Management of the COVID-19 pandemic is an ongoing challenge that requires the understanding of the full extent of the prevalence of Variants of Concern (VOCs). Inferring lineage prevalence by clinical testing is not scalable due to limited resources dedicated to testing/sequencing and reporting; that hospitalizations lag infections by weeks; and that mild or asymptomatic cases are not reported. Municipal wastewater is an informative media that can be leveraged to assess the prevalence of the COVID-19 in a scalable fashion. Challenges remain in terms of the quantification of viral RNA in the wastewater; the delineation of VOCs; and phylogenetic inference of VOCs. By applying tiling amplicon library preparation, high throughput sequencing and droplet digital PCR (ddPCR), we have shown evidence to address these urgent needs. Our results showed: (1) quantification of SARS-CoV-2 RNA at at least one order of magnitude lower that that the detection limit of RT-qPCR; (2) the solid fraction of the wastewater potentially harbours significantly higher amount of viral RNA than the liquid fraction; (3) and delineation and phylogenetic analysis of VOCs is feasible from wastewater. Ongoing work aims to further enrich our capacity to provide accurate and timely detection of pathogens from wastewater to strengthen public health management.