Agrawal Shelesh, Orschler Laura, Zachmann Kira, Lackner Susanne
Technical University of Darmstadt, Institute IWAR, Chair of Water and Environmental Biotechnology, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany.
FEMS Microbes. 2023 Mar 3;4:xtad006. doi: 10.1093/femsmc/xtad006. eCollection 2023.
Tracking SARS-CoV-2 variants in wastewater is primarily performed by detecting characteristic mutations of the variants. Unlike the Delta variant, the emergence of the Omicron variant and its sublineages as variants of concern has posed a challenge in using characteristic mutations for wastewater surveillance. In this study, we monitored the temporal and spatial variation of SARS-CoV-2 variants by including all the detected mutations and compared whether limiting the analyses to characteristic mutations for variants like Omicron impact the outcomes. We collected 24-hour composite samples from 15 wastewater treatment plants (WWTP) in Hesse and sequenced 164 wastewater samples with a targeted sequencing approach from September 2021 to March 2022. Our results show that comparing the number of all the mutations against the number of the characteristic mutations reveals a different outcome. A different temporal variation was observed for the ORF1a and S gene. As Omicron became dominant, we observed an increase in the overall number of mutations. Based on the characteristic mutations of the SARS-CoV-2 variants, a decreasing trend for the number of ORF1a and S gene mutations was noticed, though the number of known characteristic mutations in both genes is higher in Omicron than Delta.
通过检测病毒变体的特征性突变来追踪污水中的新冠病毒变体，这是目前主要的监测手段。与德尔塔变体不同，奥密克戎变体及其亚谱系作为关注变体的出现，给利用特征性突变进行污水监测带来了挑战。在本研究中，我们纳入所有检测到的突变来监测新冠病毒变体的时空变化，并比较了将分析局限于奥密克戎等变体的特征性突变是否会影响监测结果。我们从黑森州的15个污水处理厂采集了24小时混合样本，并在2021年9月至2022年3月期间采用靶向测序方法对164个污水样本进行了测序。我们的结果表明，比较所有突变的数量和特征性突变的数量会得出不同的结果。观察到开放阅读框1a（ORF1a）和刺突（S）基因存在不同的时间变化。随着奥密克戎成为优势毒株，我们观察到突变总数有所增加。基于新冠病毒变体的特征性突变，虽然奥密克戎中这两个基因的已知特征性突变数量高于德尔塔，但ORF1a和S基因突变的数量呈下降趋势。
