Whole genome sequencing of SARS-CoV-2 links wastewater RNA to individual cases in catchments.

After a limited first wave of community transmission in March 2020, Western Australia has remained largely free of COVID-19, with cases restricted to hotel quarantine, commercial vessels, and small, infrequent community clusters. Despite so few cases, whole genome sequencing (WGS) of SARS-CoV-2 from wastewater of large municipal treatments plants yielded genomic coverage up to 98% with sufficient depth to link wastewater to the WGS sequences of active cases in the catchment at the time. WGS analysis of wastewater contemporaneous with clinical cases can also be used to rule out transmission between cases in different catchments, when their SARS-CoV-2 genomes differ. These findings reveal a greater potential of wastewater WGS to inform outbreak control and disease surveillance than previously recognized.