Publications by authors named "Sejal Modha"

20 Publications

  • Page 1 of 1

NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index.

Viruses 2020 12 10;12(12). Epub 2020 Dec 10.

National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA.

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus-host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/v12121424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764237PMC
December 2020

Pingu virus: A new picornavirus in penguins from Antarctica.

Virus Evol 2019 Jul 13;5(2):vez047. Epub 2019 Dec 13.

Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Avenida dos Bandeirantes 3900, Ribeirão Preto, SP, 14049-900 Brazil.

family comprises single-stranded, positive-sense RNA viruses distributed into forty-seven genera. Picornaviruses have a broad host range and geographic distribution in all continents. In this study, we applied a high-throughput sequencing approach to examine the presence of picornaviruses in penguins from King George Island, Antarctica. We discovered and characterized a novel picornavirus from cloacal swab samples of gentoo penguins (), which we tentatively named Pingu virus. Also, using RT-PCR we detected this virus in 12.9 per cent of cloacal swabs derived from , but not in samples from adélie penguins () or chinstrap penguins (). Attempts to isolate the virus in a chicken cell line and in embryonated chicken eggs were unsuccessful. Our results expand the viral diversity, host range, and geographical distribution of the .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/ve/vez047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908804PMC
July 2019

Metaviromics Reveals Unknown Viral Diversity in the Biting Midge .

Viruses 2019 09 17;11(9). Epub 2019 Sep 17.

MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.

Biting midges ( species) are vectors of arboviruses and were responsible for the emergence and spread of (SBV) in Europe in 2011 and are likely to be involved in the emergence of other arboviruses in Europe. Improved surveillance and better understanding of risks require a better understanding of the circulating viral diversity in these biting insects. In this study, we expand the sequence space of RNA viruses by identifying a number of novel RNA viruses from (biting midge) using a meta-transcriptomic approach. A novel metaviromic pipeline called MetaViC was developed specifically to identify novel virus sequence signatures from high throughput sequencing (HTS) datasets in the absence of a known host genome. MetaViC is a protein centric pipeline that looks for specific protein signatures in the reads and contigs generated as part of the pipeline. Several novel viruses, including an alphanodavirus with both segments, a novel relative of the Hubei sobemo-like virus 49, two rhabdo-like viruses and a chuvirus, were identified in the Scottish midge samples. The newly identified viruses were found to be phylogenetically distinct to those previous known. These findings expand our current knowledge of viral diversity in arthropods and especially in these understudied disease vectors.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/v11090865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6784199PMC
September 2019

Krykféie dicistrovirus: A novel dicistrovirus in velvety free-tailed bats from Brazil.

Infect Genet Evol 2019 11 6;75:104036. Epub 2019 Sep 6.

Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.

The Dicistroviridae family comprises positive single-stranded RNA viruses that are classified into Picornavirales order. These viruses are identified in arthropod hosts, including some having devastating economic consequences. Here, we described and characterized a novel nearly complete dicistrovirus genome identified in liver samples of velvety free-tailed bats (Molossus molossus) collected in June 2010 in Araçatuba city, São Paulo State, Brazil. This novel virus presents a genome of 9262 nucleotides in length and a typical dicistrovirus genome organization. Based on our phylogenetic analysis and ICTV criteria, we propose this virus as a novel species into the Triatovirus genus. Attempts of viral propagation in Vero E6 and C6/36 cell lines were unsuccessful. The novel dicistrovirus was detected only in one out of nine liver bat samples, representing for the first time an internal organ detection from a representative of this virus family.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.meegid.2019.104036DOI Listing
November 2019

Analysis of Paramyxovirus Transcription and Replication by High-Throughput Sequencing.

J Virol 2019 09 13;93(17). Epub 2019 Aug 13.

School of Biology, Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Fife, United Kingdom

We have developed a high-throughput sequencing (HTS) workflow for investigating paramyxovirus transcription and replication. We show that sequencing of oligo(dT)-selected polyadenylated mRNAs, without considering the orientation of the RNAs from which they had been generated, cannot accurately be used to analyze the abundance of viral mRNAs because genomic RNA copurifies with the viral mRNAs. The best method is directional sequencing of infected cell RNA that has physically been depleted of ribosomal and mitochondrial RNA followed by bioinformatic steps to differentiate data originating from genomes from viral mRNAs and antigenomes. This approach has the advantage that the abundance of viral mRNA (and antigenomes) and genomes can be analyzed and quantified from the same data. We investigated the kinetics of viral transcription and replication during infection of A549 cells with parainfluenza virus type 2 (PIV2), PIV3, PIV5, or mumps virus and determined the abundances of individual viral mRNAs and readthrough mRNAs. We found that the mRNA abundance gradients differed significantly between all four viruses but that for each virus the pattern remained relatively stable throughout infection. We suggest that rapid degradation of non-poly(A) mRNAs may be primarily responsible for the shape of the mRNA abundance gradient in parainfluenza virus 3, whereas a combination of this factor and disengagement of RNA polymerase at intergenic sequences, particularly those at the NP:P and P:M gene boundaries, may be responsible in the other viruses. High-throughput sequencing (HTS) of virus-infected cells can be used to study in great detail the patterns of virus transcription and replication. For paramyxoviruses, and by analogy for all other negative-strand RNA viruses, we show that directional sequencing must be used to distinguish between genomic RNA and mRNA/antigenomic RNA because significant amounts of genomic RNA copurify with poly(A)-selected mRNA. We found that the best method is directional sequencing of total cell RNA, after the physical removal of rRNA (and mitochondrial RNA), because quantitative information on the abundance of both genomic RNA and mRNA/antigenomes can be simultaneously derived. Using this approach, we revealed new details of the kinetics of virus transcription and replication for parainfluenza virus (PIV) type 2, PIV3, PIV5, and mumps virus, as well as on the relative abundance of the individual viral mRNAs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.00571-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694822PMC
September 2019

The Third Annual Meeting of the European Virus Bioinformatics Center.

Viruses 2019 05 5;11(5). Epub 2019 May 5.

European Virus Bioinformatics Center, 07743 Jena, Germany.

The Third Annual Meeting of the European Virus Bioinformatics Center (EVBC) took place in Glasgow, United Kingdom, 28-29 March 2019. Virus bioinformatics has become central to virology research, and advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks, being successfully used to detect, control, and treat infections of humans and animals. This active field of research has attracted approximately 110 experts in virology and bioinformatics/computational biology from Europe and other parts of the world to attend the two-day meeting in Glasgow to increase scientific exchange between laboratory- and computer-based researchers. The meeting was held at the McIntyre Building of the University of Glasgow; a perfect location, as it was originally built to be a place for "rubbing your brains with those of other people", as Rector Stanley Baldwin described it. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The meeting featured eight invited and twelve contributed talks, on the four main topics: (1) systems virology, (2) virus-host interactions and the virome, (3) virus classification and evolution and (4) epidemiology, surveillance and evolution. Further, the meeting featured 34 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/v11050420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563321PMC
May 2019

Discovery of novel astrovirus and calicivirus identified in ruddy turnstones in Brazil.

Sci Rep 2019 04 3;9(1):5556. Epub 2019 Apr 3.

Virology Research Center, School of Medicine of Ribeirão Preto of University of São Paulo, Ribeirão Preto, 14049-900, SP, Brazil.

Birds are the natural reservoir of viruses with zoonotic potential, as well as contributing to the evolution, emergence, and dissemination of novel viruses. In this study, we applied a high-throughput screening approach to identify the diversity of viruses in 118 samples of birds captured between October 2006 to October 2010 in the North and Northeast regions of Brazil. We found nearly complete genomes of novel species of astrovirus and calicivirus in cloacal swabs of ruddy turnstones (Arenaria interpres) collected in Coroa do Avião islet, Pernambuco State. These viruses are positive-sense single-stranded RNA with a genome of ~7 to 8 kb, and were designated as Ruddy turnstone astrovirus (RtAstV) and Ruddy turnstone calicivirus (RTCV), respectively. Phylogenetic analysis showed that RtAstV and RTCV grouped in a monophyletic clade with viruses identified from poultry samples (i.e., chicken, goose, and turkey), including viruses associated with acute nephritis in chickens. Attempts of viral propagation in monkey and chicken cell lines for both viruses were unsuccessful. Also, we found genomes related with viral families that infect invertebrates and plants, suggesting that they might be ingested in the birds' diet. In sum, these findings shed new light on the diversity of viruses in migratory birds with the notable characterization of a novel astrovirus and calicivirus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-42110-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447618PMC
April 2019

A Novel Hepacivirus in Wild Rodents from South America.

Viruses 2019 03 24;11(3). Epub 2019 Mar 24.

Virology Research Center, Ribeirão Preto Medical School, University of São Paulo,14049-900 Ribeirão Preto, São Paulo, Brazil.

The genus comprises single-stranded positive-sense RNA viruses within the family . Several hepaciviruses have been identified in different mammals, including multiple rodent species in Africa, Asia, Europe, and North America. To date, no rodent hepacivirus has been identified in the South American continent. Here, we describe an unknown hepacivirus discovered during a metagenomic screen in , , , and from São Paulo State, Brazil. Molecular detection of this novel hepacivirus by RT-PCR showed a frequency of 11.11% (2/18) in . This is the first identification of hepavivirus in sigmondonine rodents and in rodents from South America. In sum, our results expand the host range, viral diversity, and geographical distribution of the genus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/v11030297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466192PMC
March 2019

ICTV Virus Taxonomy Profile: Parvoviridae.

J Gen Virol 2019 03 23;100(3):367-368. Epub 2019 Jan 23.

12​Centre de Recherche de Microbiologie et Biotechnologie, INRS-Institut Armand-Frappier Laval, QC H7V 1B7, Canada.

Members of the family Parvoviridae are small, resilient, non-enveloped viruses with linear, single-stranded DNA genomes of 4-6 kb. Viruses in two subfamilies, the Parvovirinae and Densovirinae, are distinguished primarily by their respective ability to infect vertebrates (including humans) versus invertebrates. Being genetically limited, most parvoviruses require actively dividing host cells and are host and/or tissue specific. Some cause diseases, which range from subclinical to lethal. A few require co-infection with helper viruses from other families. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the Parvoviridae, which is available at www.ictv.global/report/parvoviridae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/jgv.0.001212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537627PMC
March 2019

Viral diversity of Rhipicephalus microplus parasitizing cattle in southern Brazil.

Sci Rep 2018 11 5;8(1):16315. Epub 2018 Nov 5.

Virology Research Center, School of Medicine of Ribeirão Preto of University of São Paulo, Ribeirão Preto, 14049-900, SP, Brazil.

Ticks are ectoparasites spread worldwide and are well known as vectors of many viruses of great importance to human and animal health. However, the viral diversity in ticks is still poorly understood, particularly in South America. Here we characterized the viral diversity present in Rhipicephalus microplus parasitizing cattle in the southern region of Brazil using metagenomics. Our study revealed the presence of viruses that had not been previously described in the region, including lihan tick virus (Phenuiviridae family) and wuhan tick virus 2 (Chuviridae family), as well as expands the biogeography of jingmen tick virus (Flaviviridae family) in Brazil. Also, we described three novel tymoviruses (Tymovirales order), named guarapuava tymovirus-like 1 to 3. We described the genomic and phylogenetic characterization of these viruses. Our study sheds light on the viral diversity of Rhipicephalus microplus in South America, and also expands the biogeography of tick viruses that were previously described only in Asia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-34630-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218518PMC
November 2018

Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas.

PLoS Negl Trop Dis 2018 10 29;12(10):e0006884. Epub 2018 Oct 29.

MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom.

Orthobunyaviruses such as Cache Valley virus (CVV) and Kairi virus (KRIV) are important animal pathogens. Periodic outbreaks of CVV have resulted in the significant loss of lambs on North American farms, whilst KRIV has mainly been detected in South and Central America with little overlap in geographical range. Vaccines or treatments for these viruses are unavailable. One approach to develop novel vaccine candidates is based on the use of reverse genetics to produce attenuated viruses that elicit immune responses but cannot revert to full virulence. The full genomes of both viruses were sequenced to obtain up to date genome sequence information. Following sequencing, minigenome systems and reverse genetics systems for both CVV and KRIV were developed. Both CVV and KRIV showed a wide in vitro cell host range, with BHK-21 cells a suitable host cell line for virus propagation and titration. To develop attenuated viruses, the open reading frames of the NSs proteins were disrupted. The recombinant viruses with no NSs protein expression induced the production of type I interferon (IFN), indicating that for both viruses NSs functions as an IFN antagonist and that such attenuated viruses could form the basis for attenuated viral vaccines. To assess the potential for reassortment between CVV and KRIV, which could be relevant during vaccination campaigns in areas of overlap, we attempted to produce M segment reassortants by reverse genetics. We were unable to obtain such viruses, suggesting that it is an unlikely event.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pntd.0006884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245839PMC
October 2018

A novel polyomavirus in sigmodontine rodents from São Paulo State, Brazil.

Arch Virol 2018 Oct 21;163(10):2913-2915. Epub 2018 Jun 21.

Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre, Ribeirão Preto, São Paulo, 14049-900, Brazil.

The nearly complete genome sequence of a novel polyomavirus from blood samples of Akodon montensis and Calomys tener collected in Brazil was determined by high-throughput sequencing. This virus showed a typical polyomaviruses genome organization, and it was classified as a member of the genus Betapolyomavirus. Our results expand the host range and viral diversity of the family Polyomaviridae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00705-018-3913-8DOI Listing
October 2018

Novel orthohepeviruses in wild rodents from São Paulo State, Brazil.

Virology 2018 06 5;519:12-16. Epub 2018 Apr 5.

Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre, 14049-900 Ribeirão Preto, SP, Brazil.

The Hepeviridae comprise single-stranded positive-sense RNA viruses classified into two genera, Orthohepevirus and Piscihepevirus. Orthohepeviruses have a wide host range that includes rodents, but previous studies had been restricted to rodents of the Muridae family. In this study, we applied a high-throughput sequencing approach to examine the presence of orthohepeviruses in rodents from São Paulo State, Brazil. We also used RT-PCR to determine the frequency of orthohepeviruses in our sampled population. We identified novel orthohepeviruses in blood samples derived from Necromys lasiurus (1.19%) and Calomys tener (3.66%). Therefore, our results expand the host range and viral diversity of the Hepeviridae family.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virol.2018.03.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5998382PMC
June 2018

Novel Parvoviruses from Wild and Domestic Animals in Brazil Provide New Insights into Parvovirus Distribution and Diversity.

Viruses 2018 03 22;10(4). Epub 2018 Mar 22.

MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.

Parvoviruses (family ) are small, single-stranded DNA viruses. Many parvoviral pathogens of medical, veterinary and ecological importance have been identified. In this study, we used high-throughput sequencing (HTS) to investigate the diversity of parvoviruses infecting wild and domestic animals in Brazil. We identified 21 parvovirus sequences (including twelve nearly complete genomes and nine partial genomes) in samples derived from rodents, bats, opossums, birds and cattle in Pernambuco, São Paulo, Paraná and Rio Grande do Sul states. These sequences were investigated using phylogenetic and distance-based approaches and were thereby classified into eight parvovirus species (six of which have not been described previously), representing six distinct genera in the subfamily . Our findings extend the known biogeographic range of previously characterized parvovirus species and the known host range of three parvovirus genera (, ). Moreover, our investigation provides a window into the ecological dynamics of parvovirus infections in vertebrates, revealing that many parvovirus genera contain well-defined sub-lineages that circulate widely throughout the world within particular taxonomic groups of hosts.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/v10040143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5923437PMC
March 2018

ViCTree: an automated framework for taxonomic classification from protein sequences.

Bioinformatics 2018 07;34(13):2195-2200

MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.

Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualization tool that enables the tree to be explored interactively in the context of pairwise distance data.

Results: To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus.

Availability And Implementation: ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/.

Supplementary Information: Supplementary data are available at Bioinformatics online.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022645PMC
July 2018

Discovery of novel anelloviruses in small mammals expands the host range and diversity of the Anelloviridae.

Virology 2018 Jan 10;514:9-17. Epub 2017 Nov 10.

Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.

The Anelloviridae comprises single-stranded DNA viruses currently grouped in sixty-eight species classified in twelve genera. They have been found in many vertebrate hosts including primates. In this study, we describe the application of the high-throughput sequencing to examine the frequency and diversity of anelloviruses in rodents, bats and opossums captured in São Paulo State, Brazil. We report a total of twenty-six anelloviruses with sixteen nearly complete genomes and ten partial genomes, which include eleven potential novel species identified in rodents (Cricetidae), bats (Molossidae and Phyllostomidae), and opossums (Didelphidae). We also propose the inclusion of two potential new genera within the Anelloviridae family, provisionally named Omegatorquevirus and Sigmatorquevirus, including six and three novel species of anelloviruses, respectively. In summary, this study expands the diversity and the host range of the known anelloviruses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virol.2017.11.001DOI Listing
January 2018

Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution.

J Gen Virol 2017 02;98(2):225-229

MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.

Chapparvoviruses are a highly divergent group of parvoviruses (family Parvoviridae) that have recently been identified via metagenomic sampling of animal faeces. Here, we report the sequences of six novel chapparvoviruses identified through both metagenomic sampling of bat tissues and in silico screening of published vertebrate genome assemblies. The novel chapparvoviruses share several distinctive genomic features and group together as a robustly supported monophyletic clade in phylogenetic trees. Our data indicate that chapparvoviruses have a broad host range in vertebrates and a global distribution.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/jgv.0.000671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5646239PMC
February 2017

Erratum to "The use of next generation sequencing in the diagnosis and typing of respiratory infections"[J. Clin. Virol. 69 (2015) 96-100].

J Clin Virol 2015 09 18;70:128. Epub 2015 Jul 18.

MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jcv.2015.06.101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5597557PMC
September 2015

The use of next generation sequencing in the diagnosis and typing of respiratory infections.

J Clin Virol 2015 Aug 18;69:96-100. Epub 2015 Jun 18.

MRC-University of Glasgow Centre for Virus Research, Garscube Campus, 464 Bearsden Road, Glasgow, G61 1QH, UK.

Background: Molecular assays are the gold standard methods used to diagnose viral respiratory pathogens. Pitfalls associated with this technique include limits to the number of targeted pathogens, the requirement for continuous monitoring to ensure sensitivity/specificity is maintained and the need to evolve to include emerging pathogens. Introducing target independent next generation sequencing (NGS) could resolve these issues and revolutionise respiratory viral diagnostics.

Objectives: To compare the sensitivity and specificity of target independent NGS against the current standard diagnostic test.

Study Design: Diagnostic RT-PCR of clinical samples was carried out in parallel with target independent NGS. NGS sequences were analyzed to determine the proportion with viral origin and consensus sequences were used to establish viral genotypes and serotypes where applicable.

Results: 89 nasopharyngeal swabs were tested. A viral pathogen was detected in 43% of samples by NGS and 54% by RT-PCR. All NGS viral detections were confirmed by RT-PCR.

Conclusions: Target independent NGS can detect viral pathogens in clinical samples. Where viruses were detected by RT-PCR alone the Ct value was higher than those detected by both assays, suggesting an NGS detection cut-off - Ct=32. The sensitivity and specificity of NGS compared with RT-PCR was 78% and 80% respectively. This is lower than current diagnostic assays but NGS provided full genome sequences in some cases, allowing determination of viral subtype and serotype. Sequencing technology is improving rapidly and it is likely that within a short period of time sequencing depth will increase in-turn improving test sensitivity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jcv.2015.06.082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4533236PMC
August 2015

Finding a needle in the virus metagenome haystack--micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire.

PLoS One 2012 11;7(4):e34238. Epub 2012 Apr 11.

Department of Biology, University of Bergen, Bergen, Norway.

Viruses are ubiquitous in the oceans and critical components of marine microbial communities, regulating nutrient transfer to higher trophic levels or to the dissolved organic pool through lysis of host cells. Hydrothermal vent systems are oases of biological activity in the deep oceans, for which knowledge of biodiversity and its impact on global ocean biogeochemical cycling is still in its infancy. In order to gain biological insight into viral communities present in hydrothermal vent systems, we developed a method based on deep-sequencing of pulsed field gel electrophoretic bands representing key viral fractions present in seawater within and surrounding a hydrothermal plume derived from Loki's Castle vent field at the Arctic Mid-Ocean Ridge. The reduction in virus community complexity afforded by this novel approach enabled the near-complete reconstruction of a lambda-like phage genome from the virus fraction of the plume. Phylogenetic examination of distinct gene regions in this lambdoid phage genome unveiled diversity at loci encoding superinfection exclusion- and integrase-like proteins. This suggests the importance of fine-tuning lyosgenic conversion as a viral survival strategy, and provides insights into the nature of host-virus and virus-virus interactions, within hydrothermal plumes. By reducing the complexity of the viral community through targeted sequencing of prominent dsDNA viral fractions, this method has selectively mimicked virus dominance approaching that hitherto achieved only through culturing, thus enabling bioinformatic analysis to locate a lambdoid viral "needle" within the greater viral community "haystack". Such targeted analyses have great potential for accelerating the extraction of biological knowledge from diverse and poorly understood environmental viral communities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034238PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324506PMC
August 2012