Exploring the diversity of coronavirus in sewage during COVID-19 pandemic: Don't miss the forest for the trees

https://doi.org/10.1016/j.scitotenv.2021.149562Get rights and content
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Highlights

  • NGS methods have been applied to study the sewage virome during COVID-19 pandemic.

  • Coronaviridae sequences were not detected in sewage using untargeted metagenomics.

  • Target Enrichment provided with SARS-CoV-2 sequences as part of the sewage virome.

  • Human and animal CoV co-circulation in sewage only detected with Target Enrichment.

Abstract

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 from clinical samples. The use of different available NGS tools applied to 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, 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 human Coronaviridae members (CoV) present in one of those samples after applying the enrichment. One contig was identified as HCoV-OC43 and 8 contigs as SARS-CoV-2. CoVs from other animal hosts were also detected when applying this technique. These contigs were compared with those obtained from contemporary clinical specimens by applying the same target enrichment approach. The results showed that there is a co-circulation in urban areas of human and animal coronaviruses infecting domestic animals and rodents. NGS enrichment-based protocols might be crucial to describe the occurrence and genetic characteristics of SARS-CoV-2 and other Coronaviridae family members within the excreted virome present in wastewater.

Keywords

Next generation sequencing
Viral metagenomics
Coronavirus
Sewage virome
Target enrichment sequencing

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