NCM 2022: Monitoring the circulation of SARS-CoV-2 variants through community wastewater sequencing

Wastewater surveillance of SARS-CoV-2 has acted as a complementary approach to clinical surveillance to monitor levels of the virus in wastewater as an early warning indicator of increasing community infections. In this study, we evaluated the efficacy of a rapid sequencing approach for SARS-CoV-2 in wastewater to identify dominant variants circulating in communities. SARS-CoV-2 N1 and N2 genes were measured using digital PCR. Library preparation was performed using two primer pools to amplify the viral genomes and sequenced using nanopore MinION sequencer. Sequencing data were analysed using IDseq and EPI2ME bioinformatics tools. We identified that the dominant variants in wastewater by year were 20C in 2020, 21J (Delta) in 2021, and 21K (Omicron) in 2022. These results demonstrate that wastewater sequencing can be used as a rapid real-time, cost-effective public health tool to detect emerging SARS-CoV-2 variants, thus allowing public health officials to respond to virulent strains in the community adequately.