Metagenomic analysis of viruses in reclaimed water

Abstract

SummaryReclaimed water use is an important component of sustainable water resource management. However, there are concerns regarding pathogen transport through this alternative water supply. This study characterized the viral community found in reclaimed water and compared it with viruses in potable water. Reclaimed water contained 1000-fold more viruslike particles than potable water, having approximately 10 8 VLPs per millilitre. Metagenomic analyses revealed that most of the viruses in both reclaimed and potable water were novel. Bacteriophages dominated the DNA viral community in both reclaimed and potable water, but reclaimed water had a distinct phage community based on phage family distributions and host representation within each family. Eukaryotic viruses similar to plant pathogens and invertebrate picornaviruses dominated RNA metagenomic libraries. Established human pathogens were not detected in reclaimed water viral metagenomes, which contained a wealth of novel single-stranded DNA and RNA viruses related to plant, animal and insect viruses. Therefore, reclaimed water may play a role in the dissemination of highly stable viruses. Information regarding viruses present in reclaimed water but not in potable water can be used to identify new bioindicators of water quality. Future studies will need to investigate the infectivity and host range of these viruses to evaluate the impacts of reclaimed water use on human and ecosystem health.

Potential role of viruses in white plague coral disease

“…Interestingly, SCSDVs have been found to be abundant in reclaimed waters and sewage, suggesting that SCSDVs in the diseased corals examined here could be linked to environment degradation (Blinkova et al, 2009;Rosario et al, 2009). Previously it has been shown that environmental viruses such as human enteroviruses and adenoviruses are present on coral mucus, suggesting that these associations were the result of anthropogenic pollution (for example, runoff; Lipp et al, 2002Lipp et al, , 2007Futch et al, 2010).…”

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

“…In addition, the data set was supplemented with tombusvirus-like CP sequences recovered from the RNA virome obtained from Lake Needwood 45 . Notably, in none of the data sets containing information about both RNA and DNA virus communities present in the same environmental sample 34 could we detect both CHIVs and tombus-like RNA viruses (in the DNA and RNA fractions, respectively), pointing towards their divergent distribution. The tombusvirus sequences form a well-supported monophyletic clade.…”

“…To get further insight into the diversity and evolution of CHIVs, we have assembled sequence reads from 103 publicly available viromes and searched the resultant contigs for co-occurrence of genes encoding RC-Reps and RNA virus-like CPs (Supplementary Data 1). As a result, nine contigs were assembled from viromes derived from atmospheric 32 and aquatic 26,33,34 samples. As ssDNA viruses are known to integrate into the genomes of their hosts 35,36 , we also searched for the presence of CHIVs in the eukaryotic genome databases.…”

Recommended advanced techniques for waterborne pathogen detection in developing countries

“…In addition, by counting the reads of each sequence, valuable information may be learned about the contamination load in each water sample. One NGS approach, pyrosequencing, is a highthroughput molecular-level sequencing technique that has been applied to the study of microbial metagenomes in a variety of environmental samples, such as marine systems, freshwater, open ocean water, and reused wastewater [56][57][58][59][60]. Pyrosequencing delivers sequence reads up to 450 base pairs, which makes it possible to generate large amounts of data for bioinformatic analyses.…”