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Peter Tijssen - One of the best experts on this subject based on the ideXlab platform.
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The family Parvoviridae
Archives of Virology, 2014Co-Authors: Susan F. Cotmore, Peter Tijssen, Maria Söderlund-venermo, Mavis Agbandje-mckenna, Dmitry V. Mukha, John A. Chiorini, David J. Pintel, Jianming Qiu, Peter Tattersall, Derek GathererAbstract:A set of proposals to rationalize and extend the taxonomy of the family Parvoviridae is currently under review by the International Committee on Taxonomy of Viruses (ICTV). Viruses in this family infect a wide range of hosts, as reflected by the longstanding division into two subfamilies: the Parvovirinae , which contains viruses that infect vertebrate hosts, and the Densovirinae , encompassing viruses that infect arthropod hosts. Using a modified definition for classification into the family that no longer demands isolation as long as the biological context is strong, but does require a near-complete DNA sequence, 134 new viruses and virus variants were identified. The proposals introduce new species and genera into both subfamilies, resolve one misclassified species, and improve taxonomic clarity by employing a series of systematic changes. These include identifying a precise level of sequence similarity required for viruses to belong to the same genus and decreasing the level of sequence similarity required for viruses to belong to the same species. These steps will facilitate recognition of the major phylogenetic branches within genera and eliminate the confusion caused by the near-identity of species and viruses. Changes to taxon nomenclature will establish numbered, non-Latinized binomial names for species, indicating genus affiliation and host range rather than recapitulating virus names. Also, affixes will be included in the names of genera to clarify subfamily affiliation and reduce the ambiguity that results from the vernacular use of “parvovirus” and “densovirus” to denote multiple taxon levels.
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Iteradensovirus from the Monarch Butterfly, Danaus plexippus plexippus
Genome Announcements, 2014Co-Authors: Qian Yu, Peter TijssenAbstract:ABSTRACT The 5,006-nucleotide (nt)-long genome of a new virus from monarch butterfly pupae was cloned and sequenced. It was flanked by inverted terminal repeats (ITRs) of 239 nt with 163-nt hairpins. The monosense genome with three open reading frames is typical of the genus Iteradensovirus in the subfamily Densovirinae of the family Parvoviridae.
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Pseudoplusia includens Densovirus Genome Organization and Expression Strategy
Journal of virology, 2012Co-Authors: Oanh Thi Hoang Huynh, Hanh T. Pham, Peter TijssenAbstract:The genome of a densovirus of a major phytophagous pest, Pseudoplusia includens, was analyzed. It contained 5,990 nucleotides (nt) and included inverted terminal repeats of 540 nt with terminal Y-shaped hairpins of 120 nt. Its DNA sequence and ambisense organization with 4 typical open reading frames demonstrated that it belonged to the genus Densovirus in the subfamily Densovirinae of the family Parvoviridae.
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Papilio polyxenes Densovirus Has an Iteravirus-Like Genome Organization
Journal of Virology, 2012Co-Authors: Qian Yu, Max Bergoin, Ann E Hajek, Peter TijssenAbstract:The genome of Papilio polyxenes densovirus was cloned and sequenced and contained 5,053 nucleotides (nt), including inverted terminal repeats (ITRs) of 271 nt with terminal hairpins of 175 nt. Its DNA sequence and monosense organization with 3 open reading frames (ORFs) are typical of the genus Iteravirus in the subfamily Densovirinae of the Parvoviridae.
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Iteravirus-Like Genome Organization of a Densovirus from Sibine fusca Stoll
Journal of Virology, 2012Co-Authors: Qian Yu, Gilles Fédière, Max Bergoin, Adly M. M. Abd-alla, Peter TijssenAbstract:The complete genome of Sibine fusca densovirus was cloned and sequenced. The genome contained 5,012 nucleotides (nt), including inverted terminal repeats (ITRs) of 230 nt with terminal hairpins of 161 nt. Its DNA sequence and monosense organization with 3 open reading frames (ORFs) is typical of the genus Iteravirus in the subfamily Densovirinae of the Parvoviridae.
Eric Delwart - One of the best experts on this subject based on the ideXlab platform.
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A new densovirus in cerebrospinal fluid from a case of anti-NMDA-receptor encephalitis
Archives of Virology, 2016Co-Authors: Tung Gia Phan, Kevin Messacar, Samuel R. Dominguez, Antonio Charlys Costa, Xutao Deng, Eric DelwartAbstract:We characterized the genome of a densovirus, tentatively called human CSF-associated densovirus 1 (HuCSFDV1), in cerebrospinal fluid (CSF) from a human case of encephalitis with antibodies against the N-methyl D-aspartate receptor. The presence of the viral genome in CSF was independently confirmed. This virus, which is proposed to be a member of a new species in the genus Iteradensovirus of the subfamily Densovirinae , showed the typical two ORFs encoding nonstructural and structural proteins with low-level identities of 22 and 16 % to the closest known densovirus relative. No other eukaryotic viral sequences were detected using deep sequencing. The replication and pathogenicity in humans of this virus, which belongs to a viral subfamily whose members are only known to replicate in invertebrates, remain to be demonstrated. Alternative explanations for the detection of densovirus DNA in CSF are discussed.
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The Fecal Viral Flora of Wild Rodents
PLoS Pathogens, 2011Co-Authors: Tung Gia Phan, Beatrix Kapusinszky, Robe K. Rose, Chunlin Wang, Howard L. Lipton, Eric DelwartAbstract:The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially new viral families were characterized. In the Picornaviridae family two new candidate genera as well as a close genetic relative of the human pathogen Aichi virus were characterized. Fragments of the first mouse sapelovirus and picobirnaviruses were identified and the first murine astrovirus genome was characterized. A mouse papillomavirus genome and fragments of a novel adenovirus and adenovirus-associated virus were also sequenced. The next largest fraction of the rodent fecal virome was related to insect viruses of the Densoviridae, Iridoviridae, Polydnaviridae, Dicistroviriade, Bromoviridae, and Virgaviridae families followed by plant virus-related sequences in the Nanoviridae, Geminiviridae, Phycodnaviridae, Secoviridae, Partitiviridae, Tymoviridae, Alphaflexiviridae, and Tombusviridae families reflecting the largely insect and plant rodent diet. Phylogenetic analyses of full and partial viral genomes therefore revealed many previously unreported viral species, genera, and families. The close genetic similarities noted between some rodent and human viruses might reflect past zoonoses. This study increases our understanding of the viral diversity in wild rodents and highlights the large number of still uncharacterized viruses in mammals.
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Bat Guano Virome: Predominance of Dietary Viruses from Insects and Plants plus Novel Mammalian Viruses
Journal of virology, 2010Co-Authors: Joseph Victoria, Chunlin Wang, Gary M. Fellers, Thomas H. Kunz, Morris S. Jones, Eric DelwartAbstract:Bats are hosts to a variety of viruses capable of zoonotic transmissions. Because of increased contact between bats, humans, and other animal species, the possibility exists for further cross-species transmissions and ensuing disease outbreaks. We describe here full and partial viral genomes identified using metagenomics in the guano of bats from California and Texas. A total of 34% and 58% of 390,000 sequence reads from bat guano in California and Texas, respectively, were related to eukaryotic viruses, and the largest proportion of those infect insects, reflecting the diet of these insectivorous bats, including members of the viral families Dicistroviridae, Iflaviridae, Tetraviridae, and Nodaviridae and the subfamily Densovirinae. The second largest proportion of virus-related sequences infects plants and fungi, likely reflecting the diet of ingested insects, including members of the viral families Luteoviridae, Secoviridae, Tymoviridae, and Partitiviridae and the genus Sobemovirus. Bat guano viruses related to those infecting mammals comprised the third largest group, including members of the viral families Parvoviridae, Circoviridae, Picornaviridae, Adenoviridae, Poxviridae, Astroviridae, and Coronaviridae. No close relative of known human viral pathogens was identified in these bat populations. Phylogenetic analysis was used to clarify the relationship to known viral taxa of novel sequences detected in bat guano samples, showing that some guano viral sequences fall outside existing taxonomic groups. This initial characterization of the bat guano virome, the first metagenomic analysis of viruses in wild mammals using second-generation sequencing, therefore showed the presence of previously unidentified viral species, genera, and possibly families. Viral metagenomics is a useful tool for genetically characterizing viruses present in animals with the known capability of direct or indirect viral zoonosis to humans.
Marta Canuti - One of the best experts on this subject based on the ideXlab platform.
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Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis.
Viruses, 2021Co-Authors: Marta Canuti, Joost T. P. Verhoeven, Hannah J. Munro, Sheena Roul, Davor Ojkic, Gregory J. Robertson, Hugh Whitney, Suzanne C. Dufour, Andrew S. LangAbstract:Parvoviruses are small single-stranded DNA viruses that can infect both vertebrates and invertebrates. We report here the full characterization of novel viruses we identified in ducks, including two viral species within the subfamily Hamaparvovirinae (duck-associated chapparvovirus, DAC) and a novel species within the subfamily Densovirinae (duck-associated ambidensovirus, DAAD). Overall, 5.7% and 21.1% of the 123 screened ducks (American black ducks, mallards, northern pintail) were positive for DAC and DAAD, respectively, and both viruses were more frequently detected in autumn than in winter. Genome organization and predicted transcription profiles of DAC and DAAD were similar to viruses of the genera Chaphamaparvovirus and Protoambidensovirus, respectively. Their association to these genera was also demonstrated by subfamily-wide phylogenetic and distance analyses of non-structural protein NS1 sequences. While DACs were included in a highly supported clade of avian viruses, no definitive conclusions could be drawn about the host type of DAAD because it was phylogenetically close to viruses found in vertebrates and invertebrates and analyses of codon usage bias and nucleotide frequencies of viruses within the family Parvoviridae showed no clear host-based viral segregation. This study highlights the high parvoviral diversity in the avian reservoir with many avian-associated parvoviruses likely yet to be discovered.
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Reorganizing the family Parvoviridae: a revised taxonomy independent of the canonical approach based on host association
Archives of Virology, 2020Co-Authors: Judit J. Pénzes, Maria Söderlund-venermo, Marta Canuti, Anna Maria Eis-hübinger, Joseph Hughes, Susan F. Cotmore, Balázs HarrachAbstract:Parvoviridae , a diverse family of small single-stranded DNA viruses was established in 1975. It was divided into two subfamilies, Parvovirinae and Densovirinae , in 1993 to accommodate parvoviruses that infect vertebrate and invertebrate animals, respectively. This relatively straightforward segregation, using host association as the prime criterion for subfamily-level classification, has recently been challenged by the discovery of divergent, vertebrate-infecting parvoviruses, dubbed “chapparvoviruses”, which have proven to be more closely related to viruses in certain Densovirinae genera than to members of the Parvovirinae . Viruses belonging to these genera, namely Brevi -, Hepan - and Penstyldensovirus , are responsible for the unmatched heterogeneity of the subfamily Densovirinae when compared to the Parvovirinae in matters of genome organization, protein sequence homology, and phylogeny. Another genus of Densovirinae , Ambidensovirus , has challenged traditional parvovirus classification, as it includes all newly discovered densoviruses with an ambisense genome organization, which introduces genus-level paraphyly. Lastly, current taxon definition and virus inclusion criteria have significantly limited the classification of certain long-discovered parvoviruses and impedes the classification of some potential family members discovered using high-throughput sequencing methods. Here, we present a new and updated system for parvovirus classification, which includes the introduction of a third subfamily, Hamaparvovirinae , resolves the paraphyly within genus Ambidensovirus , and introduces new genera and species into the subfamily Parvovirinae . These proposals were accepted by the ICTV in 2020 March.
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ICTV Virus Taxonomy Profile: Parvoviridae
Journal of General Virology, 2019Co-Authors: Susan Cotmore, Marta Canuti, Anna Maria Eis-hübinger, Joseph Hughes, Mavis Agbandje-mckenna, John Chiorini, Mario Mietzsch, Sejal Modha, Mylène Ogliastro, Judit PénzesAbstract: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.
Max Bergoin - One of the best experts on this subject based on the ideXlab platform.
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Papilio polyxenes Densovirus Has an Iteravirus-Like Genome Organization
Journal of Virology, 2012Co-Authors: Qian Yu, Max Bergoin, Ann E Hajek, Peter TijssenAbstract:The genome of Papilio polyxenes densovirus was cloned and sequenced and contained 5,053 nucleotides (nt), including inverted terminal repeats (ITRs) of 271 nt with terminal hairpins of 175 nt. Its DNA sequence and monosense organization with 3 open reading frames (ORFs) are typical of the genus Iteravirus in the subfamily Densovirinae of the Parvoviridae.
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Iteravirus-Like Genome Organization of a Densovirus from Sibine fusca Stoll
Journal of Virology, 2012Co-Authors: Qian Yu, Gilles Fédière, Max Bergoin, Adly M. M. Abd-alla, Peter TijssenAbstract:The complete genome of Sibine fusca densovirus was cloned and sequenced. The genome contained 5,012 nucleotides (nt), including inverted terminal repeats (ITRs) of 230 nt with terminal hairpins of 161 nt. Its DNA sequence and monosense organization with 3 open reading frames (ORFs) is typical of the genus Iteravirus in the subfamily Densovirinae of the Parvoviridae.
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Organization of the Ambisense Genome of the Helicoverpa armigera Densovirus
Journal of Virology, 2012Co-Authors: Jozsef Szelei, Gilles Fédière, Max Bergoin, Qian Yu, Peter TijssenAbstract:A natural densovirus (DNV) of a serious phytophagous pest, Helicoverpa armigera, was isolated. The genome of HaDNV contained 6,039 nucleotides (nt) and included inverted terminal repeats (ITRs) of 545 nt with terminal Y-shaped hairpins of 126 nt. Its DNA sequence and ambisense organization with four typical open reading frames (ORFs) demonstrated that it belonged to the genus Densovirus in the subfamily Densovirinae of the family Parvoviridae.
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Structure and Expression Strategy of the Genome of Culex pipiens Densovirus, a Mosquito Densovirus with an Ambisense Organization
Journal of virology, 2009Co-Authors: Elizabeth Baquerizo-audiot, Peter Tijssen, Adly M. M. Abd-alla, Françoise-xavière Jousset, Françoise Cousserans, Max BergoinAbstract:The genome of all densoviruses (DNVs) so far isolated from mosquitoes or mosquito cell lines consists of a 4-kb single-stranded DNA molecule with a monosense organization (genus Brevidensovirus, subfamily Densovirinae). We previously reported the isolation of a Culex pipiens DNV (CpDNV) that differs significantly from brevidensoviruses by (i) having a approximately 6-kb genome, (ii) lacking sequence homology, and (iii) lacking antigenic cross-reactivity with Brevidensovirus capsid polypeptides. We report here the sequence organization and transcription map of this virus. The cloned genome of CpDNV is 5,759 nucleotides (nt) long, and it possesses an inverted terminal repeat (ITR) of 285 nt and an ambisense organization of its genes. The nonstructural (NS) proteins NS-1, NS-2, and NS-3 are located in the 5' half of one strand and are organized into five open reading frames (ORFs) due to the split of both NS-1 and NS-2 into two ORFs. The ORF encoding capsid polypeptides is located in the 5' half of the complementary strand. The expression of NS proteins is controlled by two promoters, P7 and P17, driving the transcription of a 2.4-kb mRNA encoding NS-3 and of a 1.8-kb mRNA encoding NS-1 and NS-2, respectively. The two NS mRNAs species are spliced off a 53-nt sequence. Capsid proteins are translated from an unspliced 2.3-kb mRNA driven by the P88 promoter. CpDNV thus appears as a new type of mosquito DNV, and based on the overall organization and expression modalities of its genome, it may represent the prototype of a new genus of DNV.
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Biochemical Characterization of Junonia coenia Densovirus Nonstructural Protein NS-1
Journal of virology, 2002Co-Authors: Chuantian Ding, Max Bergoin, Masashi Urabe, Robert M. KotinAbstract:The Parvoviridae consist of two subfamilies: the Parvovirinae, which infect vertebrates, and the Densovirinae, which infect invertebrates. Junonia coenia densovirus (JcDNV) is an autonomously replicating densovirus that infects the larvae of the common buckeye butterfly, Junonia coenia. The JcDNV genome is a single-stranded, linear DNA molecule of approximately 6 kb in length (13, 32). JcDNV genomic organization differs from that of the Parvovirinae in that coding regions occur on both strands of the double-stranded replicative form viral genome (13). On one strand, a single open reading frame (ORF1) encodes four structural proteins, VP1, VP2, VP3, and VP4. On the complementary strand, ORF2, ORF3, and ORF4 encode nonstructural proteins NS-1, NS-2, and NS-3. NS-1, NS-2, and NS-3 are 545, 275, and 232 amino acids in length, respectively. The predicted molecular masses of the proteins encoded by the nonstructural NS-1, NS-2, and NS-3 ORFs are 60, 30, and 28 kDa. ORF1 and ORF2 are regulated by promoters at map positions 9 and 93 (P9 and P93), respectively (Fig. (Fig.1A).1A). Similar to adeno-associated virus (AAV) and some of the autonomous parvoviruses (2, 4, 6, 7, 23, 25), an infectious particle of JcDNV may contain either strand of the virus genome, so that in a population of infectious particles half of the virions contain a plus strand and half contain a minus strand. Relatively long terminal repeat (TR) sequences (Fig. (Fig.2A)2A) flank the coding sequences. The first 96 nucleotides (nt) of the TR, from either the 5′ or 3′ end of the genome, can fold into a T-shaped hairpin structure similar to those predicted for certain vertebrate parvoviruses (Fig. 2D and E). As a result of the strand transfers and inversions that occur during replication, flip and flop conformations arise (17, 18, 30). This phenomenon is common to the ends of all vertebrate parvoviruses with TRs (1, 5, 31). The presence of terminal palindromic sequences is a common feature for members of the Parvoviridae family, and this element acts as the origin of DNA replication (8, 21). Parvovirus replication initiator proteins possess the following activities: binding to a sequence element within the viral TRs, sequence- and strand-specific nicking activity, and helicase activity. These activities are necessary for efficient virus DNA replication (11, 12, 20, 24, 26, 34). FIG. 1. (A) Diagrammatic representation of JcDNV genomic organization. The JcDNV genome contains four major open translational reading frames, and both strands of the genome encode polypeptides. The largest is ORF1, which occupies the 5′ half of one strand, ... FIG. 2. Organization of the terminal palindrome and oligodeoxynucleotide probes used in this study. (A) The end of the JcDNV genome is represented with the positions of the GGTC and GAC repeats denoted. The filled triangle is positioned at the nick site. The ... Among the rolling-circle replication (RCR) initiator protein superfamily, three conserved motifs have been identified which are associated with single-strand nicking activities (19). Two of these conserved motifs are readily identifiable in the Parvoviridae nonstructural proteins (Fig. (Fig.1C).1C). Inspection of the JcDNV NS-1 sequence reveals that the RCR motifs are located in the amino terminal half of NS-1. Motif 2, uHuHuuu (where u is a hydrophobic amino acid) is located at residues 132 to 140 of JcDNV NS-1. Motif 3, uxxYuxxxK (with x representing any amino acid), contains the active tyrosine involved in nicking activity. Within the carboxy-terminal half of NS-1 are sequences associated with nucleoside triphosphate binding and hydrolysis (Fig. (Fig.1C,1C, ATPase motif). The Walker A-site, GxxxxGK(T/S), contains a lysine residue that interacts with a nucleoside triphosphate, typically ATP (33). The B-site, which consists of two acidic residues preceded by four hydrophobic residues, uuuu(D/E)(D/E), is thought to complex with the metal cation cofactor. Thus, sequence analysis of the JcDNV NS-1 protein indicates that NS-1 is a nickase with ATPase activities. In order to confirm these predictions, we investigated the ability of JcDNV NS-1 to function as a nickase and helicase. For this purpose, we cloned the coding region of NS-1 (or ORF2) in frame with the coding sequence of the Escherichia coli malE gene, which encodes the maltose binding protein (MBP). The MBP-NS-1 fusion protein was overexpressed in E. coli and analyzed for biochemical activities. We report here that recombinant NS-1 fusion protein binds specifically to the motif (GAC)4 located within the terminal 96 nt of the TR sequence of the JcDNV genome. The sequence-specific binding activity appears to function independently of DNA secondary structure. The results of nicking activity assays demonstrated that MBP-NS-1 specifically cleaves single-stranded DNA (ssDNA) substrates derived from the predicted JcDNV origin of replication. This nicking activity is dependent on a metal divalent cation cofactor but does not require ATP. In addition, we show here that MBP-NS-1 possesses helicase activity as judged by its ability to unwind partial duplex DNA substrates. The helicase activity is strictly dependent upon the presence of both ATP and metal divalent cation cofactors.
Joseph Hughes - One of the best experts on this subject based on the ideXlab platform.
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Reorganizing the family Parvoviridae: a revised taxonomy independent of the canonical approach based on host association
Archives of Virology, 2020Co-Authors: Judit J. Pénzes, Maria Söderlund-venermo, Marta Canuti, Anna Maria Eis-hübinger, Joseph Hughes, Susan F. Cotmore, Balázs HarrachAbstract:Parvoviridae , a diverse family of small single-stranded DNA viruses was established in 1975. It was divided into two subfamilies, Parvovirinae and Densovirinae , in 1993 to accommodate parvoviruses that infect vertebrate and invertebrate animals, respectively. This relatively straightforward segregation, using host association as the prime criterion for subfamily-level classification, has recently been challenged by the discovery of divergent, vertebrate-infecting parvoviruses, dubbed “chapparvoviruses”, which have proven to be more closely related to viruses in certain Densovirinae genera than to members of the Parvovirinae . Viruses belonging to these genera, namely Brevi -, Hepan - and Penstyldensovirus , are responsible for the unmatched heterogeneity of the subfamily Densovirinae when compared to the Parvovirinae in matters of genome organization, protein sequence homology, and phylogeny. Another genus of Densovirinae , Ambidensovirus , has challenged traditional parvovirus classification, as it includes all newly discovered densoviruses with an ambisense genome organization, which introduces genus-level paraphyly. Lastly, current taxon definition and virus inclusion criteria have significantly limited the classification of certain long-discovered parvoviruses and impedes the classification of some potential family members discovered using high-throughput sequencing methods. Here, we present a new and updated system for parvovirus classification, which includes the introduction of a third subfamily, Hamaparvovirinae , resolves the paraphyly within genus Ambidensovirus , and introduces new genera and species into the subfamily Parvovirinae . These proposals were accepted by the ICTV in 2020 March.
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ICTV Virus Taxonomy Profile: Parvoviridae
Journal of General Virology, 2019Co-Authors: Susan Cotmore, Marta Canuti, Anna Maria Eis-hübinger, Joseph Hughes, Mavis Agbandje-mckenna, John Chiorini, Mario Mietzsch, Sejal Modha, Mylène Ogliastro, Judit PénzesAbstract: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.
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ViCTree: an automated framework for taxonomic classification from protein sequences.
Bioinformatics (Oxford England), 2018Co-Authors: Sejal Modha, Susan F. Cotmore, Anil S. Thanki, Andrew J. Davison, Joseph HughesAbstract: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.