Wastewater Tiling Amplicon Sequencing Reveals Longitudinal Dynamics of SARS-CoV-2 Variants Prevalence in the Community

Abstract

AbstractSARS-CoV-2 continues to evolve, while the decline in clinical sequencing efforts hampers public health sectors to prepare for the menace of ongoing variant emergence and future COVID-19 surges.1Wastewater-based epidemiology (WBE) has been proposed to provide complementary insights on the variants being transmitted in communities.2However, limited research has been dedicated to the use sequencing methods for tracking disease prevalence and variant dynamics in wastewater, particularly on a large scale. Here, we employed a tiling amplicon sequencing to track the dynamics of variant of concern (VOC) in wastewater collected from Queensland, Australia from 2020 to 2022. RNA concentrations in wastewater measured by ATOPlex showed a stronger correlation and greater consistency with the number of daily new cases than a PCR-based method. The VOC dynamics observed in wastewater were largely in line with clinical reports. These findings support that WBE and sensitive sequencing methods can serve as a long-term approach for disease surveillance, thus aiding in disease outbreak prevention, control, and management.