Detection of SARS-CoV-2 with VirCapSeq capture on wastewater metagenomic samples

In the wake of the COVID-19 pandemic, the use of next generation sequencing (NGS) has proved to be an important tool for the genetic characterization of SARS-CoV-2, both from clinical isolates as well as wastewater-based epidemiology for early warning outbreak containment. The use of NGS in wastewater samples could be the key for an in-depth study of the excreted virome, not only focusing on SARS-CoV-2 circulation and typing, but also to detect other potentially pandemic viruses within the same family. With this aim, two 24-hours composite wastewater samples from March and July 2020 were sequenced by applying specific viral NGS as well as target enrichment NGS. The full virome of the analyzed samples was obtained, with Coronaviridae members (CoV) in one of those samples after applying the enrichment. One contig was identified as HCoV-OC43 and 8 contigs as SARS-CoV-2. These contigs were compared with those obtained from clinical specimens by applying the same target enrichment approach. CoVs with other animal hosts were also detected when applying this technique. The results showed that there is a co-circulation of human and animal coronaviruses in urban areas infecting domestic animals and rodents. NGS enrichment-based protocols might be crucial to describe the occurrence and genetic characteristics of Coronaviridae family members within the excreted virome present in wastewater.