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1. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2024).

Author

Simmonds, Peter, Adriaenssens, Evelien, Lefkowitz, Elliot, Oksanen, Hanna, Siddell, Stuart, Zerbini, Francisco, Alfenas-Zerbini, Poliane, Aylward, Frank, Dempsey, Donald, Dutilh, Bas, Freitas-Astúa, Juliana, García, María, Hendrickson, R, Hughes, Holly, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens, Lambert, Amy, Łobocka, Małgorzata, Mushegian, Arcady, Penzes, Judit, Muñoz, Alejandro, Robertson, David, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Smith, Donald, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, and Varsani, Arvind

Subjects
Viruses, Terminology as Topic, Classification, Phylogeny, Virology
Abstract

This article reports changes to virus taxonomy and taxon nomenclature that were approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2024. The entire ICTV membership was invited to vote on 203 taxonomic proposals that had been approved by the ICTV Executive Committee (EC) in July 2023 at the 55th EC meeting in Jena, Germany, or in the second EC vote in November 2023. All proposals were ratified by online vote. Taxonomic additions include one new phylum (Ambiviricota), one new class, nine new orders, three new suborders, 51 new families, 18 new subfamilies, 820 new genera, and 3547 new species (excluding taxa that have been abolished). Proposals to complete the process of species name replacement to the binomial (genus + species epithet) format were ratified. Currently, a total of 14,690 virus species have been established.

Published
2024

9. 2024 taxonomy update for the family Circoviridae

Author

Varsani, Arvind, Harrach, Balázs, Roumagnac, Philippe, Benkő, Mária, Breitbart, Mya, Delwart, Eric, Franzo, Giovanni, Kazlauskas, Darius, Rosario, Karyna, Segalés, Joaquim, Dunay, Emily, Rukundo, Joshua, Goldberg, Tony L., Fehér, Enikő, Kaszab, Eszter, Bányai, Krisztián, and Krupovic, Mart

Published
2024
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11. A predicted CRISPR-mediated symbiosis between uncultivated archaea

Author

Esser, Sarah P, Rahlff, Janina, Zhao, Weishu, Predl, Michael, Plewka, Julia, Sures, Katharina, Wimmer, Franziska, Lee, Janey, Adam, Panagiotis S, McGonigle, Julia, Turzynski, Victoria, Banas, Indra, Schwank, Katrin, Krupovic, Mart, Bornemann, Till LV, Figueroa-Gonzalez, Perla Abigail, Jarett, Jessica, Rattei, Thomas, Amano, Yuki, Blaby, Ian K, Cheng, Jan-Fang, Brazelton, William J, Beisel, Chase L, Woyke, Tanja, Zhang, Ying, and Probst, Alexander J

Subjects
Microbiology, Biological Sciences, Human Genome, Genetics, Archaea, Symbiosis, Genomics, Plasmids, DNA, Medical Microbiology
Abstract

CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.

Published
2023

12. Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota).

Author

Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles, Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi, Kumar Chaturvedi, Krishna, Chooi, Kar, Crane, Anya, Dal Bó, Elena, Carlos de la Torre, Juan, de Souza, William, de Swart, Rik, Debat, Humberto, Dheilly, Nolwenn, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf, Digiaro, Michele, Drexler, J, Duprex, W, Dürrwald, Ralf, Easton, Andrew, Elbeaino, Toufic, Ergünay, Koray, Feng, Guozhong, Firth, Andrew, Fooks, Anthony, Formenty, Pierre, Freitas-Astúa, Juliana, Gago-Zachert, Selma, Laura García, María, García-Sastre, Adolfo, Garrison, Aura, Gaskin, Thomas, Gong, Wenjie, Gonzalez, Jean-Paul, de Bellocq, JoëlleGoüy, Griffiths, Anthony, Groschup, Martin, Günther, Ines, Günther, Stephan, Hammond, John, Hasegawa, Yusuke, Hayashi, Kazusa, Hepojoki, Jussi, Higgins, Colleen, Hongō, Seiji, Horie, Masayuki, Hughes, Holly, Hume, Adam, Hyndman, Timothy, Ikeda, Kenichi, Jiāng, Dàohóng, Jonson, Gilda, Junglen, Sandra, Klempa, Boris, Klingström, Jonas, Kondō, Hideki, Koonin, Eugene, Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy, Lǐ, Jiànróng, Li, Jun-Min, Liu, Ran, Lukashevich, Igor, MacDiarmid, Robin, Maes, Piet, Marklewitz, Marco, Marshall, Sergio, Marzano, Shin-Yi, McCauley, John, Mirazimi, Ali, Mühlberger, Elke, Nabeshima, Tomoyuki, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José, Neriya, Yutaro, Netesov, Sergey, Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio, Ochoa-Corona, Francisco, Okada, Tomoyuki, Palacios, Gustavo, Pallás, Vicente, Papa, Anna, Paraskevopoulou, Sofia, Parrish, Colin, Pauvolid-Corrêa, Alex, Pawęska, Janusz, Pérez, Daniel, and Pfaff, Florian

Subjects
Aliusviridae, Arenaviridae, Articulavirales, Artoviridae, Aspiviridae, Bornaviridae, Bunyavirales, Crepuscuviridae, Discoviridae, Filoviridae, Fimoviridae, Goujianvirales, Hantaviridae, ICTV, International Committee on Taxonomy of Viruses, Jingchuvirales, Lispiviridae, Mononegavirales, Muvirales, Mymonaviridae, Myriaviridae, Nairoviridae, Natareviridae, Negarnaviricota, Nyamiviridae, Orthomyxoviridae, Orthornavirae, Paramyxoviridae, Peribunyaviridae, Phasmaviridae, Phenuiviridae, Pneumoviridae, Rhabdoviridae, Riboviria, Serpentovirales, Sunviridae, Tenuivirus, Tosoviridae, Tospoviridae, Tulasviridae, articulaviral, bunyaviral, bunyavirus, goujianviral, megaclassification, megataxonomy, mononegaviral, muviral, negarnaviricot, serpentoviral, virus classification, virus nomenclature, virus taxonomy, Negative-Sense RNA Viruses, RNA Viruses, RNA-Dependent RNA Polymerase
Abstract

In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Published
2023

13. MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets

Author

Vik, Dean, Bolduc, Benjamin, Roux, Simon, Sun, Christine L, Pratama, Akbar Adjie, Krupovic, Mart, and Sullivan, Matthew B

Subjects
Microbiology, Biological Sciences, Bioengineering, Infection, Ecology
Abstract

Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal viruses outside of extreme environments is limited. This largely stems from the lack of a robust, high-throughput, and systematic way to distinguish between bacterial and archaeal viruses in datasets of curated viruses. Here we upgrade our prior text-based tool (MArVD) via training and testing a random forest machine learning algorithm against a newly curated dataset of archaeal viruses. After optimization, MArVD2 presented a significant improvement over its predecessor in terms of scalability, usability, and flexibility, and will allow user-defined custom training datasets as archaeal virus discovery progresses. Benchmarking showed that a model trained with viral sequences from the hypersaline, marine, and hot spring environments correctly classified 85% of the archaeal viruses with a false detection rate below 2% using a random forest prediction threshold of 80% in a separate benchmarking dataset from the same habitats.

Published
2023

14. Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Author

Adriaenssens, Evelien M, Roux, Simon, Brister, J Rodney, Karsch-Mizrachi, Ilene, Kuhn, Jens H, Varsani, Arvind, Yigang, Tong, Reyes, Alejandro, Lood, Cédric, Lefkowitz, Elliot J, Sullivan, Matthew B, Edwards, Robert A, Simmonds, Peter, Rubino, Luisa, Sabanadzovic, Sead, Krupovic, Mart, and Dutilh, Bas E

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Genome, Viral, Phylogeny, Databases, Factual
Published
2023

16. Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

Author

Lee, Benjamin D, Neri, Uri, Roux, Simon, Wolf, Yuri I, Camargo, Antonio Pedro, Krupovic, Mart, Consortium, RNA Virus Discovery, Simmonds, Peter, Kyrpides, Nikos, Gophna, Uri, Dolja, Valerian V, and Koonin, Eugene V

Subjects
Biological Sciences, Genetics, Infectious Diseases, RNA, Circular, Viroids, RNA, Catalytic, RNA, Viral, Ecosystem, Plant Diseases, RNA Virus Discovery Consortium, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.

Published
2023

17. Four principles to establish a universal virus taxonomy

Author

Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola GA, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos

Subjects
Infectious Diseases, Infection, Humans, Bacteriophages, Metagenomics, Phylogeny, Viruses, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology
Abstract

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

Published
2023

18. 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.

Author

Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles, Candresse, Thierry, Carson, Jeremy, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi, Chiaki, Yuya, Crane, Anya, Crane, Mark, Dacheux, Laurent, Bó, Elena, de la Torre, Juan, de Lamballerie, Xavier, de Souza, William, de Swart, Rik, Dheilly, Nolwenn, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf, Digiaro, Michele, Drexler, J, Duprex, W, Dürrwald, Ralf, Easton, Andrew, Elbeaino, Toufic, Ergünay, Koray, Feng, Guozhong, Feuvrier, Claudette, Firth, Andrew, Fooks, Anthony, Formenty, Pierre, Freitas-Astúa, Juliana, Gago-Zachert, Selma, García, María, García-Sastre, Adolfo, Garrison, Aura, Godwin, Scott, Gonzalez, Jean-Paul, de Bellocq, Joëlle, Griffiths, Anthony, Groschup, Martin, Günther, Stephan, Hammond, John, Hepojoki, Jussi, Hierweger, Melanie, Hongō, Seiji, Horie, Masayuki, Horikawa, Hidenori, Hughes, Holly, Hume, Adam, Hyndman, Timothy, Jiāng, Dàohóng, Jonson, Gilda, Junglen, Sandra, Kadono, Fujio, Karlin, David, Klempa, Boris, Klingström, Jonas, Koch, Michel, Kondō, Hideki, Koonin, Eugene, Krásová, Jarmila, Krupovic, Mart, Kubota, Kenji, Kuzmin, Ivan, Laenen, Lies, Lambert, Amy, Lǐ, Jiànróng, Li, Jun-Min, Lieffrig, François, Lukashevich, Igor, Luo, Dongsheng, Maes, Piet, Marklewitz, Marco, Marshall, Sergio, Marzano, Shin-Yi, McCauley, John, Mirazimi, Ali, Mohr, Peter, Moody, Nick, Morita, Yasuaki, Morrison, Richard, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José, Neriya, Yutaro, Netesov, Sergey, Neumann, Gabriele, Nowotny, Norbert, Ochoa-Corona, Francisco, Palacios, Gustavo, Pallandre, Laurane, Pallás, Vicente, Papa, Anna, Paraskevopoulou, Sofia, and Parrish, Colin

Subjects
Humans, Mononegavirales, Phylogeny, Viruses
Abstract

In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Published
2022

22. Perspective on taxonomic classification of uncultivated viruses

Author

Dutilh, Bas E, Varsani, Arvind, Tong, Yigang, Simmonds, Peter, Sabanadzovic, Sead, Rubino, Luisa, Roux, Simon, Muñoz, Alejandro Reyes, Lood, Cédric, Lefkowitz, Elliot J, Kuhn, Jens H, Krupovic, Mart, Edwards, Robert A, Brister, J Rodney, Adriaenssens, Evelien M, and Sullivan, Matthew B

Subjects
Microbiology, Biological Sciences, Infectious Diseases, Networking and Information Technology R&D (NITRD), Animals, Evolution, Molecular, Humans, Metagenomics, Phylogeny, Viruses, Medical Microbiology
Abstract

Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on an astounding number of previously unknown viruses. As metagenomes are relatively free of biases, these data provide an unprecedented insight into the vastness of the virosphere, but to properly value the extent of this diversity it is critical that the viruses are taxonomically classified. Inclusion of uncultivated viruses has already improved the process as well as the understanding of the taxa, viruses, and their evolutionary relationships. The continuous development and testing of computational tools will be required to maintain a dynamic virus taxonomy that can accommodate the new discoveries.

Published
2021

25. Correction to: Changes to virus taxonomy and the ICTV Statutes ratifed by the International Committee on Taxonomy of Viruses (2023)

Author

Zerbini, Francisco Murilo, Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas‑Zerbini, Poliane, Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Hendrickson, R. Curtis, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne‑Mieke, and Varsani, Arvind

Published
2023
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30. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes

Author

Liu, Ying, Demina, Tatiana A, Roux, Simon, Aiewsakun, Pakorn, Kazlauskas, Darius, Simmonds, Peter, Prangishvili, David, Oksanen, Hanna M, and Krupovic, Mart

Subjects
Microbiology, Biological Sciences, Genetics, Biotechnology, Infection, Archaeal Viruses, Biological Evolution, DNA, DNA, Viral, Genetic Variation, Genome, Viral, Host Specificity, Mutation, Phylogeny, Prokaryotic Cells, Viral Proteins, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments.

Published
2021

31. Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

Author

Roux, Simon, Krupovic, Mart, Daly, Rebecca A, Borges, Adair L, Nayfach, Stephen, Schulz, Frederik, Sharrar, Allison, Matheus Carnevali, Paula B, Cheng, Jan-Fang, Ivanova, Natalia N, Bondy-Denomy, Joseph, Wrighton, Kelly C, Woyke, Tanja, Visel, Axel, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A

Subjects
Microbiology, Biological Sciences, Medical Microbiology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

34. 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Alkhovsky, Sergey V., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Bandte, Martina, Beer, Martin, Bejerman, Nicolas, Bergeron, Éric, Biedenkopf, Nadine, Bigarré, Laurent, Blair, Carol D., Blasdell, Kim R., Bradfute, Steven B., Briese, Thomas, Brown, Paul A., Bruggmann, Rémy, Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Candresse, Thierry, Carson, Jeremy, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Chiaki, Yuya, Crane, Anya, Crane, Mark, Dacheux, Laurent, Bó, Elena Dal, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Souza, William M., de Swart, Rik L., Dheilly, Nolwenn M., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Drexler, J. Felix, Duprex, W. Paul, Dürrwald, Ralf, Easton, Andrew J., Elbeaino, Toufic, Ergünay, Koray, Feng, Guozhong, Feuvrier, Claudette, Firth, Andrew E., Fooks, Anthony R., Formenty, Pierre B. H., Freitas-Astúa, Juliana, Gago-Zachert, Selma, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Godwin, Scott E., Gonzalez, Jean-Paul J., de Bellocq, Joëlle Goüy, Griffiths, Anthony, Groschup, Martin H., Günther, Stephan, Hammond, John, Hepojoki, Jussi, Hierweger, Melanie M., Hongō, Seiji, Horie, Masayuki, Horikawa, Hidenori, Hughes, Holly R., Hume, Adam J., Hyndman, Timothy H., Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Karlin, David G., Klempa, Boris, Klingström, Jonas, Koch, Michel C., Kondō, Hideki, Koonin, Eugene V., Krásová, Jarmila, Krupovic, Mart, Kubota, Kenji, Kuzmin, Ivan V., Laenen, Lies, Lambert, Amy J., Lǐ, Jiànróng, Li, Jun-Min, Lieffrig, François, Lukashevich, Igor S., Luo, Dongsheng, Maes, Piet, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., McCauley, John W., Mirazimi, Ali, Mohr, Peter G., Moody, Nick J. G., Morita, Yasuaki, Morrison, Richard N., Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Neriya, Yutaro, Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Ochoa-Corona, Francisco M., Palacios, Gustavo, Pallandre, Laurane, Pallás, Vicente, Papa, Anna, Paraskevopoulou, Sofia, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Pérez, Daniel R., Pfaff, Florian, Plemper, Richard K., Postler, Thomas S., Pozet, Françoise, Radoshitzky, Sheli R., Ramos-González, Pedro L., Rehanek, Marius, Resende, Renato O., Reyes, Carina A., Romanowski, Víctor, Rubbenstroth, Dennis, Rubino, Luisa, Rumbou, Artemis, Runstadler, Jonathan A., Rupp, Melanie, Sabanadzovic, Sead, Sasaya, Takahide, Schmidt-Posthaus, Heike, Schwemmle, Martin, Seuberlich, Torsten, Sharpe, Stephen R., Shi, Mang, Sironi, Manuela, Smither, Sophie, Song, Jin-Won, Spann, Kirsten M., Spengler, Jessica R., Stenglein, Mark D., Takada, Ayato, Tesh, Robert B., Těšíková, Jana, Thornburg, Natalie J., Tischler, Nicole D., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Tsunekawa, Kenta, Turina, Massimo, Tzanetakis, Ioannis E., Vaira, Anna Maria, van den Hoogen, Bernadette, Vanmechelen, Bert, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Yamasaki, Junki, Yanagisawa, Hironobu, Ye, Gongyin, Zhang, Yong-Zhen, and Økland, Arnfinn Lodden

Published
2022
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36. Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022)

Author

Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Curtis Hendrickson, R., Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Orton, Richard J., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Zerbini, Francisco Murilo

Published
2022
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37. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023)

Author

Zerbini, Francisco Murilo, Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas‑Zerbini, Poliane, Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Hendrickson, R. Curtis, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne‑Mieke, and Varsani, Arvind

Published
2023
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38. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Author

Bin Jang, Ho, Bolduc, Benjamin, Zablocki, Olivier, Kuhn, Jens H, Roux, Simon, Adriaenssens, Evelien M, Brister, J Rodney, Kropinski, Andrew M, Krupovic, Mart, Lavigne, Rob, Turner, Dann, and Sullivan, Matthew B

Subjects
Microbiology, Biological Sciences, Infectious Diseases, Biotechnology, Genetics, Infection, Bacteriophages, Classification, Gene Regulatory Networks, Genome, Viral, Metagenome, Metagenomics, Phylogeny, Prokaryotic Cells, Viruses
Abstract

Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.

Published
2019

39. Cryptic inoviruses are pervasive in bacteria and archaea across Earth’s biomes

Author

Roux, Simon, Krupovic, Mart, Daly, Rebecca, Borges, Adair, Nayfach, Stephen, Schulz, Frederik, Cheng, Jan-Fang, Ivanova, Natalia, Bondy-Denomy, Joseph, Wrighton, Kelly, Woyke, Tanja, Visel, Axel, Kyrpides, Nikos, and Eloe-Fadrosh, Emiley

Subjects
Prevention, Biotechnology, Biodefense, Infectious Diseases, Rare Diseases, Vaccine Related, Emerging Infectious Diseases, Genetics, 2.2 Factors relating to the physical environment, Infection
Abstract

Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content, and infection cycle. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications such as phage display, or because of their impact on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis . Here we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a new machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like genomes from microbial genomes and metagenomes. Collectively, these represent six distinct proposed inovirus families infecting nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that these viruses may have occasionally transferred from bacterial to archaeal hosts. Finally, we identified an expansive diversity of inovirus-encoded toxin-antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere sparks new avenues for microbial manipulation approaches and innovative biotechnological applications.

Published
2019

40. Numerous cultivated and uncultivated viruses encode ribosomal proteins.

Author

Mizuno, Carolina M, Guyomar, Charlotte, Roux, Simon, Lavigne, Régis, Rodriguez-Valera, Francisco, Sullivan, Matthew B, Gillet, Reynald, Forterre, Patrick, and Krupovic, Mart

Subjects
Vaccine Related, Prevention, Biodefense, Genetics, Infectious Diseases, 2.2 Factors relating to physical environment, Infection, MD Multidisciplinary
Abstract

Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses. Viruses tend to encode dynamic RPs, easily exchangeable between ribosomes, suggesting these proteins can replace cellular versions in host ribosomes. Functional assays confirm that the two most common virus-encoded RPs, bS21 and bL12, are incorporated into 70S ribosomes when expressed in Escherichia coli. Ecological distribution of virus-encoded RPs suggests some level of ecosystem adaptations as aquatic viruses and viruses of animal-associated bacteria are enriched for different subsets of RPs. Finally, RP genes are under purifying selection and thus likely retained an important function after being horizontally transferred into virus genomes.

Published
2019

45. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author

Turner, Dann, Shkoporov, Andrey N., Lood, Cédric, Millard, Andrew D., Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K., Oksanen, Hanna M., Poranen, Minna M., Kropinski, Andrew M., Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A., Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, BL, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M.

Published
2023
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50. Differentiating between viruses and virus species by writing their names correctly

Author

Zerbini, Francisco Murilo, Siddell, Stuart G., Mushegian, Arcady R., Walker, Peter J., Lefkowitz, Elliot J., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Dutilh, Bas E., García, María Laura, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, and Varsani, Arvind

Published
2022
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