Targeted amplicon sequencing of wastewater samples for detecting SARS-CoV-2 variants with high sensitivity and resolution. Severe acute respiratory syndrome coronavirus 2

We developed a next-generation sequencing (NGS)-based method to determine the identity and composition of individual SARS-CoV-2 sublineages in wastewater samples through this project. The combination and optimization of targeted amplicon sequencing and nested PCR allowed detection of each variant with sensitivity comparable to that of qPCR.