Abstract
Sewage-associated viruses can cause several human and animal diseases, such as gastroenteritis, hepatitis, and respiratory infections. Therefore, their detection in wastewater can reflect current infections within the source population. To date, no viral study has been performed using the sewage of any large South American city. In this study, we used viral metagenomics to obtain a single sample snapshot of the RNA virosphere in the wastewater from Santiago de Chile, the seventh largest city in the Americas. Despite the overrepresentation of dsRNA viruses, our results show that Santiago’s sewage RNA virosphere was composed mostly of unknown sequences (88%), while known viral sequences were dominated by viruses that infect bacteria (60%), invertebrates (37%) and humans (2.4%). Interestingly, we discovered three novel genogroups within the Picobirnaviridae family that can fill major gaps in this taxa’s evolutionary history. We also demonstrated the dominance of emerging Rotavirus genotypes, such as G8 and G6, that have displaced other classical genotypes, which is consistent with recent clinical reports. This study supports the usefulness of sewage viral metagenomics for public health surveillance. Moreover, it demonstrates the need to monitor the viral component during the wastewater treatment and recycling process, where this virome can constitute a reservoir of human pathogens.
Highlights
Viruses are the most abundant biological entities on Earth, with an estimated 1031 particles worldwide [1]
Urban environments impacted by human activity, such as wastewater treatment plants (WWTPs) and sewage are not an exception
Viruses associated with the biological waste of a city are mixed with viruses from all the organisms living in the WWTP, forming an untapped source of viral diversity [2,3]
Summary
Viruses are the most abundant biological entities on Earth, with an estimated 1031 particles worldwide [1]. To solve this, recycled water derived from WWTP effluent has been intensively used for industrial operations, agricultural irrigation and even recreational activities [8] In this way, recycling of treated sewage generates a potential public health risk, as well as a critical risk for agricultural and animal production industries, due to insufficient removal of pathogenic viruses [6,8,9]. We unveiled abundant and emergent Rotavirus A genotypes never before recorded in Chile, representing changes in the prevalence of the classical genotypes The latter discovery provides evidence for the benefits of using viral metagenomics to aid public health surveillance based on excreted viruses in sewage. Viruses 2020, 12, x FOR PEER REVIEW of analyzing viral dark matter through self-clustering of the sequences independent of their direct comparison to databases, Materials and Methodswhich can result in the discovery and classification of new viral sequences
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