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Journal ArticleDOI

Eukaryotic Viruses in Wastewater Samples from the United States

01 Mar 2009-Applied and Environmental Microbiology (American Society for Microbiology)-Vol. 75, Iss: 5, pp 1402-1409
TL;DR: A baseline understanding of viruses in raw sewage will enable educated decisions to be made regarding the use of different viruses in water quality assessments, and uncovered previously unknown sequence diversity in human picobirnaviruses.
Abstract: Human fecal matter contains a large number of viruses, and current bacterial indicators used for monitoring water quality do not correlate with the presence of pathogenic viruses. Adenoviruses and enteroviruses have often been used to identify fecal pollution in the environment; however, other viruses shed in fecal matter may more accurately detect fecal pollution. The purpose of this study was to develop a baseline understanding of the types of viruses found in raw sewage. PCR was used to detect adenoviruses, enteroviruses, hepatitis B viruses, herpesviruses, morbilliviruses, noroviruses, papillomaviruses, picobirnaviruses, reoviruses, and rotaviruses in raw sewage collected throughout the United States. Adenoviruses and picobirnaviruses were detected in 100% of raw sewage samples and 25% and 33% of final effluent samples, respectively. Enteroviruses and noroviruses were detected in 75% and 58% of raw sewage samples, respectively, and both viral groups were found in 8% of final effluent samples. This study showed that adenoviruses, enteroviruses, noroviruses, and picobirnaviruses are widespread in raw sewage. Since adenoviruses and picobirnaviruses were detected in 100% of raw sewage samples, they are potential markers of fecal contamination. Additionally, this research uncovered previously unknown sequence diversity in human picobirnaviruses. This baseline understanding of viruses in raw sewage will enable educated decisions to be made regarding the use of different viruses in water quality assessments.
Citations
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Journal ArticleDOI
TL;DR: The results suggest that absorption-extraction methods with minimal pretreatment or without manipulation can provide suitably rapid, cost-effective and relatively straightforward recovery of enveloped viruses in wastewater.

372 citations


Cites background or methods from "Eukaryotic Viruses in Wastewater Sa..."

  • ...Thesemethods have been previously used to concentrate viruses from (waste)water (Symonds et al., 2009; Ikner et al., 2011) and recently used for SARS-CoV-2 RNA detection in untreated wastewater (Ahmed et al....

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  • ...This centrifugal concentration step was repeated three times to pass through the entire supernatant volume (Symonds et al., 2009; Ikner et al., 2011; Ahmed et al., 2015)....

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  • ...Methods D and E were ultrafiltration methods that use centrifugal devices that have previously been used to concentrate viruses from (waste)water (Symonds et al., 2009; Ikner et al., 2011)....

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Journal ArticleDOI
01 Nov 2011-Mbio
TL;DR: Deep sequencing nucleic acids obtained from virion populations enriched from raw sewage revealed 234 known viruses, including 17 that infect humans, making untreated wastewater the most diverse viral metagenome examined thus far.
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 vi- ruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA (ssRNA()), and dsRNA ge- nomes. 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 stud- ied 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.

277 citations

Journal ArticleDOI
TL;DR: It is demonstrated that the plant pathogen Pepper mild mottle virus (PMMoV) is widespread and abundant in wastewater from the United States, suggesting the utility of this virus as an indicator of human fecal pollution.
Abstract: Accurate indicators of fecal pollution are needed in order to minimize public health risks associated with wastewater contamination in recreational waters. However, the bacterial indicators currently used for monitoring water quality do not correlate with the presence of pathogens. Here we demonstrate that the plant pathogen Pepper mild mottle virus (PMMoV) is widespread and abundant in wastewater from the United States, suggesting the utility of this virus as an indicator of human fecal pollution. Quantitative PCR was used to determine the abundance of PMMoV in raw sewage, treated wastewater, seawater exposed to wastewater, and fecal samples and/or intestinal homogenates from a wide variety of animals. PMMoV was present in all wastewater samples at concentrations greater than 1 million copies per milliliter of raw sewage. Despite the ubiquity of PMMoV in human feces, this virus was not detected in the majority of animal fecal samples tested, with the exception of chicken and seagull samples. PMMoV was detected in four out of six seawater samples collected near point sources of secondary treated wastewater off southeastern Florida, where it co-occurred with several other pathogens and indicators of fecal pollution. Since PMMoV was not found in nonpolluted seawater samples and could be detected in surface seawater for approximately 1 week after its initial introduction, the presence of PMMoV in the marine environment reflects a recent contamination event. Together, these data demonstrate that PMMoV is a promising new indicator of fecal pollution in coastal environments.

253 citations


Cites background from "Eukaryotic Viruses in Wastewater Sa..."

  • ...Wastewater samples were collected from 12 treatment facilities in 11 coastal states from the United States to determine the prevalence of PMMoV....

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  • ...This study analyzed the presence of PMMoV in raw sewage and treated wastewater samples collected from wastewater treatment facilities throughout the coastal United States....

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  • ...Here we demonstrate that the plant pathogen Pepper mild mottle virus (PMMoV) is widespread and abundant in wastewater from the United States, suggesting the utility of this virus as an indicator of human fecal pollution....

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  • ...Ten-milliliter samples of raw sewage and treated wastewater were gathered from 12 wastewater treatment facilities throughout the coastal United States (Table 1) and were concentrated according to the methods of Symonds et al. (41)....

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  • ...Picobirnaviruses and Torque teno virus are abundant in raw sewage from some regions and thus have also been proposed as indicator viruses (15, 41)....

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Journal ArticleDOI
TL;DR: The utility of analyzing sewage to monitor shedding of viral pathogens and the high viral diversity found in this common pollutant are highlighted and genetic information is provided to facilitate future studies of these newly characterized viruses.
Abstract: Deep sequencing of untreated sewage provides an opportunity to monitor enteric infections in large populations and for high-throughput viral discovery. A metagenomics analysis of purified viral particles in untreated sewage from the United States (San Francisco, CA), Nigeria (Maiduguri), Thailand (Bangkok), and Nepal (Kathmandu) revealed sequences related to 29 eukaryotic viral families infecting vertebrates, invertebrates, and plants (BLASTx E score, 90% protein identities) in numerous viral families infecting humans (Adenoviridae, Astroviridae, Caliciviridae, Hepeviridae, Parvoviridae, Picornaviridae, Picobirnaviridae, and Reoviridae), plants (Alphaflexiviridae, Betaflexiviridae, Partitiviridae, Sobemovirus, Secoviridae, Tombusviridae, Tymoviridae, Virgaviridae), and insects (Dicistroviridae, Nodaviridae, and Parvoviridae). The full and partial genomes of a novel kobuvirus, salivirus, and sapovirus are described. A novel astrovirus (casa astrovirus) basal to those infecting mammals and birds, potentially representing a third astrovirus genus, was partially characterized. Potential new genera and families of viruses distantly related to members of the single-stranded RNA picorna-like virus superfamily were genetically characterized and named Picalivirus, Secalivirus, Hepelivirus, Nedicistrovirus, Cadicistrovirus, and Niflavirus. Phylogenetic analysis placed these highly divergent genomes near the root of the picorna-like virus superfamily, with possible vertebrate, plant, or arthropod hosts inferred from nucleotide composition analysis. Circular DNA genomes distantly related to the plant-infecting Geminiviridae family were named Baminivirus, Nimivirus, and Niminivirus. These results highlight the utility of analyzing sewage to monitor shedding of viral pathogens and the high viral diversity found in this common pollutant and provide genetic information to facilitate future studies of these newly characterized viruses.

248 citations

Journal ArticleDOI
TL;DR: The high excretion level and dissemination of PMMoV in human sewage and river water suggest thatPMMoV could be a promising indicator of fecal pollution in surface water.

192 citations


Cites background from "Eukaryotic Viruses in Wastewater Sa..."

  • ...The selection of the hPBV for the present study was due to its high prevalence in wastewater samples (Symonds et al., 2009)....

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References
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Journal ArticleDOI
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.

88,255 citations

Journal ArticleDOI
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

70,111 citations

Journal ArticleDOI
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Abstract: CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

38,522 citations


"Eukaryotic Viruses in Wastewater Sa..." refers methods in this paper

  • ...8 (73), and phylogenetic analyses were carried out with MEGA v....

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Journal ArticleDOI
TL;DR: Version 4 of MEGA software expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses.
Abstract: We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).

29,021 citations

Journal ArticleDOI
01 Jul 1971-Ecology
TL;DR: It is suggested that species diversity has become a meaningless concept, that the term be abandoned, and that ecologists take a more critical approach to species-number relations and rely less on information theoretic and other analogies.
Abstract: The recent literature on species diversity contains many semantic, conceptual, and technical problems. It is suggested that, as a result of these problems, species diversity has become a meaningless concept, that the term be abandoned, and that ecologists take a more critical approach to species—number relations and rely less on information theoretic and other analogies. As multispecific collections of organisms possess numerous statistical properties which conform to the conventional criteria for diversity indices, such collections are not intrinsically arrangeable in linear order along some diversity scale. Several such properties or "species composition parameters" having straightforward biological interpretations are presented as alternatives to the diversity approach. The two most basic of these are simply ▵1=[n/n—1][1—Σi(N_i/_N)2] =the proportion of potential interindividual encounters which is interspecific (as opposed to intraspecific), assuming every individual in the collection can encounter all other individuals, E(Sn) = Σi [1—(N—Nin)/(Nn)] =the expected number of species in a sample of n individuals selected at random from a collection containing N individuals, S species, and Ni individuals in the ith species.

3,924 citations


"Eukaryotic Viruses in Wastewater Sa..." refers methods in this paper

  • ...In addition to dereplicating sequences, FastGroup II (81) was also used to calculate the Chao1 value, a richness estimator (22, 23), and to plot a rarefaction curve, which displays the number of unique sequences versus the number of clones sequenced (42, 46)....

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