配置文件与其临床对应的配置文件相关，并受益于近乎实时和便捷的数据收集和报告渠道。这种检测方法可以在目前的SARS-CoV-2 WBE框架内以最低的成本快速实施；允许在临床筛查和鉴定之前或代替临床筛查和鉴定对B.1.1.7社区传播进行早期和同期估计。我们的研究表明，这一策略可以为公共卫生单位提供一个额外的和迫切需要的工具，以高灵敏度和谱系特异性快速三角测量VOC的发病率/流行率。
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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DOI：
10.1016/j.scitotenv.2021.149618
发表时间：
2021-12-20
期刊：
The Science of the total environment
影响因子：
--
作者：
D'Aoust PM;Towhid ST;Mercier É;Hegazy N;Tian X;Bhatnagar K;Zhang Z;Naughton CC;MacKenzie AE;Graber TE;Delatolla R
通讯作者：
Delatolla R
影响因子：
64.8
作者：
Gaebler C;Wang Z;Lorenzi JCC;Muecksch F;Finkin S;Tokuyama M;Cho A;Jankovic M;Schaefer-Babajew D;Oliveira TY;Cipolla M;Viant C;Barnes CO;Bram Y;Breton G;Hägglöf T;Mendoza P;Hurley A;Turroja M;Gordon K;Millard KG;Ramos V;Schmidt F;Weisblum Y;Jha D;Tankelevich M;Martinez-Delgado G;Yee J;Patel R;Dizon J;Unson-O'Brien C;Shimeliovich I;Robbiani DF;Zhao Z;Gazumyan A;Schwartz RE;Hatziioannou T;Bjorkman PJ;Mehandru S;Bieniasz PD;Caskey M;Nussenzweig MC
通讯作者：
Nussenzweig MC
影响因子：
7.7
作者：
Chen AT;Altschuler K;Zhan SH;Chan YA;Deverman BE
通讯作者：
Deverman BE
影响因子：
10.7
作者：
Kustin T;Stern A
通讯作者：
Stern A
影响因子：
9.3
作者：
Lefever, Steve;Pattyn, Filip;Vandesompele, Jo
通讯作者：
Vandesompele, Jo