Metagenomic Insights into the Sewage RNA Virosphere of a Large City

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.

The True Host/s of Picobirnaviruses

“…Since PBVs have been mostly detected in feces/gut contents of animals and humans with or without diarrhea, they were considered as opportunistic enteric pathogens of mammals (2,3). However, the identification of the prokaryotic RBS sequence upstream of putative ORF/s in PBV and PBV-like sequences indicate that PBVs might actually infect bacteria (7,8,13,21). Furthermore, by phylogenetic analysis of viral RdRp sequences, the partitivirus-picobirnavirus clade has been hypothesized to have originated in an as-yet-undiscovered lineage of prokaryotic RNA viruses (76).…”

“…Certain viruses that infect prokaryotes have been shown to be highly enriched for RBS sequences, such as the bacteriophages with segmented dsRNA genomes of family Cystoviridae (13,21,64,65). Similar to prokaryotic mRNAs and the cystoviruses, the RBS sequence, or its subset has been found to be conserved upstream of putative ORF/s (putative ORF1, 2 and 3 in gene segment-1 and putative ORF for RdRp in gene segment-2) in published PBV sequences from humans, animals and environmental samples (4,7,8,(11)(12)(13)(14)(15)(16)(17)(18)21). The presence of the conserved prokaryotic RBS sequence upstream of the putative start codon/s in representative PBV gene segment-1 sequences, gene segment-2 sequences of PBV GI and GII strains, and PBVlike RdRp sequences are shown in Table 1.…”

“…Traditionally, PBVs are considered as opportunistic enteric pathogens of mammals and avian species (1)(2)(3)(4)(5). On the other hand, PBVs have also been detected in invertebrates and environmental samples (6)(7)(8)(9). During the past few years, the whole genomes, or at least the complete/nearly complete gene segment-2 sequences of several PBV strains from humans, different animal species and environmental samples have been obtained using next generation sequencing technologies, or a modified non-specific primer-based amplification method (1,4,(6)(7)(8)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20).…”

“…On the other hand, PBVs have also been detected in invertebrates and environmental samples (6)(7)(8)(9). During the past few years, the whole genomes, or at least the complete/nearly complete gene segment-2 sequences of several PBV strains from humans, different animal species and environmental samples have been obtained using next generation sequencing technologies, or a modified non-specific primer-based amplification method (1,4,(6)(7)(8)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). Analyses of the expanded repertoire of diverse full-length/nearly full-length PBV sequences revealed remarkable features in the PBV genome including those that suggest that PBVs might be actually prokaryotic or fungal viruses (1,4,(6)(7)(8)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21).…”

Viromes in Marine Ecosystems Reveal Remarkable Invertebrate RNA Virus Diversity

“…The oceans, which cover 71% of the Earth, are the most valuable resource for investigating the ecological and geographical diversity of viruses. However, to date, aquatic viromic studies tended to study phages but already showed enormous genetic diversity and ecological distributions (Roux, et al 2016; Vlok, et al 2019; Guajardo-Leiva, et al 2020; Gulino, et al 2020; Moon, et al 2020; Zhang, et al 2020). Although some studies included aquatic invertebrates (Magbanua, et al 2000; Thakur, et al 2002; Shi, et al 2016; Rosani, et al 2019), there is a lack of systematic study of these animals in a whole.…”