Abstract：
Wastewater surveillance locally and globally is important for the investigation of the molecular epidemiological features of SARS-CoV-2 in the environment. The current study investigated the genomic diversity and mutation profile of SARS-CoV-2 variants in wastewater for the period spanning COVID-19 pandemic up to December, 2022. A total of 3618 complete SARS-CoV-2 genome sequences from waste water samples submitted to the GISAID database were retrieved. The SARS-CoV-2 sequences were subjected to pairwise alignment against reference, followed by clade and lineage assignment (based on Nextstrain, GISAID and Pango), distance metric phylogenetic analysis, and detection of substitution mutations. Following GISAID, Nextstrain, and Pango nomenclatures, an overall agreement in clade and lineage determination in wastewater samples was observed. There was successive appearance, dissemination, and disappearance of SARS-CoV-2 lineages along time in wastewater. The SARS-CoV-2 genomes from wastewater were clustered into the variants of concern (VOC) as Alpha GRY (B.1.1.7 + Q.7), Delta GK (B.1.617.2 + AY.*), and Omicron GRA (BA.1*, BA.2* + B.1.1.529, BA.5*). The evolutionary rate was 9.63e-04 substitutions/site/year for SARS-CoV-2 in wastewater. B.1.1.7 was less prevalent than B.1.617.2 in 2021, appeared in succession, and BA.1, BA.2, BA.5 were serially detected in 2022, the latter strain continued to persist in wastewater. The N501Y, E484K/Q, K417N/T, L452R, T478K spike substitutions remained dominant attribute of SARS-CoV-2 VOCs. The study underlines the importance of wastewater surveillance for enumerating spatiotemporal diversity of SARS-CoV-2 variants and mutations, which might pave the way for novel antiviral and vaccine designing towards management and prevention of SARS-CoV-2 infection.
摘要：
本地和全球的废水监测对于调查环境中SARS-CoV-2的分子流行病学特征具有重要意义。目前的研究调查了截至12月COVID-19大流行期间废水中SARS-CoV-2变体的基因组多样性和突变谱，2022年。从提交给GISAID数据库的废水样品中总共检索了3618个完整的SARS-CoV-2基因组序列。SARS-CoV-2序列与参考进行成对比对，其次是进化枝和谱系分配(基于Nextstrain，GISAID和Pango)，距离度量系统发育分析，和检测替代突变。在GISAID之后,Nextstrain,和潘戈命名法，观察到废水样品中进化枝和谱系测定的总体一致性。连续出现，传播,以及废水中SARS-CoV-2谱系随时间的消失。来自废水的SARS-CoV-2基因组被聚类为AlphaFRY（B.1.1.7Q.7）的关注变体（VOC），三角洲GK（B.1.617.2+AY。*),和OmicronGRA(BA.1*，BA.2*+B.1.1.529,BA.5*)。废水中SARS-CoV-2的进化率为9.63e-04替换/站点/年。B.1.1.7在2021年不如B.1.617.2流行，相继出现，2022年连续检测到BA.1、BA.2、BA.5，后一种菌株在废水中继续存在。N501Y,E484K/Q,K417N/T,L452R,T478K穗取代仍然是SARS-CoV-2挥发性有机化合物的主要属性。该研究强调了废水监测对于列举SARS-CoV-2变体和突变的时空多样性的重要性，这可能为新型抗病毒和疫苗设计铺平道路，以管理和预防SARS-CoV-2感染。
