Viruses In Aquatic Environments Research Articles

Activation of peroxymonosulfate by sustainable biomass-based carbon nanotubes for controlling the spread of plant viruses in water environments

With the increasing demand for water in hydroponic systems and agricultural irrigation, viral diseases have seriously affected the yield and quality of crops. By removing plant viruses in water environments, virus transmission can be prevented and agricultural production and ecosystems can be protected. But so far, there have been few reports on the removal of plant viruses in water environments. Herein, in this study, easily recyclable biomass-based carbon nanotubes catalysts were synthesized with varying metal activities to activate peroxymonosulfate (PMS). Among them, the magnetic 0.125Fe@NCNTs-1/PMS system showed the best overall removal performance against pepper mild mottle virus, with a 5.9 log10 removal within 1 min. Notably, the key reactive species in the 0.125Fe@NCNTs-1/PMS system is 1O2, which can maintain good removal effect in real water matrices (river water and tap water). Through RNA fragment analyses and label free analysis, it was found that this system could effectively cleave virus particles, destroy viral proteins and expose their genome. The capsid protein of pepper mild mottle virus was effectively decomposed where serine may be the main attacking sites by 1O2. Long viral RNA fragments (3349 and 1642 nt) were cut into smaller fragments (∼160 nt) and caused their degradation. In summary, this study contributes to controlling the spread of plant viruses in real water environment, which will potentially help protect agricultural production and food safety, and improve the health and sustainability of ecosystems.

Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments.

The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the followingaims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.

Tracing the fate of wastewater viruses reveals catchment-scale virome diversity and connectivity

The discharge of wastewater-derived viruses in aquatic environments impacts catchment-scale virome composition. To explore this, we used viromic analysis of RNA and DNA virus-like particles to holistically track virus communities entering and leaving wastewater treatment plants and the connecting river catchment system and estuary. We reconstructed >40 000 partial viral genomes into 10 149 species-level groups, dominated by dsDNA and (+)ssRNA bacteriophages (Caudoviricetes and Leviviricetes) and a small number of genomes that could pose a risk to human health. We found substantial viral diversity and geographically distinct virus communities associated with different wastewater treatment plants. River and estuarine water bodies harboured more diverse viral communities in downstream locations, influenced by tidal movement and proximity to wastewater treatment plants. Shellfish and beach sand were enriched in viral communities when compared with the surrounding water, acting as entrapment matrices for virus particles. Extensive phylogenetic analyses of environmental-derived and reference sequences showed the presence of human-associated sapovirus GII in all sample types, multiple rotavirus A strains in wastewater and a diverse set of picorna-like viruses associated with shellfish. We conclude that wastewater-derived viral genetic material is commonly deposited in the environment and can be traced throughout the freshwater-marine continuum of the river catchment, where it is influenced by local geography, weather events and tidal effects. Our data illustrate the utility of viromic analyses for wastewater- and environment-based ecology and epidemiology, and we present a conceptual model for the circulation of all types of viruses in a freshwater catchment.

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla.

Sequential treatment using a hydrophobic resin and gel filtration to improve viral gene quantification from highly complex environmental concentrates

Assays based on the polymerase chain reaction (PCR) are widely applied to quantify enteric viruses in aquatic environments to study their fates and potential infection risks. However, inhibitory substances enriched by virus concentration processes can result in inaccurate quantification. This study aimed to find a method for improving virus quantification by mitigating the effects of inhibitory environmental concentrates, using previous knowledge of the properties of the inhibitory substances. Performances of anion exchange resins, gel filtration, and a hydrophobic resin (DAX-8) were comparatively evaluated using poliovirus and its extracted RNA spiked into humic acid solutions. These solutions served as good representatives of the inhibitory environmental concentrates. A sequential treatment using DAX-8 resin and gel filtration produced the most favorable results, i.e., low virus losses that were stable and a reduced inhibitory effect. Furthermore, the sequential treatment was applied to another set of 15 environmental concentrates. Without the sequential treatment, serious underestimation (>4.0 log10 to 1.1 log10) of a molecular process control (murine norovirus) was measured for eight samples. With the treatment, the control was detected with <1.0 log10 underestimation for all samples. The treatment improved the quantification of seven types of indigenous viruses. In summary, the sequential treatment is effective in improving the viral quantification in various of environmental concentrates.

Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages.

Viruses in aquatic environments play a key role in microbial population dynamics and nutrient cycling. In particular, bacteria of the phylum Bacteriodetes are known to participate in recycling algal blooms. Studies of phage–host interactions involving this phylum are hence important to understand the processes shaping bacterial and viral communities in the ocean as well as nutrient cycling. In this study, we isolated and sequenced three strains of flavobacteria—LMO6, LMO9, LMO8—and 38 virulent phages infecting them. These phages represent 15 species, occupying three novel genera. Additionally, one temperate phage was induced from LMO6 and was found to be competent at infecting LMO9. Functions could be predicted for a limited number of phage genes, mainly representing roles in DNA replication and virus particle formation. No metabolic genes were detected. While the phages isolated on LMO8 could infect all three bacterial strains, the LMO6 and LMO9 phages could not infect LMO8. Of the phages isolated on LMO9, several showed a host-derived reduced efficiency of plating on LMO6, potentially due to differences in DNA methyltransferase genes. Overall, these phage–host systems contribute novel genetic information to our sequence databases and present valuable tools for the study of both virulent and temperate phages.

Microcosm environment models for studying the stability of adenovirus and murine norovirus in water and sediment.

Microcosms are useful tools for understanding the survival and fate of enteric viruses in aquatic environments. This study set out to determine the stability of infectious enteric viruses in an aquatic environment using a laboratory scale microcosm. Sediment and overlaying water were collected from a lagoon and inoculated with known concentrations of recombinant adenovirus (AdV-GFP) and murine norovirus (MNV-1). Infectious particles of these viruses were measured using fluorescence microscopy (AdV-GFP) or the plaque assay method (MNV-1), over 85 days in two different conditions: under natural sunlight and in fully darkened environments. The time required to reach one log reduction in viral titres (T90) of viable viruses in a natural condition microcosm for AdV-GFP and MNV-1 was shorter than in a dark condition microcosm. There was also a negative correlation between the temperature and infectivity of these viruses in both water and sediment samples. Considering that microcosms aim to mimic natural environment conditions and that AdV-GFP and MNV-1 are excellent surrogates for measuring the infectivity of the respective viruses strains, the results presented here have the potential to be applied in future health hazard studies and also would be useful for future climate scenarios.

Interaction of Microcystis and Phix174 in the Aquatic Environment

AbstractThis study aimed to explore the potential impact of algal blooms on the survival of viruses in aquatic environments by using Microcystis and somatic coliphage phiX174 as a model algae and m...

Cannibalistic viruses in the aquatic environment: role of virophages in manipulating microbial communities

The ecological role of viruses in aquatic environments is gaining interest due to their abundance and overall diversity. Much focus has been on bacteriophages since they were found to play an important role in the diversification and sustainment at both the micro- and macro-scale. However, the discovery of virophages coexisting with giant viruses in a diverse set of eukaryotic hosts has recently gained attention. Virophages are small double-stranded DNA viruses found parasitizing giant viruses of eukaryotes. Since the discovery of the first virophage (Sputnik) many virophage signatures have been detected from a variety of environmental samples with specific infection cycles. In addition, these parasites display important roles in equilibrating microbial biomass, nutrient cycling and population dynamics. Moreover, virophage-induced evolution between giant viruses and their hosts have also been described. Considering the ongoing discovery of virophages and their dynamics in aquatic ecosystems, this review intends to provide an update of the virophage signatures identified to date, also tending to provide insight on the mechanisms of coinfection as well as their role as agents of biodiversity and nutrient cyclers in water environments.

Sunlight inactivation of somatic coliphage in the presence of natural organic matter

Long wavelengths of sunlight spectrum (UVA and visible light), as well as natural organic matter (NOM) are important environmental factors affecting survival of viruses in aquatic environment through direct and indirect inactivation. In order to understand the virus inactivation kinetics under such conditions, this study investigated the effects of Suwannee River natural organic matter (NOM) on the inactivation of a somatic coliphage, phiX174, by UVA and visible light. Experiments were carried out to examine the virucidal effects of UVA/visible light, assess the influence of SRNOM at different concentrations, and identify the effective ROS in virus inactivation. The results from this study showed that the presence of NOM could either enhance virus inactivation or reduce virus inactivation depending on the concentration, where the inactivation rate followed a parabolic relationship against NOM concentration. The results indicated that moderate levels of NOM (11ppm) had the strongest antiviral activity, while very low or very high NOM concentrations prolonged virus survival. The results also showed that OH▪ was the primary ROS in causing phiX174 (ssDNA virus) inactivation, unlike previous findings where 1O2 was the primary ROS causing MS2 (ssRNA virus) inactivation. The phiX174 inactivation by OH∙ could be described as k=3.7✕1013[OH∙]+1.404 (R2=0.8527).

Detection of peramivir and laninamivir, new anti-influenza drugs, in sewage effluent and river waters in Japan.

This is the first report of the detection of two new anti-influenza drugs, peramivir (PER) and laninamivir (LAN), in Japanese sewage effluent and river waters. Over about 1 year from October 2013 to July 2014, including the influenza prevalence season in January and February 2014, we monitored for five anti-influenza drugs—oseltamivir (OS), oseltamivir carboxylate (OC), zanamivir (ZAN), PER, and LAN—in river waters and in sewage effluent flowing into urban rivers of the Yodo River system in Japan. The dynamic profiles of these anti-influenza drugs were synchronized well with that of the numbers of influenza patients treated with the drugs. The highest levels in sewage effluents and river waters were, respectively, 82 and 41 ng/L (OS), 347 and 125 ng/L (OC), 110 and 35 ng/L (ZAN), 64 and 11 ng/L (PER), and 21 and 9 ng/L (LAN). However, application of ozone treatment before discharge from sewage treatment plants was effective in reducing the levels of these anti-influenza drugs in effluent. The effectiveness of the ozone treatment and the drug dependent difference in susceptibility against ozone were further evidenced by ozonation of a STP effluent in a batch reactor. These findings should help to promote further environmental risk assessment of the generation of drug-resistant influenza viruses in aquatic environments.

The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics

ABSTRACTViruses have a profound influence on the ecology and evolution of plankton, but our understanding of the composition of the aquatic viral communities is still rudimentary. This is especially true of those viruses having RNA genomes. The limited data that have been published suggest that the RNA virioplankton is dominated by viruses with positive-sense, single-stranded (+ss) genomes that have features in common with those of eukaryote-infecting viruses in the order Picornavirales (picornavirads). In this study, we investigated the diversity of the RNA virus assemblages in tropical coastal seawater samples using targeted PCR and metagenomics. Amplification of RNA-dependent RNA polymerase (RdRp) genes from fractions of a buoyant density gradient suggested that the distribution of two major subclades of the marine picornavirads was largely congruent with the distribution of total virus-like RNA, a finding consistent with their proposed dominance. Analyses of the RdRp sequences in the library revealed the presence of many diverse phylotypes, most of which were related only distantly to those of cultivated viruses. Phylogenetic analysis suggests that there were hundreds of unique picornavirad-like phylotypes in one 35-liter sample that differed from one another by at least as much as the differences among currently recognized species. Assembly of the sequences in the metagenome resulted in the reconstruction of six essentially complete viral genomes that had features similar to viruses in the families Bacillarna-, Dicistro-, and Marnaviridae. Comparison of the tropical seawater metagenomes with those from other habitats suggests that +ssRNA viruses are generally the most common types of RNA viruses in aquatic environments, but biases in library preparation remain a possible explanation for this observation.

Geochemistry of Virus–Prokaryote Interactions in Freshwater and Acid Mine Drainage Environments, Ontario, Canada

An extensive water sample survey was conducted in southern Ontario, Canada across a variety of freshwater systems in order to further understand the role of viruses in aquatic environments. Backwards stepwise multiple regression analysis found that VLP (virus-like particle) abundance, phosphate, pH, sulfate, and magnesium are predictors of prokaryotic abundance with the model describing 90% of the variability in the data (R2 = 0.90). Statistically significant (P < 0.05) predictors of VLP abundance were mineral saturation indices (SI) of goethite (R2 = 0.78) although moderate Pearson component analysis correlations (r) were noted with ferrihydrite, jarosite, and pyrolusite. These relationships indicate that viral inactivation through mineral attachment may be a contributor to the moderate relationship between VLP and prokaryotic abundance (rs = 0.45). In addition, VLP abundance is shown to have a stronger correlation with minerals SI values than prokaryotes indicating a stronger mineral influence with viruses.

Freshwater Clams As Bioconcentrators of Avian Influenza Virus in Water

We report experimental evidence for bioconcentration of a low-pathogenicity avian influenza virus (H6N8) in the tissue of freshwater clams. Our results support the concept that freshwater clams may provide an effective tool for use in the early detection of influenza A viruses in aquatic environments.

Highly Pathogenic Influenza A(H5N1) Virus Survival in Complex Artificial Aquatic Biotopes

BackgroundVery little is known regarding the persistence of Highly Pathogenic Avian Influenza (HPAI) H5N1 viruses in aquatic environments in tropical countries, although environmental materials have been suggested to play a role as reservoirs and sources of transmission for H5N1 viruses.Methodology/Principal FindingsThe survival of HPAI H5N1 viruses in experimental aquatic biotopes (water, mud, aquatic flora and fauna) relevant to field conditions in Cambodia was investigated. Artificial aquatic biotopes, including simple ones containing only mud and water, and complex biotopes involving the presence of aquatic flora and fauna, were set up. They were experimentally contaminated with H5N1 virus. The persistence of HPAI H5N1 virus (local avian and human isolates) was determined by virus isolation in embryonated chicken eggs and by real-time reverse-polymerase chain reaction. Persistence of infectious virus did not exceed 4 days, and was only identified in rain water. No infectious virus particles were detected in pond and lake water or mud even when high inoculum doses were used. However, viral RNA persisted up to 20 days in rain water and 7 days in pond or lake water. Viral RNA was also detected in mud samples, up to 14 days post-contamination in several cases. Infectious virus and viral RNA was detected in few cases in the aquatic fauna and flora, especially in bivalves and labyrinth fish, although these organisms seemed to be mostly passive carriers of the virus rather than host allowing virus replication.Conclusions/SignificanceAlthough several factors for the survival and persistence of HPAI viruses in the environment are still to be elucidated, and are particularly hard to control in laboratory conditions, our results, along with previous data, support the idea that environmental surveillance is of major relevance for avian influenza control programs.

Validation of Internal Controls for Extraction and Amplification of Nucleic Acids from Enteric Viruses in Water Samples

Inhibitors that reduce viral nucleic acid extraction efficiency and interfere with cDNA synthesis and/or polymerase activity affect the molecular detection of viruses in aquatic environments. To overcome these significant problems, we developed a methodology for assessing nucleic acid yields and DNA amplification efficiencies for environmental water samples. This involved adding particles of adenovirus type 5 and murine norovirus and newly developed primer-sharing controls, which are amplified with the same primer pairs and result in the same amplicon sizes as the targets, to these samples. We found that nucleic acid loss during the extraction process, rather than reverse transcription-PCR (RT-PCR) inhibition, more significantly attributed to underestimation of the presence of viral genomes in the environmental water samples tested in this study. Our success rate for satisfactorily amplifying viral RNAs and DNAs by RT-PCR was higher than that for obtaining adequate nucleic acid preparations. We found that inhibitory properties were greatest when we used larger sample volumes. A magnetic silica bead-based RNA extraction method effectively removed inhibitors that interfere with viral nucleic acid extraction and RT-PCR. To our knowledge, this is the first study to assess the inhibitory properties of environmental water samples by using both control virus particles and primer-sharing controls.

Physical fractionation of aquatic viral assemblages

Aquatic viruses are extraordinarily diverse and have major influences on plankton ecology and evolution, but the majority of these viruses remain uncharacterized. Most viruses have not been cultivated and cultivationindependent means to explore viral diversity have provided only a fragmented view of viral genomic information. In this study, ultracentrifugation and chromatographic methods were evaluated for their ability to fractionate aquatic viruses based on their differing physical properties with the aim of physically enriching subsets of aquatic viruses for further study. Centrifugation in continuous cesium chloride gradients, strong and weak anion‐exchange chromatography, and size‐exclusion chromatography with Sephacryl S‐1000 were found to separate aquatic viruses based on their differing buoyant densities, surface charges, and sizes, respectively. Sucrose density gradients, cation‐exchange chromatography, and size‐exclusion chromatography using controlled‐pore glass were found to have insufficient resolution to effectively separate viral assemblages. Using the successful methods listed above, we were able to separate complex assemblages of viruses into fractions that had distinguishable subsets of the viruses present in the original community as determined by pulsed‐field gel electrophoresis. Strong anion‐exchange chromatography was particularly effective at separating viruses in the samples and resulted in one to six dominant viral genome bands in most fractions. Our results suggest that individual populations of viruses may be physically enriched, and possibly isolated, from complex assemblages without cultivation. These fractionation methods are expected to improve our ability to characterize the genotypes and phenotypes of the uncultivated majority of viruses in aquatic environments.

Chemical and microbiological parameters as possible indicators for human enteric viruses in surface water

There are still conflicting results on the suitability of chemical and microbiological parameters as indicators for the viral contamination of surface waters. In this study, conducted over 20 months, the abundance of human adenovirus, human polyomavirus, enterovirus, group A rotavirus and norovirus was determined in Ruhr and Rhine rivers, Germany. Additionally, prevalence of different possible indicators such as somatic coliphages, E. coli, intestinal enterococci, and total coliforms was also considered. Moreover, the chemical parameter TCPP (tris-(2-chloro-, 1-methyl-ethyl)-phosphate), characterized by environmental stability and human origin, was included. Furthermore, chemical parameters (fluoride, chloride, nitrate, nitrite, bromide, phosphate, and sulfate) which may influence the stability and subsequently the detection rates of viruses in aquatic environment were measured. Quantitative Real-Time (RT-)PCR and double agar layer test were used for the quantification of human enteric viruses and somatic coliphages, respectively. The analyses for E. coli, total coliforms, and intestinal enterococci were done with respect to the standard reference method. The chemical parameters were measured by liquid chromatography of ions and by gas chromatography-flame photometer detector (GC-FPD), respectively. We demonstrated that human adenovirus had the highest detection rate (96.3%), followed by somatic coliphages (73.5%), human polyomavirus (68.6%), and rotavirus (63.5%). However, norovirus GII and enterovirus were found in only 25.7 and 17.8%, respectively. The concentration of the viral genome ranged between 16 and 1.1 xs 10(6) gen. equ./l (genome equivalents/l) whereas the concentrations for TCPP ranged between 0.01 and 0.9 microg/l. The results of the Pearson correlation showed no association between TCPP and any other microbiological parameter. None of the other tested chemical parameters correlated negatively, and therefore they do not influence the stability of enteric viruses. We conclude that neither TCPP nor any other chemical or microbiological parameter can be used as a reliable indicator for the presence of enteric viruses in river water.

Application of real-time PCR assays to genotyping of F-specific phages in river water and sediments in Japan

Genotyping of F-specific RNA phages is currently one of the most promising approaches to differentiate between human and animal fecal contamination in aquatic environments. In this study, a total of 18 river water and sediment samples were collected from the Tonegawa River basin, Japan, in order to describe the genogroup distribution of F-specific RNA and DNA phages using genogroup-specific real-time PCR assays. F-specific phages were detected in nine (100%) river water and six (67%) sediment samples. Eighty-five phage plaques were isolated from these samples and subjected to real-time PCR assays specific for the phages. F-specific RNA phages of human genogroups (II and III) were detected in 32 (38%) plaques, whereas those of animal genogroups (I and IV) were detected in 17 (20%) plaques. No correlation was observed between the genogroup distribution of F-specific RNA phages and the occurrence of human adenovirus genomes, suggesting that genotyping of the phages alone is inadequate for the evaluation of the occurrence of viruses in aquatic environments. SYBR Green-based real-time PCR assay revealed the presence of F-specific DNA phages in four (5%) plaques, which were further classified into two genogroups (fd- and f1-like phages) by sequence analysis. Thirty-two (38%) plaques were not classified as the F-specific phage genogroups, indicating the limited applicability of these real-time PCR assays to a wide range of aquatic environmental samples worldwide.

VIRUS REPLICATION FACTOR MAY BE A CONTROLLING AGENT FOR OBTAINING DISEASE-FREE SYSTEM IN A MULTI-SPECIES ECO-EPIDEMIOLOGICAL SYSTEM

The role of viruses in marine phytoplankton-zooplankton community structure is undoubtedly very important. In this paper, we propose a simple mathematical model for phytoplankton-zooplankton (prey-predator) system with an additional factor that the viral disease is spreading only among the prey species. Considering high abundance and importance of viruses in aquatic environments we have explicitly considered here the growth equation of free viruses and have studied this four-dimensional model analytically. It is observed that the disease-free system can be obtained when the virus replication factor lies in-between certain critical values. Numerical simulations have also been performed to substantiate the analytical findings.