Genetic sequencing detected the SARS-CoV-2 delta variant in wastewater a month prior to the first COVID-19 case in Ahmedabad (India).
Genetic sequencing detected the SARS-CoV-2 delta variant in wastewater a month prior to the first COVID-19 case in Ahmedabad (India).
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DOI：
10.1016/j.envpol.2022.119757
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发表时间：
2022-10-01
影响因子：
8.9
通讯作者：
Joshi, Chaitanya G.
中科院分区：
文献类型：
--
作者：
Joshi, Madhvi;Kumar, Manish;Srivastava, Vaibhav;Kumar, Dinesh;Rathore, Dalip Singh;Pandit, Ramesh;Graham, David W.;Joshi, Chaitanya G.
基于废水的基因组监测可以识别人群中受感染个体传播的绝大多数变异，这超出了基于临床样本（即仅针对有症状的患者）的基因组监测。我们分析了四个样本，以检测SARS-CoV-2基因组的关键突变，并追踪印度第一波（2020年9月/ 11月）和第二波（2021年2月）之前艾哈迈达巴德的流行变异。该分析在23种类型的样本中发现了刺突蛋白的34个突变。刺突蛋白突变与VOC-21APR-02相关；B.1.617.2谱系（Delta变体），在2021年2月的废水样本中频率为57%。关键刺突蛋白突变位点为T19R、L452R、T478K、D614G和P681R，缺失位点分别为22029 （6 bp）、28248 （6 bp）和28271 （1 bp）。有趣的是，这些突变在2020年9月/ 11月的样本中没有发现，但在2021年4月初印度开始的第二波大规模COVID-19病例之前确实出现了。事实上，在2021年2月初的样本中发现了Delta变异的遗传痕迹，这比2021年3月在古吉拉特邦艾哈迈达巴德出现首例临床确诊病例早了一个多月。本工作描述了SARS-CoV-2变体在艾哈迈达巴德的传播，并证实了废水监测对早期发现关注的变体（VOCs）的相应价值。这种监测必须作为未来健康保护系统的一个主要组成部分。在艾哈迈达巴德的废水中发现的Delta变异比首次确诊的临床患者报告早一个月。
Wastewater-based genomic surveillance can identify a huge majority of variants shed by the infected individuals within a population, which goes beyond genomic surveillance based on clinical samples (i.e., symptomatic patients only). We analyzed four samples to detect key mutations in the SARS-CoV-2 genome and track circulating variants in Ahmedabad during the first wave (Sep/Nov 2020) and before the second wave (in Feb 2021) of COVID-19 in India. The analysis identified a total of 34 mutations in the spike protein across samples categorized into 23 types. The spike protein mutations were linked to the VOC-21APR-02; B.1.617.2 lineage (Delta variant) with 57% frequency in wastewater samples of Feb 2021. The key spike protein mutations were T19R, L452R, T478K, D614G, & P681R and deletions at 22029 (6 bp), 28248 (6 bp), & 28271 (1 bp). Interestingly, these mutations were not seen in the samples from Sep/Nov 2020 but did appear before the massive second wave of COVID-19 cases, which in India started in early April 2021. In fact, genetic traces of the Delta variant were found in samples of early Feb 2021, more than a month before the first clinically confirmed case of this in March 2021 in Ahmedabad, Gujarat. The present work describes the circulating of SARS-CoV-2 variants in Ahmedabad and confirms the consequential value of wastewater surveillance for the early detection of variants of concerns (VOCs). Such monitoring must be included as a major component of future health protection systems. Delta variant found a month earlier in the wastewater of Ahmedabad than the first confirmed clinical patient report.
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DOI：
10.1016/j.scitotenv.2020.143578
发表时间：
2021-03-01
期刊：
The Science of the total environment
影响因子：
--
作者：
Hata A;Hara-Yamamura H;Meuchi Y;Imai S;Honda R
通讯作者：
Honda R
影响因子：
12.8
作者：
Pérez-Cataluña A;Chiner-Oms Á;Cuevas-Ferrando E;Díaz-Reolid A;Falcó I;Randazzo W;Girón-Guzmán I;Allende A;Bracho MA;Comas I;Sánchez G
通讯作者：
Sánchez G
影响因子：
13.6
作者：
Kumar M;Dhangar K;Thakur AK;Ram B;Chaminda T;Sharma P;Kumar A;Raval N;Srivastava V;Rinklebe J;Kuroda K;Sonne C;Barcelo D
通讯作者：
Barcelo D
DOI：
10.1016/j.scitotenv.2021.148367
发表时间：
2021-10-20
期刊：
The Science of the total environment
影响因子：
--
作者：
Kumar M;Joshi M;Shah AV;Srivastava V;Dave S
通讯作者：
Dave S
影响因子：
64.5
作者：
Korber, Bette;Fischer, Will M.;Montefiori, David C.
通讯作者：
Montefiori, David C.