Wastewater surveillance of SARS-CoV-2 variants to track community outbreaks in Hong Kong

Sewage surveillance of SARS-CoV-2 serves as an effective tool to monitor the progression of the pandemic. Although standard qPCR confirms the presence of SARS-CoV-2 in sewage, the variant identity of SARS-CoV-2 is not addressed. We developed a cost-effective solution to track SARS-CoV-2 variants in Hong Kong, which utilizes 3 rd generation amplicon sequencing and bioinformatics to process samples within 24 hours from extraction to reporting. SARS-CoV-2 variants were identified in 1168 sewage samples collected from May 2022 to July 2023 that were initially tested positive for SARS-CoV-2 by qPCR. The distribution of SARS-CoV-2 variants in sewage predicted and overlapped with their clinical rise and decline. The discovery of SARS-CoV-2 variants in sewage also appeared around the same time in clinical testing. Moreover, infection trends of BQ.1.1 and XBB were preceded by their surge in sewage, confirming the predictive power of wastewater surveillance of SARS-CoV-2 variants. Based on the variant data, it was expected that XBB variants continued to dominate infections till late 2023. Successful analysis of low titer samples (Ct ≥ 30) suggests the high sensitivity of our platform. The cloud-based bioinformatic pipeline is automated from raw data to report generation and accessible through our web interface. In summary, this workflow can be used to monitor infection dynamics of circulating variants and predict emerging variants. Our solution can be used in the surveillance of SARS-CoV-2 variants and as an indicator of future outbreaks.