从德国南部的废水中提取的全面突变图谱扩大了循环 SARS-CoV-2 多样性的证据范围,使其超越了 Omicron 的突变特征。

FEMS microbes Pub Date : 2023-03-03 eCollection Date: 2023-01-01 DOI:10.1093/femsmc/xtad006
Shelesh Agrawal, Laura Orschler, Kira Zachmann, Susanne Lackner
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摘要

跟踪废水中的 SARS-CoV-2 变异体主要是通过检测变体的特征突变来进行的。与德尔塔变异体不同,欧米克隆变异体及其亚系变异体的出现引起了人们的关注,这给利用特征变异体进行废水监测带来了挑战。在本研究中,我们通过纳入所有检测到的变异来监测 SARS-CoV-2 变异的时间和空间变化,并比较了仅限于对 Omicron 等变异的特征变异进行分析是否会影响结果。我们收集了黑森州 15 家污水处理厂 (WWTP) 的 24 小时综合样本,并在 2021 年 9 月至 2022 年 3 月期间采用定向测序方法对 164 份污水样本进行了测序。我们的结果表明,将所有突变的数量与特征突变的数量进行比较会发现不同的结果。在 ORF1a 和 S 基因上观察到了不同的时间变化。随着 Omicron 成为优势基因,我们观察到突变的总数有所增加。根据 SARS-CoV-2 变异株的特征突变,我们注意到 ORF1a 和 S 基因突变的数量呈下降趋势,尽管这两个基因中已知的特征突变数量在 Omicron 中高于 Delta。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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Comprehensive mutation profiling from wastewater in southern Germany extends evidence of circulating SARS-CoV-2 diversity beyond mutations characteristic for Omicron.

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.

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