Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)

Walker, Peter; Siddell, Stuart G.; Lefkowitz, Elliot J.; Mushegian, Arcady; Adriaenssens, Evelien M.; Dempsey, Donald M.; Dutilh, Bas E.; Harrach, Balázs; Harrison, Robert L.; Hendrickson, R. Curtis; Junglen, Sandra; Knowles, Nick J.; Kropinski, Andrew M.; Krupovìč, Mart; Kuhn, Jens H.; Nibert, Max L.; Orton, Richard; Rubino, Luisa; Sabanadzovic, Sead; Simmonds, Peter; Smith, Donald B.; Varsani, Arvind; Zerbini, F. Murilo; Davison, Andrew J.

doi:10.1007/s00705-020-04752-x

Cited by 227 publications

(188 citation statements)

References 6 publications

(4 reference statements)

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“…None of the 15 Group-1 proviruses identified here (including the three characterized temperate viruses and the incomplete proviruses), exhibits significant nucleotide similarity with viral genomes in the NCBI virus database. Following taxonomic criteria where viruses belonging to the same genus display > 50-70% nucleotide identity over the full genome while species display > 95% nucleotide identity [36][37], the VIRIDIC tool suggested that the complete Group-1 proviruses identified here, correspond to 13 new species and at least 11 new genera (Supplementary Table S2). Two provirus pairs, MCV1-MCV2 and M1135V1 - M1138V1, may be assigned to the same genus having intergenomic similarity scores of 56% and 60% respectively (Supplementary Table S2).…”

Section: Resultsmentioning

confidence: 99%

Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing

Haverkamp

Lossouarn

Zhaxybayeva

et al. 2020

Preprint

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Viruses are drivers of microbial ecology and evolution controlling populations and disseminating DNA laterally among the cells they infect. Phylogenetic and comparative genomic analyses of Thermotogota bacteria have shown high levels of lateral gene transfer with distantly related organisms, particularly with Firmicutes. One likely source of such DNA transfers is viruses, however, to date only three temperate viruses infecting Marinitoga bacteria have been characterized in this phylum. Here we use a bioinformatic approach to identify an additional 17 proviruses integrated into genomes of eight Thermotogota genera including Marinitoga. We also induce viral particle production from one of the newly identified proviruses. The proviruses fall into two groups based on sequence similarities, gene synteny and virus classification tools. Group-1 shows similar genome structure to the three previously identified Marinitoga viruses while Group-2 are distantly related to these viruses and have different genome organization. Both groups show close connections to Firmicutes in genomic- and phylogenetic analyses, and the Group-2 viruses show evidence of very recent transfer between these lineages and are likely capable of infecting cells from both phyla. We suggest that viruses are responsible for a large portion of the laterally transferred DNA between these distantly related lineages.

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Section: Resultsmentioning

confidence: 99%

Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing

Haverkamp

Lossouarn

Zhaxybayeva

et al. 2020

Preprint

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“…The first was the VirHostMatcher (VHM) benchmark dataset obtained from Ahlgren’s study [ 16 ]. The taxonomic information of both viral and prokaryotic genomes in the dataset was updated according to the International Committee on Taxonomy of Viruses (ICTV) [ 20 ] and NCBI Taxonomy database [ 21 ]. One pair of virus-host interaction (Tetraselmis viridis virus - Tetraselmis sp.)…”

Section: Methodsmentioning

confidence: 99%

Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics

Zhang

Cai

et al. 2021

BMC Biol

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Background Viruses are ubiquitous biological entities, estimated to be the largest reservoirs of unexplored genetic diversity on Earth. Full functional characterization and annotation of newly discovered viruses requires tools to enable taxonomic assignment, the range of hosts, and biological properties of the virus. Here we focus on prokaryotic viruses, which include phages and archaeal viruses, and for which identifying the viral host is an essential step in characterizing the virus, as the virus relies on the host for survival. Currently, the method for determining the viral host is either to culture the virus, which is low-throughput, time-consuming, and expensive, or to computationally predict the viral hosts, which needs improvements at both accuracy and usability. Here we develop a Gaussian model to predict hosts for prokaryotic viruses with better performances than previous computational methods. Results We present here Prokaryotic virus Host Predictor (PHP), a software tool using a Gaussian model, to predict hosts for prokaryotic viruses using the differences of k-mer frequencies between viral and host genomic sequences as features. PHP gave a host prediction accuracy of 34% (genus level) on the VirHostMatcher benchmark dataset and a host prediction accuracy of 35% (genus level) on a new dataset containing 671 viruses and 60,105 prokaryotic genomes. The prediction accuracy exceeded that of two alignment-free methods (VirHostMatcher and WIsH, 28–34%, genus level). PHP also outperformed these two alignment-free methods much (24–38% vs 18–20%, genus level) when predicting hosts for prokaryotic viruses which cannot be predicted by the BLAST-based or the CRISPR-spacer-based methods alone. Requiring a minimal score for making predictions (thresholding) and taking the consensus of the top 30 predictions further improved the host prediction accuracy of PHP. Conclusions The Prokaryotic virus Host Predictor software tool provides an intuitive and user-friendly API for the Gaussian model described herein. This work will facilitate the rapid identification of hosts for newly identified prokaryotic viruses in metagenomic studies.

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“…All lyssavirus species are capable of causing fatal neurological disease with symptomatic presentation and disease progression that is indistinguishable from clinical rabies. Phylogenetic analyses have enabled the subdivision of lyssavirus isolates into at least two phylogroups and several ungrouped viruses [13,14]. Phylogroup I includes the prototype lyssavirus, Rabies lyssavirus (RABV), ABLV, Duvenhage lyssavirus (DUVV), Aravan lyssavirus (ARAV), Bokeloh bat lyssavirus (BBLV), Irkut lyssavirus (IRKV), Khujand lyssavirus (KHUV), Gannoruwa bat lyssavirus (GBLV), European bat 1 lyssavirus (EBLV-1), European bat 2 lyssavirus (EBLV-2), Taiwan bat lyssavirus (TWBLV), and Kotalahti bat virus (KBLV).…”

Section: Introductionmentioning

confidence: 99%

“…Shimoni bat lyssavirus (SHIBV), Lagos bat lyssavirus (LBV), and Mokola lyssavirus form phylogroup II. Finally, the most genetically divergent lyssaviruses are ungrouped and include West Caucasian bat lyssavirus (WCBV), Ikoma lyssavirus (IKOV), and Lleida bat lyssavirus (LLEBV) [14]. While genetically and serologically distinct from one another, all lyssaviruses are enveloped bullet-shaped viruses with 12 kb negative-sense single-stranded RNA genomes that encode five major viral proteins: nucleoprotein (N), phosphoprotein (P), matrix (M), glycoprotein (G), and viral RNA polymerase (L) [15].…”

Section: Introductionmentioning

confidence: 99%

Isolation and Characterization of Cross-Reactive Human Monoclonal Antibodies That Potently Neutralize Australian Bat Lyssavirus Variants and Other Phylogroup 1 Lyssaviruses

Weir

Coggins

et al. 2021

Viruses

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Australian bat lyssavirus (ABLV) is a rhabdovirus that circulates in four species of pteropid bats (ABLVp) and the yellow-bellied sheath-tailed bat (ABLVs) in mainland Australia. In the three confirmed human cases of ABLV, rabies illness preceded fatality. As with rabies virus (RABV), post-exposure prophylaxis (PEP) for potential ABLV infections consists of wound cleansing, administration of the rabies vaccine and injection of rabies immunoglobulin (RIG) proximal to the wound. Despite the efficacy of PEP, the inaccessibility of human RIG (HRIG) in the developing world and the high immunogenicity of equine RIG (ERIG) has led to consideration of human monoclonal antibodies (hmAbs) as a passive immunization option that offers enhanced safety and specificity. Using a recombinant vesicular stomatitis virus (rVSV) expressing the glycoprotein (G) protein of ABLVs and phage display, we identified two hmAbs, A6 and F11, which completely neutralize ABLVs/ABLVp, and RABV at concentrations ranging from 0.39 and 6.25 µg/mL and 0.19 and 0.39 µg/mL respectively. A6 and F11 recognize overlapping epitopes in the lyssavirus G protein, effectively neutralizing phylogroup 1 lyssaviruses, while having little effect on phylogroup 2 and non-grouped diverse lyssaviruses. These results suggest that A6 and F11 could be effective therapeutic and diagnostic tools for phylogroup 1 lyssavirus infections.

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Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)

Cited by 227 publications

References 6 publications

Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing

Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing

Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics

Isolation and Characterization of Cross-Reactive Human Monoclonal Antibodies That Potently Neutralize Australian Bat Lyssavirus Variants and Other Phylogroup 1 Lyssaviruses

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