Raw Sewage Harbors Diverse Viral Populations

Abstract

At this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(+)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity.Importance At this time, virology is focused on the study of a relatively small number of viral species. Specific viruses are studied either because they are easily propagated in the laboratory or because they are associated with disease. The lack of knowledge of the size and characteristics of the viral universe and the diversity of viral genomes is a roadblock to understanding important issues, such as the origin of emerging pathogens and the extent of gene exchange among viruses. Untreated wastewater is an ideal system for assessing viral diversity because virion populations from large numbers of individuals are deposited and because raw sewage itself provides a rich environment for the growth of diverse host species and thus their viruses. These studies suggest that the viral universe is far more vast and diverse than previously suspected.

Papillomavirus

“…This nested PCR system, validated on clinical samples, has proved to be a powerful tool for HPV detection even in environmental samples Iaconelli et al, 2015;La Rosa et al, 2015) . Recently, next generation sequencing has been shown to be effective in the detection of a wide range of HPVs, including novel types, in both clinical and environmental samples (Bibby & Peccia, 2013;Bzhalava et al, 2014;Cantalupo et al, 2011;Johansson et al, 2013;Kocjan et al, 2015). Since deep sequencing technologies are continuously evolving with increasing throughput and decreasing costs, it is likely that an expanding diversity of HPVs will continue to be revealed.…”

“…Table 3 summarizes the studies on HPVs in environmental samples. NR -Not Reported a GC/L= Genome copy number per liter; assuming 1GC =1 viron Cantalupo et al, 2011;Bibby and Peccia, 2013 described observations of HPV 112 and 7, 10, 16, 18, 34, 49, 53, 63, 90, 92, 129 in sewage and sewage sludge in Spain and USA but no quantitative data were available.…”

“…Recently, the possibility of waterborne transmission has been raised Reynolds, 2012), due to the fact that HPVs are excreted both in the urine and in the feces. And indeed, HPV has recently been detected both in sewage and in sewage sludge (Bibby & Peccia, 2013;Cantalupo et al, 2011;Symonds, 2008). Consequently, these viruses may reach waters receiving sewage discharge.…”

Polioviruses and other Enteroviruses

“…More recent, deep-sequencing analysis of viral metagenomes from sewage and sewage sludge (also known as sewage viromes) has indicated that these novel human picornaviruses can be found in most cases at relatively higher abundance and occurrence than members of the Enterovirus genus (Aw et al, 2014;Bibby and Peccia, 2013;Cantalupo et al, 2011;Ng et al, 2012). Taken together, these studies have demonstrated the importance of targeted molecular assays and unbiased high-throughput sequencing (i.e., metagenomics viral pathogen detection technologies) to the study of virus diversity in waste waters and to monitor shedding of known and newly characterized viral human pathogens on a population level scale.…”

Whole‐Genome Sequencing of a Single Viral Species from a Highly Heterogeneous Sample

“…Previous metagenomic studies reveal that wastewater harbors diverse viral species including previously undescribed viruses with unknown viral sequences outnumbering known viral sequences by a factor of 10 to 1,000 [3] . This indicates that raw sewage is an excellent source for previously undescribed viruses.…”