Viral Eco-Genomic Tools: Development and Implementation for Aquatic Biomonitoring (2024)

Viral indicators for tracking domestic wastewater contamination in the aquatic environment

Water Research, 2020

Metagenomics and the development of viral water quality tools

npj clean water, 2019

Application of enteric viruses for fecal pollution source tracking in environmental waters

2012

Rapid Detection of Enteroviruses in Small Volumes of Natural Waters by Real-Time Quantitative Reverse Transcriptase PCR

Applied and Environmental Microbiology, 2005

Despite viral contamination of recreational waters, only bacterial, not viral, indicators are monitored routinely, due to a lack of rapid and cost-effective assays. We used negatively charged filters to capture enteroviruses from seawater and freshwater. Viral RNA was extracted using a commercial kit, and the viruses were quantified by real-time quantitative reverse transcriptase PCR (qRT-PCR). Poliovirus (6.6 to 330,000 virus particles/ml) was added to samples from watersheds in Los Angeles, California, and analysis showed that with 50-ml samples, a cellulose acetate/nitrate (HA) filter yielded final recovery of 51% (r 2 = 0.99) in fresh water and 23% (r 2 = 0.90) in seawater. However, for additions of low levels of virus (more likely to represent field samples; <104 enterovirus particles/ml), the recovery was lower and more variable, with HA being best in freshwater (17%, r 2 = 0.97) and the type GF/F glass filter having higher average recovery in seawater (GF/F, 17%; r 2 = 0.9...

Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control

Frontiers in microbiology, 2016

Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensively expounded mainly because of the lack of appropriate tools for environmental studies on aquatic viruses. However, the upcoming of metagenomics analyses opens great avenues in which environmental samples can be used to study the epidemiology of viral diseases outside their host species. Hence, in this review I have shown that epidemiological factors that influence the composition of viruses in different aquatic environments include ecological factors, anthropogenic activities and stocking densities of cultured organisms based on environmental metagenomics studies carried out this far. Ballast water transportation and global trade of aquatic organisms are the most common virus dispersal process identified this far. In terms of dise...

Current Advances on Virus Discovery and Diagnostic Role of Viral Metagenomics in Aquatic Organisms

Frontiers in microbiology, 2017

The global expansion of the aquaculture industry has brought with it a corresponding increase of novel viruses infecting different aquatic organisms. These emerging viral pathogens have proved to be a challenge to the use of traditional cell-cultures and immunoassays for identification of new viruses especially in situations where the novel viruses are unculturable and no antibodies exist for their identification. Viral metagenomics has the potential to identify novel viruses without prior knowledge of their genomic sequence data and may provide a solution for the study of unculturable viruses. This review provides a synopsis on the contribution of viral metagenomics to the discovery of viruses infecting different aquatic organisms as well as its potential role in viral diagnostics. High throughput Next Generation sequencing (NGS) and library construction used in metagenomic projects have simplified the task of generating complete viral genomes unlike the challenge faced in traditio...

Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis

Frontiers in Microbiology, 2015

Viral Communities Distribution and Diversity in a Wastewater Treatment Plants Using High-throughput Sequencing Analysis

2021

Waterborne pathogens are still considered a threat to human health. Wastewater treatment plants (WWTPs), contain a high populace and diversity of viruses that can significantly affect the aquatic ecosystem. Subsequently, the occurrence and recurrence of viral pathogens are alarming that exist in human populations, which are potentially discharged into sewage systems. This study investigated the distribution and diversity of the viral communities from three WWTPs in Gauteng Province, South Africa using next-generation sequencing technology. The results uncovered that most of the viral populaces in the wastewater plants belong to the families Siphoviridae, Microviridae, and Myoviridae of the order Caudovirales. Other families including Baculoviridae, Partitiviridae, Virgaviridae, and Tymoviridae were likewise recorded. On the other hand, enteric pathogens detected were Astroviridae, Reoviridae, and Coronaviridae. The predicted functional features for the viromes revealed that the DNA ...

From Lab to Lake - Evaluation of Current Molecular Methods for the Detection of Infectious Enteric Viruses in Complex Water Matrices in an Urban Area

PloS one, 2016

Quantitative PCR methods are commonly used to monitor enteric viruses in the aquatic environment because of their high sensitivity, short reaction times and relatively low operational cost. However, conclusions for public health drawn from results of such molecular techniques are limited due to their inability to determine viral infectivity. Ethidium monoazide (EMA) and propidium monoazide (PMA) are capable to penetrate the damaged or compromised capsid of the inactivated viruses and bind to the viral nucleic acids. We assessed whether dye treatment is a suitable approach to improve the ability of qPCR to distinguish between infectious and non-infectious human adenovirus, enterovirus and rotavirus A in surface water of an urban river and sewage before and after UV disinfection. Like the gold standard of cell culture assays, pretreatment EMA-/PMA-qPCR succeeded in removing false positive results which would lead to an overestimation of the viral load if only qPCR of the environmental...

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

mSystems

Detection of viruses in the environment is heavily dependent on PCR-based approaches that require reference sequences for primer design. While this strategy can accurately detect known viruses, it will not find novel genotypes or emerging and invasive viral species. In this study, we investigated the use of viromics, i.e., high-throughput sequencing of the biosphere's viral fraction, to detect human-/animal-pathogenic RNA viruses in the Conwy river catchment area in Wales, United Kingdom. Using a combination of filtering and nuclease treatment, we extracted the viral fraction from wastewater and estuarine river water and sediment, followed by high-throughput RNA sequencing (RNA-Seq) analysis on the Illumina HiSeq platform, for the discovery of RNA virus genomes. We found a higher richness of RNA viruses in wastewater samples than in river water and sediment, and we assembled a complete norovirus genotype GI.2 genome from wastewater effluent, which was not contemporaneously detec...