Setting a baseline for global urban virome surveillance in sewage

Abstract

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.

Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

“…NGS analysis can unravel the diversity of viruses within a complex sample such as wastewater, particularly by using unbiased sequencing of the sewage virome ( 43 ). Nevertheless, the detection of variants of a virus in a single sample can be challenging because of the relatively low number of reads obtained for each virus.…”

Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing

“…In depth NGS analysis could help to unravel the diversity of viruses within a complex sample such as wastewater, particularly unbiased sequencing of the sewage virome can give a good picture of the general viral diversity contained in a sample 36 . Nevertheless, the detection of variants of a particular virus in a single sample can be difficult due to the relative low number of reads obtained for each virus type.…”

Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams

“…In our previous work, we proposed methodological approaches that aimed to eliminate as much as possible bacteria, shellfish tissues, or free DNA or RNA (Strubbia et al, 2020), to focus on RNA viruses. This likely explains the low amount of DNA and phages viruses reads in our study unlike agnostic metagenomic studies where these viruses constituted the largest viral fraction (Bačnik et al, 2020;Nieuwenhuijse et al, 2020). We also performed technical triplicates of cDNA synthesis and libraries as we observed that it increases the odds to recover sequences from viruses present at low concentrations (Strubbia et al, 2020).…”