Spatiotemporal genome diversity of SARS-CoV-2 in wastewater: a two-year global epidemiological study

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.