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33 results on '"International Committee on Taxonomy of Viruses"'

1. Promotion of order Bunyavirales to class Bunyaviricetes to accommodate a rapidly increasing number of related polyploviricotine viruses.

Author: Kuhn, Jens H., Brown, Katherine, Adkins, Scott, de la Torre, Juan Carlos, Digiaro, Michele, Ergünay, Koray, Firth, Andrew E., Hughes, Holly R., Junglen, Sandra, Lambert, Amy J., Maes, Piet, Marklewitz, Marco, Palacios, Gustavo, Takahide Sasaya (笹谷孝英), Mang Shi (施莽), Yong-Zhen Zhang (张永振), Wolf, Yuri I., and Massimo Turina
Subjects: *RNA replicase, *ARENAVIRUSES, *BUNYAVIRUSES, *GENOMES, *RNA
Abstract: Prior to 2017, the family Bunyaviridae included five genera of arthropod and rodent viruses with tri-segmented negative-sense RNA genomes related to the Bunyamwera virus. In 2017, the International Committee on Taxonomy of Viruses (ICTV) promoted the family to order Bunyavirales and subsequently greatly expanded its composition by adding multiple families for non-segmented to polysegmented viruses of animals, fungi, plants, and protists. The continued and accelerated discovery of bunyavirals highlighted that an order would not suffice to depict the evolutionary relationships of these viruses. Thus, in April 2024, the order was promoted to class Bunyaviricetes. This class currently includes two major orders, Elliovirales (Cruliviridae, Fimoviridae, Hantaviridae, Peribunyaviridae, Phasmaviridae, Tospoviridae, and Tulasviridae) and Hareavirales (Arenaviridae, Discoviridae, Konkoviridae, Leishbuviridae, Mypoviridae, Nairoviridae, Phenuiviridae, and Wupedeviridae), for hundreds of viruses, many of which are pathogenic for humans and other animals, plants, and fungi. [ABSTRACT FROM AUTHOR]
Published: 2024
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2. 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

3. Ambiviricota, a novel ribovirian phylum for viruses with viroidlike properties.

Author: Kuhn, Jens H., Botella, Leticia, de la Peña, Marcos, Vainio, Eeva J., Krupovic, Mart, Lee, Benjamin D., Navarro, Beatriz, Sabanadzovic, Sead, Simmonds, Peter, and Turina, Massimo
Subjects: *RNA replicase, *MOBILE genetic elements, *GENETIC variation, *CATALYTIC RNA, *GENOMES
Abstract: Fungi harbor a vast diversity of mobile genetic elements (MGEs). Recently, novel fungal MGEs, tentatively referred to as ‘ambiviruses,’ were described. ‘Ambiviruses’ have single-stranded RNA genomes of about 4–5 kb in length that contain at least two open reading frames (ORFs) in non-overlapping ambisense orientation. Both ORFs are conserved among all currently known ‘ambiviruses,’ and one of them encodes a distinct viral RNA-directed RNA polymerase (RdRP), the hallmark gene of ribovirian kingdom Orthornavirae. However, ‘ambivirus’ genomes are circular and predicted to replicate via a rolling-circle mechanism. Their genomes are also predicted to form rod-like structures and contain ribozymes in various combinations in both sense and antisense orientations—features reminiscent of viroids, virusoids, ribozyvirian kolmiovirids, and yet-unclassified MGEs (such as ‘epsilonviruses,’ ‘zetaviruses,’ and some ‘obelisks’). As a first step toward the formal classification of ‘ambiviruses,’ the International Committee on Taxonomy of Viruses (ICTV) recently approved the establishment of a novel ribovirian phylum, Ambiviricota, to accommodate an initial set of 20 members with well-annotated genome sequences. [ABSTRACT FROM AUTHOR]
Published: 2024
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4. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials.

Author: Postler, Thomas S, Clawson, Anna N, Amarasinghe, Gaya K, Basler, Christopher F, Bavari, Sbina, Benko, Mária, Blasdell, Kim R, Briese, Thomas, Buchmeier, Michael J, Bukreyev, Alexander, Calisher, Charles H, Chandran, Kartik, Charrel, Rémi, Clegg, Christopher S, Collins, Peter L, Juan Carlos, De La Torre, Derisi, Joseph L, Dietzgen, Ralf G, Dolnik, Olga, Dürrwald, Ralf, Dye, John M, Easton, Andrew J, Emonet, Sébastian, Formenty, Pierre, Fouchier, Ron AM, Ghedin, Elodie, Gonzalez, Jean-Paul, Harrach, Balázs, Hewson, Roger, Horie, Masayuki, Jiang, Dàohóng, Kobinger, Gary, Kondo, Hideki, Kropinski, Andrew M, Krupovic, Mart, Kurath, Gael, Lamb, Robert A, Leroy, Eric M, Lukashevich, Igor S, Maisner, Andrea, Mushegian, Arcady R, Netesov, Sergey V, Nowotny, Norbert, Patterson, Jean L, Payne, Susan L, PaWeska, Janusz T, Peters, Clarence J, Radoshitzky, Sheli R, Rima, Bertus K, Romanowski, Victor, Rubbenstroth, Dennis, Sabanadzovic, Sead, Sanfaçon, Hélène, Salvato, Maria S, Schwemmle, Martin, Smither, Sophie J, Stenglein, Mark D, Stone, David M, Takada, Ayato, Tesh, Robert B, Tomonaga, Keizo, Tordo, Noël, Towner, Jonathan S, Vasilakis, Nikos, Volchkov, Viktor E, Wahl-Jensen, Victoria, Walker, Peter J, Wang, Lin-Fa, Varsani, Arvind, Whitfield, Anna E, Zerbini, F Murilo, and Kuhn, Jens H
Subjects: Classification, Terminology as Topic, Viruses, Arenaviridae, binomials, ICTV, International Committee on Taxonomy of Viruses, Mononegavirales, virus nomenclature, virus taxonomy, Evolutionary Biology, Genetics
Abstract: Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted to convert all currently official names of species included in the virus family Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment. [Arenaviridae; binomials; ICTV; International Committee on Taxonomy of Viruses; Mononegavirales; virus nomenclature; virus taxonomy.].
Published: 2017

5. Bunyavirales Order

Author: D. K. Lvov and S. V. Alkhovsky
Subjects: bunyaviruses, virus taxonomy, international committee on taxonomy of viruses, Infectious and parasitic diseases, RC109-216
Abstract: In 2017 the International Committee on Taxonomy of Viruses (ICTY) established and approved a new order Bunyavirales that unite evolutionary related viruses whose genome is represented by a segmented linear single-stranded RNA of negative or ambisense polarity. Currently, the order Bunyavirales includes 10 families that infect vertebrate animals, invertebrates (arthropods), and plants. At least 41 zoonotic bunyaviruses, including pathogenic for human, were isolated on the territory of Northern Eurasia. This review presents the data on the composition of the families belonging to the order Bunyavirales and a list of zoonotic bunyaviruses, isolated in Northern Eurasia, indicating their modern taxonomy. Most of them are arboviruses, associated with different species of mosquitoes or ticks.
Published: 2018
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6. Guide to the Correct Use of Filoviral Nomenclature

Author: Kuhn, Jens H., Compans, Richard W, Series editor, Honjo, Tasuku, Series editor, Malissen, Bernard, Series editor, Aktories, Klaus, Series editor, Rappuoli, Rino, Series editor, Galan, Jorge E., Series editor, Ahmed, Rafi, Series editor, Palme, Klaus, Series editor, Casadevall, Arturo, Series editor, Garcia-Sastre, Adolfo, Series editor, Iwasaki, Akiko, Series editor, Mühlberger, Elke, editor, Hensley, Lisa L., editor, and Towner, Jonathan S., editor
Published: 2017
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7. Cressdnaviricota: a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes.

Author: Krupovic, Mart, Varsani, Arvind, Kazlauskas, Darius, Breitbart, Mya, Delwart, Eric, Rosario, Karyna, Yutin, Natalya, Wolf, Yuri I., Harrach, Balázs, Zerbini, F. Murilo, Dolja, Valerian V., Kuhn, Jens H., and Koonin, Eugene V.
Subjects: *SINGLE-stranded DNA, *CIRCULAR DNA, *VIRUSES, *GENOMES
Published: 2020
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8. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Author: Siddell, Stuart G, Smith, Donald B, Adriaenssens, Evelien, Alfenas-Zerbini, Poliane, Dutilh, Bas E, Garcia, Maria Laura, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Mushegian, Arcady R, Oksanen, Hanna M, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Zerbini, F Murilo, Siddell, Stuart G, Smith, Donald B, Adriaenssens, Evelien, Alfenas-Zerbini, Poliane, Dutilh, Bas E, Garcia, Maria Laura, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Mushegian, Arcady R, Oksanen, Hanna M, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Zerbini, F Murilo
Abstract: The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy of Viruses (ICTV), which scrutinizes, approves and ratifies taxonomic proposals, and maintains a list of virus taxa with approved names (https://ictv.global). The ICTV has approximately 180 members who vote by simple majority. Taxon-specific Study Groups established by the ICTV have a combined membership of over 600 scientists from the wider virology community; they provide comprehensive expertise across the range of known viruses and are major contributors to the creation and evaluation of taxonomic proposals. Proposals can be submitted by anyone and will be considered by the ICTV irrespective of Study Group support. Thus, virus taxonomy is developed from within the virology community and realized by a democratic decision-making process. The ICTV upholds the distinction between a virus or replicating genetic element as a physical entity and the taxon category to which it is assigned. This is reflected by the nomenclature of the virus species taxon, which is now mandated by the ICTV to be in a binomial format (genus + species epithet) and is typographically distinct from the names of viruses. Classification of viruses below the rank of species (such as, genotypes or strains) is not within the remit of the ICTV. This article, authored by the ICTV Executive Committee, explains the principles of virus taxonomy and the organization, function, processes and resources of the ICTV, with the aim of encouraging greater understanding and interaction among the wider virology community.
Published: 2023

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

Author: Kuhn, Jens H., Abe, Junya, Adkins, Scott, Alkhovsky, Sergey V., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Baranwal, Virendra Kumar, Beer, Martin, Bejerman, Nicolas, Bergeron, Éric, Biedenkopf, Nadine, Blair, Carol D., Blasdell, Kim R., Blouin, Arnaud G., Bradfute, Steven B., Briese, Thomas, Brown, Paul A., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Chaturvedi, Krishna Kumar, Chooi, Kar Mun, Crane, Anya, Bó, Elena Dal, de la Torre, Juan Carlos, de Souza, William M., de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Drexler, J.F., Duprex, W.P., Dürrwald, Ralf, Easton, Andrew J., Elbeaino, Toufic, Ergünay, Koray, Feng, Guozhong, 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., Gaskin, Thomas R., Gong, Wenjie, Gonzalez, Jean Paul J., de Bellocq, Joëlle Goüy, Griffiths, Anthony, Groschup, Martin H., Günther, Ines, Günther, Stephan, Hammond, John, Hasegawa, Yusuke, Hayashi, Kazusa, Hepojoki, Jussi, Higgins, Colleen M., Hongō, Seiji, Horie, Masayuki, Hughes, Holly R., Hume, Adam J., Hyndman, Timothy H., Ikeda, Kenichi, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Klempa, Boris, Klingström, Jonas, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Lǐ, Jiànróng, Li, Jun Min, Liu, Ran, Lukashevich, Igor S., MacDiarmid, Robin M., Maes, Piet, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin Yi L., McCauley, John W., Mirazimi, Ali, Mühlberger, Elke, Nabeshima, Tomoyuki, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Neriya, Yutaro, Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R.T., Ochoa-Corona, Francisco M., Okada, Tomoyuki, Palacios, Gustavo, 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., Rabbidge, Lee O., Radoshitzky, Sheli R., Ramos-González, Pedro L., Rehanek, Marius, Resende, Renato O., Reyes, Carina A., Rodrigues, Thaís C.S., Romanowski, Víctor, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sadiq, Sabrina, Salvato, Maria S., Sasaya, Takahide, Schwemmle, Martin, Sharpe, Stephen R., Shi, Mang, Shimomoto, Yoshifumi, Sidharthan, Venkidusamy Kavi, Sironi, Manuela, Smither, Sophie, Song, Jin Won, Spann, Kirsten M., Spengler, Jessica R., Stenglein, Mark D., Takada, Ayato, Takeyama, Sawana, Tatara, Akio, Tesh, Robert B., Thornburg, Natalie J., Tian, Xin, Tischler, Nicole D., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Tu, Changchun, 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., Waltzek, Thomas B., Whitfield, Anna E., Wolf, Yuri I., Xia, Han, Xylogianni, Evanthia, Yanagisawa, Hironobu, Yano, Kazutaka, Ye, Gongyin, Yuan, Zhiming, Zerbini, F.M., Zhang, Guilin, Zhang, Song, Zhang, Yong Zhen, Zhao, Lu, Økland, Arnfinn Lodden, Kuhn, Jens H., Abe, Junya, Adkins, Scott, Alkhovsky, Sergey V., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Baranwal, Virendra Kumar, Beer, Martin, Bejerman, Nicolas, Bergeron, Éric, Biedenkopf, Nadine, Blair, Carol D., Blasdell, Kim R., Blouin, Arnaud G., Bradfute, Steven B., Briese, Thomas, Brown, Paul A., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Chaturvedi, Krishna Kumar, Chooi, Kar Mun, Crane, Anya, Bó, Elena Dal, de la Torre, Juan Carlos, de Souza, William M., de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Drexler, J.F., Duprex, W.P., Dürrwald, Ralf, Easton, Andrew J., Elbeaino, Toufic, Ergünay, Koray, Feng, Guozhong, 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., Gaskin, Thomas R., Gong, Wenjie, Gonzalez, Jean Paul J., de Bellocq, Joëlle Goüy, Griffiths, Anthony, Groschup, Martin H., Günther, Ines, Günther, Stephan, Hammond, John, Hasegawa, Yusuke, Hayashi, Kazusa, Hepojoki, Jussi, Higgins, Colleen M., Hongō, Seiji, Horie, Masayuki, Hughes, Holly R., Hume, Adam J., Hyndman, Timothy H., Ikeda, Kenichi, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Klempa, Boris, Klingström, Jonas, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Lǐ, Jiànróng, Li, Jun Min, Liu, Ran, Lukashevich, Igor S., MacDiarmid, Robin M., Maes, Piet, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin Yi L., McCauley, John W., Mirazimi, Ali, Mühlberger, Elke, Nabeshima, Tomoyuki, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Neriya, Yutaro, Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R.T., Ochoa-Corona, Francisco M., Okada, Tomoyuki, Palacios, Gustavo, 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., Rabbidge, Lee O., Radoshitzky, Sheli R., Ramos-González, Pedro L., Rehanek, Marius, Resende, Renato O., Reyes, Carina A., Rodrigues, Thaís C.S., Romanowski, Víctor, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sadiq, Sabrina, Salvato, Maria S., Sasaya, Takahide, Schwemmle, Martin, Sharpe, Stephen R., Shi, Mang, Shimomoto, Yoshifumi, Sidharthan, Venkidusamy Kavi, Sironi, Manuela, Smither, Sophie, Song, Jin Won, Spann, Kirsten M., Spengler, Jessica R., Stenglein, Mark D., Takada, Ayato, Takeyama, Sawana, Tatara, Akio, Tesh, Robert B., Thornburg, Natalie J., Tian, Xin, Tischler, Nicole D., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Tu, Changchun, 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., Waltzek, Thomas B., Whitfield, Anna E., Wolf, Yuri I., Xia, Han, Xylogianni, Evanthia, Yanagisawa, Hironobu, Yano, Kazutaka, Ye, Gongyin, Yuan, Zhiming, Zerbini, F.M., Zhang, Guilin, Zhang, Song, Zhang, Yong Zhen, Zhao, Lu, and Økland, Arnfinn Lodden
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.
Published: 2023

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

Author: National Institute of Allergy and Infectious Diseases (US), Antiviral Countermeasures Development Center (US), Department of Agriculture (US), Department of the Army (US), Department of Health and Human Services (US), US Department of Homeland Security, Federal Government of the United States, Kuhn, Jens H. [0000-0002-7800-6045], Abe, Junya [0000-0003-3627-7071], Adkins, Scott [0000-0003-0095-8414], Alkhovsky, Sergey V. [0000-0001-6913-5841], Avsic-Zupanc, Tatjana [0000-0001-6243-0688], Ayllón, María A. [0000-0001-7893-6106], Bahl, Justin [0000-0001-7572-4300], Balkema-Buschmann, A. [0000-0001-7613-9592], Ballinger, Matthew J. [0000-0001-7453-8725], Bejerman, Nicolas [0000-0002-7851-3506], Biedenkopf, Nadine [0000-0002-6061-8019], Blair, Carol D.[0000-0002-2803-0354], Blasdell, Kim R.[0000-0003-2121-0376], Bradfute, Steven B.[0000-0002-1985-751X], Briese, Thomas [0000-0002-4819-8963], Buchholz, Ursula J. [0000-0002-2329-3198], Buchmeier, Michael J.[0000-0002-2387-9287], Bukreyev, Alexander [0000-0002-0342-4824], Burt, Felicity [0000-0002-7238-7799], Büttner, Carmen [0000-0002-2086-2594], Calisher, Charles H. [0000-0003-0213-294X], Cao, Mengji [0000-0003-0396-262X], Casas, Inmaculada [0000-0003-1840-1198], Chandran, Kartik [0000-0003-0232-7077], Charrel, Rémi N.[0000-0002-7675-8251], Chaturvedi, Krishna Kumar [0000-0002-6529-5466], Crane, Anya [0000-0002-2060-2469], De Swart, Rik L.[0000-0003-3599-8969], Debat, Humberto [0000-0003-3056-3739], Dheilly, Nolwenn M.[0000-0002-3675-5013], Di Paola, Nicholas [0000-0002-9694-3913], Di Serio, Francesco [0000-0003-2822-704X], Dietzgen, Ralf G.[0000-0002-7772-2250], Digiaro, Michele [0009-0006-3089-3606], Drexler, J. Felix [0000-0002-3509-0232], Duprex, W. Paul [0000-0003-1716-6376], Elbeaino, Toufic [0000-0003-2211-7907], Ergünay, Koray [0000-0001-5422-1982], Feng, Guozhong [0000-0002-9489-9322], Fooks, Anthony R.[0000-0002-3243-6154], Formenty, Pierre B.H.[0000-0002-9482-5411], Freitas-Astúa, Juliana [0000-0002-0506-6880], Gago-Zachert, Selma [0000-0002-1084-2119], García, María Laura [0000-0001-6468-6943], Garrison, Aura R.[0000-0003-3034-6400], Gaskin, Thomas R. [0000-0002-5644-4431], Gouy de Bellocq, Joelle [0000-0001-5831-6284], Griffiths, Anthony [0000-0001-5435-8364], Groschup, M. H.[0000-0003-0215-185X], Günther, Stephan [0000-0002-6562-0230], Hayashi, Kazusa [0009-0002-9395-0066], Hepojoki, Jussi [0000-0001-5699-214X], Higgins, Colleen M. 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H., Günther, Ines, Günther, Stephan, Hammond, John, Hasegawa, Yusuke, Hayashi, Kazusa, Hepojoki, Jussi, Higgins, Colleen M., Hongo, Seiji, Horie, Masayuki, Hughes, Holly R., Hume, Adam J., Hyndman, Timothy, Ikeda, Kenichi, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Klempa, B., Klingström, Jonas, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Li, Jianrong, Li, Jun-Min, Liu, Ran, Lukashevich, Igor S., MacDiarmid, Robin M, Maes, Piet, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., McCauley, John W., Mirazimi, Ali, Mühlberger, Elke, Nabeshima, Tomoyuki, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Neriya, Yutaro, Netesov, Sergey V., Neumann, Gabriele, Nowotny, N., Nunes, Márcio R.T., Ochoa-Corona, Francisco M., Okada, Tomoyuki, Palacios, Gustavo, 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., Rabbidge, Lee O., Radoshitzky, Sheli R., Ramos-González, Pedro L., Rehanek, Marius, Resende, Renato O., Reyes, Carina A., Rodrigues, Thaís C.S., Romanowski, Víctor, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sadiq, Sabrina, Salvato, Maria S., Sasaya, Takahide, Schwemmle, Martin, Sharpe, Stephen R., Shi, Mang, Shimomoto, Yoshifumi, Kavi Sidharthan, Venkidusamy, Sironi, Manuela, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Takada, Ayato, Takeyama, Sawana, Tatara, Akio, Tesh, Robert B., Thornburg, Natalie J., Tian, Xin, Tischler, Nicole D., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Tu, Changchun, 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., Waltzek, Thomas B., Whitfield, Anna E., Wolf, Yuri I., Xia, Han, Xylogianni, Evanthia, Yanagisawa, Hironobu, Yano, Kazutaka, Ye, Gongyin, Yuan, Zhiming, Zerbini, F. Murilo, Zhang, Guilin, Zhang, Song, Zhang, Yong-Zhen, Zhao, Lu, and Okland, Arnfinn Lodden
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

11. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Author: Siddell, Stuart G., Smith, Donald B., Adriaenssens, Evelien, Alfenas-Zerbini, Poliane, Dutilh, Bas E., Garcia, Maria Laura, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Lefkowitz, Elliot J., Łobocka, Małgorzata, Mushegian, Arcady R., Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Zerbini, F. Murilo, University of Bristol [Bristol], University of Oxford, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Utrecht University [Utrecht], Instituto de Biotecnología y Biología Molecular [La Plata] (IBBM), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas [La Plata], Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), Free University of Berlin (FU), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), University of Alabama at Birmingham [ Birmingham] (UAB), Institute of Biochemistry and Biophysics [Warsaw] (IBB), National Science Foundation [Arlington] (NSF), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, MRC - University of Glasgow Centre for Virus Research, CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], Okayama University, University of Arizona, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Arizona State University [Tempe] (ASU), D.B.S. is supported by a grant from the Microbiology Society. B.E.D. is supported by the European Research Council (ERC) Consolidator grant 865694: DiversiPHI, the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany ́s Excellence Strategy – EXC 2051 – Project-ID 390713860, the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt-Professorship founded by German Federal Ministry of Education and Research, and the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie Actions Innovative Training Networks grant agreement no. 955 974 (VIROINF). E.J.L. – this publication was supported by the National Institutes of Health (NIH) National Institute of Allergy And Infectious Diseases (NIAID), under Award Number U24AI162625. This work was also supported in part through the Laulima Government Solutions, LLC, prime contract with the NIH NIAID, under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), the statements and opinions expressed herein are made in a personal capacity and do not constitute endorsement by NSF or the government of the United States. H.M.O. was supported by the University of Helsinki and Academy of Finland funding for FINStruct, part of Biocenter Finland and Instruct-ERIC. D.L.R. is funded by the MRC (MC_UU_12014/12). S.S. acknowledges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project, under Accession Number 1021 494., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Instituto de Higiene e Medicina Tropical (IHMT), Global Health and Tropical Medicine (GHTM), and TB, HIV and opportunistic diseases and pathogens (THOP)
Subjects: ICTV, Infectious Diseases, Science & Technology, SDG 3 - Good Health and Well-being, Biotechnology & Applied Microbiology, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, virus nomenclature, virus taxonomy, virus classification, QR355 Virology, Life Sciences & Biomedicine, International Committee on Taxonomy of Viruses
Abstract: The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy of Viruses (ICTV), which scrutinizes, approves and ratifies taxonomic proposals, and maintains a list of virus taxa with approved names (https://ictv.global). The ICTV has approximately 180 members who vote by simple majority. Taxon-specific Study Groups established by the ICTV have a combined membership of over 600 scientists from the wider virology community; they provide comprehensive expertise across the range of known viruses and are major contributors to the creation and evaluation of taxonomic proposals. Proposals can be submitted by anyone and will be considered by the ICTV irrespective of Study Group support. Thus, virus taxonomy is developed from within the virology community and realized by a democratic decision-making process. The ICTV upholds the distinction between a virus or replicating genetic element as a physical entity and the taxon category to which it is assigned. This is reflected by the nomenclature of the virus species taxon, which is now mandated by the ICTV to be in a binomial format (genus + species epithet) and is typographically distinct from the names of viruses. Classification of viruses below the rank of species (such as, genotypes or strains) is not within the remit of the ICTV. This article, authored by the ICTV Executive Committee, explains the principles of virus taxonomy and the organization, function, processes and resources of the ICTV, with the aim of encouraging greater understanding and interaction among the wider virology community.
Published: 2023
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12. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species.

Author: Calisher, Charles H, Briese, Thomas, Brister, J Rodney, Charrel, Rémi N, Dürrwald, Ralf, Ebihara, Hideki, Fulhorst, Charles F, Gāo, George Fú, Groschup, Martin H, Haddow, Andrew D, Hyndman, Timothy H, Junglen, Sandra, Klempa, Boris, Klingström, Jonas, Kropinski, Andrew M, Krupovic, Mart, LaBeaud, A Desiree, Maes, Piet, Nowotny, Norbert, and Nunes, Márcio Roberto Teixeira
Subjects: *VIROLOGY, *VIRUSES, *TAXONOMY, *SPECIES
Abstract: The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV's official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology. [ABSTRACT FROM AUTHOR]
Published: 2019
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13. Guidance for creating individual and batch latinized binomial virus species names

Author: Postler, Thomas S., Rubino, Luisa, Adriaenssens, Evelien M., Dutilh, Bas E., Harrach, Balázs, Junglen, Sandra, Kropinski, Andrew M., Krupovic, Mart, Wada, Jiro, Crane, Anya, Kuhn, Jens H., Mushegian, Arcady, Rūmnieks, Jānis, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, F. Murilo, Callanan, Julie, Draper, Lorraine A., Hill, Colin, Stockdale, Stephen R., Theoretical Biology and Bioinformatics, Sub Bioinformatics, Columbia University Irving Medical Center (CUIMC), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Utrecht University [Utrecht], Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Humboldt University Of Berlin, University of Guelph, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Institutes of Health [Bethesda] (NIH), National Science Foundation [Arlington] (NSF), Latvian Biomedical Research and Study Centre [Rīga], Mississippi State University [Mississippi], University of Oxford, Arizona State University [Tempe] (ASU), University of Cape Town, Universidade Federal de Viçosa = Federal University of Viçosa (UFV), University College Cork (UCC), This work was supported in part through Laulima Government Solutions, LLC prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. A.C. and J.W. performed this work as employees or affiliates of Laulima Government Solutions, LLC. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. This publication has emanated from research conducted with the financial support of Science Foundation Ireland under grant numbers SFI/12/RC/2273_P2 and SFI/14/SP APC/B3032 (J.C., L.A.D, C.H. and S.R.S). E.M.A. gratefully acknowledges the support of the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Program Gut Microbes and Health BB/R012490/1 and its constituent project(s) BBS/E/F/000PR10353 and BBS/E/F/000PR10356. B.E.D. was supported by the European Research Council (ERC) Consolidator grant 865694: DiversiPHI and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy EXC 2051 Project-ID 390713860. B.H. is supported by the National Research, Development and Innovation Office—NKFIH (NN140356). A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), but the statements and opinions expressed herein are made in the personal capacity and do not constitute the endorsement by NSF or the government of the United States. S.S. acknowledges partial support from the Special Research Initiative (MAFES) USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch Project 1021494., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Theoretical Biology and Bioinformatics, and Sub Bioinformatics
Subjects: Virus taxonomy, Binomial, virus nomenclature, virus taxonomy, Virus nomenclature, International Committee on Taxonomy of Viruses, binomial, Ictv, ICTV, Virology, Latinization, Species name, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, species name
Abstract: The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages.
Published: 2022
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14. Spumaretroviruses: Updated taxonomy and nomenclature.

Author: Khan, Arifa S., Bodem, Jochen, Buseyne, Florence, Gessain, Antoine, Johnson, Welkin, Kuhn, Jens H., Kuzmak, Jacek, Lindemann, Dirk, Linial, Maxine L., Löchelt, Martin, Materniak-Kornas, Magdalena, Soares, Marcelo A., and Switzer, William M.
Subjects: *FOAMY viruses, *RETROVIRUSES, *TAXONOMY, *RHESUS monkeys, *VIROLOGY, *PHYSIOLOGY
Abstract: Spumaretroviruses, commonly referred to as foamy viruses, are complex retroviruses belonging to the subfamily Spumaretrovirinae, family Retroviridae , which naturally infect a variety of animals including nonhuman primates (NHPs). Additionally, cross-species transmissions of simian foamy viruses (SFVs) to humans have occurred following exposure to tissues of infected NHPs. Recent research has led to the identification of previously unknown exogenous foamy viruses, and to the discovery of endogenous spumaretrovirus sequences in a variety of host genomes. Here, we describe an updated spumaretrovirus taxonomy that has been recently accepted by the International Committee on Taxonomy of Viruses (ICTV) Executive Committee, and describe a virus nomenclature that is generally consistent with that used for other retroviruses, such as lentiviruses and deltaretroviruses. This taxonomy can be applied to distinguish different, but closely related, primate (e.g., human, ape, simian) foamy viruses as well as those from other hosts. This proposal accounts for host-virus co-speciation and cross-species transmission. [ABSTRACT FROM AUTHOR]
Published: 2018
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15. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names

Author: Jens H. Kuhn, Kristian G. Andersen, Yīmíng Bào, Sina Bavari, Stephan Becker, Richard S. Bennett, Nicholas H. Bergman, Olga Blinkova, Steven Bradfute, J. Rodney Brister, Alexander Bukreyev, Kartik Chandran, Alexander A. Chepurnov, Robert A. Davey, Ralf G. Dietzgen, Norman A. Doggett, Olga Dolnik, John M. Dye, Sven Enterlein, Paul W. Fenimore, Pierre Formenty, Alexander N. Freiberg, Robert F. Garry, Nicole L. Garza, Stephen K. Gire, Jean-Paul Gonzalez, Anthony Griffiths, Christian T. Happi, Lisa E. Hensley, Andrew S. Herbert, Michael C. Hevey, Thomas Hoenen, Anna N. Honko, Georgy M. Ignatyev, Peter B. Jahrling, Joshua C. Johnson, Karl M. Johnson, Jason Kindrachuk, Hans-Dieter Klenk, Gary Kobinger, Tadeusz J. Kochel, Matthew G. Lackemeyer, Daniel F. Lackner, Eric M. Leroy, Mark S. Lever, Elke Mühlberger, Sergey V. Netesov, Gene G. Olinger, Sunday A. Omilabu, Gustavo Palacios, Rekha G. Panchal, Daniel J. Park, Jean L. Patterson, Janusz T. Paweska, Clarence J. Peters, James Pettitt, Louise Pitt, Sheli R. Radoshitzky, Elena I. Ryabchikova, Erica Ollmann Saphire, Pardis C. Sabeti, Rachel Sealfon, Aleksandr M. Shestopalov, Sophie J. Smither, Nancy J. Sullivan, Robert Swanepoel, Ayato Takada, Jonathan S. Towner, Guido van der Groen, Viktor E. Volchkov, Valentina A. Volchkova, Victoria Wahl-Jensen, Travis K. Warren, Kelly L. Warfield, Manfred Weidmann, and Stuart T. Nichol
Subjects: Bundibugyo virus, cDNA clone, cuevavirus, Ebola, Ebola virus, ebolavirus, filovirid, Filoviridae, filovirus, genome annotation, ICTV, International Committee on Taxonomy of Viruses, Lloviu virus, Marburg virus, marburgvirus, mononegavirad, Mononegavirales, mononegavirus, Ravn virus, RefSeq, Reston virus, reverse genetics, Sudan virus, Taï Forest virus, virus classification, virus isolate, virus nomenclature, virus strain, virus taxonomy, virus variant, Microbiology, QR1-502
Abstract: Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.
Published: 2014
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16. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae.

Author: Demina, Tatiana A., Pietilä, Maija K., Svirskaitė, Julija, Ravantti, Janne J., Atanasova, Nina S., Bamford, Dennis H., and Oksanen, Hanna M.
Subjects: *ICOSAHEDRA, *HALOPHILIC organisms, *CLASSIFICATION of viruses, *VIRAL genes, *BACTERIOPHAGES
Abstract: Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1), has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV) in 2016. [ABSTRACT FROM AUTHOR]
Published: 2017
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17. Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria : kingdom Orthornavirae : phylum Negarnaviricota ).

Author: Kuhn JH, Abe J, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Kumar Baranwal V, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Blair CD, Blasdell KR, Blouin AG, Bradfute SB, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Kumar Chaturvedi K, Chooi KM, Crane A, Dal Bó E, Carlos de la Torre J, de Souza WM, de Swart RL, Debat H, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, Laura García M, García-Sastre A, Garrison AR, Gaskin TR, Gong W, Gonzalez JJ, de Bellocq J, Griffiths A, Groschup MH, Günther I, Günther S, Hammond J, Hasegawa Y, Hayashi K, Hepojoki J, Higgins CM, Hongō S, Horie M, Hughes HR, Hume AJ, Hyndman TH, Ikeda K, Jiāng D, Jonson GB, Junglen S, Klempa B, Klingström J, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Lǐ J, Li JM, Liu R, Lukashevich IS, MacDiarmid RM, Maes P, Marklewitz M, Marshall SH, Marzano SL, McCauley JW, Mirazimi A, Mühlberger E, Nabeshima T, Naidu R, Natsuaki T, Navarro B, Navarro JA, Neriya Y, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Ochoa-Corona FM, Okada T, Palacios G, Pallás V, Papa A, Paraskevopoulou S, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Pérez DR, Pfaff F, Plemper RK, Postler TS, Rabbidge LO, Radoshitzky SR, Ramos-González PL, Rehanek M, Resende RO, Reyes CA, Rodrigues TCS, Romanowski V, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sadiq S, Salvato MS, Sasaya T, Schwemmle M, Sharpe SR, Shi M, Shimomoto Y, Kavi Sidharthan V, Sironi M, Smither S, Song JW, Spann KM, Spengler JR, Stenglein MD, Takada A, Takeyama S, Tatara A, Tesh RB, Thornburg NJ, Tian X, Tischler ND, Tomitaka Y, Tomonaga K, Tordo N, Tu C, Turina M, Tzanetakis IE, Maria Vaira A, van den Hoogen B, Vanmechelen B, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Waltzek TB, Whitfield AE, Wolf YI, Xia H, Xylogianni E, Yanagisawa H, Yano K, Ye G, Yuan Z, Zerbini FM, Zhang G, Zhang S, Zhang YZ, Zhao L, and Økland AL
Subjects: RNA-Dependent RNA Polymerase genetics, Negative-Sense RNA Viruses, RNA Viruses genetics
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
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18. PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses

Author: Tatiana Tatusova, Vyacheslav Chetvernin, and Yiming Bao
Subjects: Filoviridae, filovirus, ICTV, International Committee on Taxonomy of Viruses, National Center for Biotechnology Information, NCBI, PAirwise Sequence Comparison, PASC, virus classification, virus taxonomy, Microbiology, QR1-502
Abstract: PAirwise Sequence Comparison (PASC) is a tool that uses genome sequence similarity to help with virus classification. The PASC tool at NCBI uses two methods: local alignment based on BLAST and global alignment based on Needleman-Wunsch algorithm. It works for complete genomes of viruses of several families/groups, and for the family of Filoviridae, it currently includes 52 complete genomes available in GenBank. It has been shown that BLAST-based alignment approach works better for filoviruses, and therefore is recommended for establishing taxon demarcation criteria. When more genome sequences with high divergence become available, these demarcations will most likely become more precise. The tool can compare new genome sequences of filoviruses with the ones already in the database, and propose their taxonomic classification.
Published: 2012
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19. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae

Author: Tatiana A. Demina, Maija K. Pietilä, Julija Svirskaitė, Janne J. Ravantti, Nina S. Atanasova, Dennis H. Bamford, and Hanna M. Oksanen
Subjects: Sphaerolipoviridae, Alphasphaerolipovirus, halovirus, archaeal virus, tailless icosahedral virus, membrane virus, halophilic archaea, virus classification, International Committee on Taxonomy of Viruses, structure-based viral lineage, Microbiology, QR1-502
Abstract: Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1), has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV) in 2016.
Published: 2017
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20. Past, present, and future of arenavirus taxonomy.

Author: Radoshitzky, Sheli, Bào, Yīmíng, Buchmeier, Michael, Charrel, Rémi, Clawson, Anna, Clegg, Christopher, DeRisi, Joseph, Emonet, Sébastien, Gonzalez, Jean-Paul, Kuhn, Jens, Lukashevich, Igor, Peters, Clarence, Romanowski, Victor, Salvato, Maria, Stenglein, Mark, and Torre, Juan
Subjects: *ARENAVIRUSES, *CLADISTIC analysis, *CLASSIFICATION of viruses, *SEQUENCE analysis, *AMINO acid sequence, *VIRUSES
Abstract: Until recently, members of the monogeneric family Arenaviridae (arenaviruses) have been known to infect only muroid rodents and, in one case, possibly phyllostomid bats. The paradigm of arenaviruses exclusively infecting small mammals shifted dramatically when several groups independently published the detection and isolation of a divergent group of arenaviruses in captive alethinophidian snakes. Preliminary phylogenetic analyses suggest that these reptilian arenaviruses constitute a sister clade to mammalian arenaviruses. Here, the members of the International Committee on Taxonomy of Viruses (ICTV) Arenaviridae Study Group, together with other experts, outline the taxonomic reorganization of the family Arenaviridae to accommodate reptilian arenaviruses and other recently discovered mammalian arenaviruses and to improve compliance with the Rules of the International Code of Virus Classification and Nomenclature (ICVCN). PAirwise Sequence Comparison (PASC) of arenavirus genomes and NP amino acid pairwise distances support the modification of the present classification. As a result, the current genus Arenavirus is replaced by two genera, Mammarenavirus and Reptarenavirus, which are established to accommodate mammalian and reptilian arenaviruses, respectively, in the same family. The current species landscape among mammalian arenaviruses is upheld, with two new species added for Lunk and Merino Walk viruses and minor corrections to the spelling of some names. The published snake arenaviruses are distributed among three new separate reptarenavirus species. Finally, a non-Latinized binomial species name scheme is adopted for all arenavirus species. In addition, the current virus abbreviations have been evaluated, and some changes are introduced to unequivocally identify each virus in electronic databases, manuscripts, and oral proceedings. [ABSTRACT FROM AUTHOR]
Published: 2015
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21. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names.

Author: Kuhn, Jens H., Andersen, Kristian G., Bào, Yīmíng, Bavari, Sina, Becker, Stephan, Bennett, Richard S., Bergman, Nicholas H., Blinkova, Olga, Bradfute, Steven, Brister, J. Rodney, Bukreyev, Alexander, Chandran, Kartik, Chepurnov, Alexander A., Davey, Robert A., Dietzgen, Ralf G., Doggett, Norman A., Dolnik, Olga, Dye, John M., Enterlein, Sven, and Fenimore, Paul W.
Subjects: *GENETICS of virus diseases, *FILOVIRIDAE, *VIRAL genomes, *MEDICAL coding, *VIRAL ecology
Abstract: Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information's (NCBI's) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences. [ABSTRACT FROM AUTHOR]
Published: 2014
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22. Guidance for creating individual and batch latinized binomial virus species names.

Author: Postler TS, Rubino L, Adriaenssens EM, Dutilh BE, Harrach B, Junglen S, Kropinski AM, Krupovic M, Wada J, Crane A, Kuhn JH, Mushegian A, Rūmnieks J, Sabanadzovic S, Simmonds P, Varsani A, Zerbini FM, Callanan J, Draper LA, Hill C, and Stockdale SR
Subjects: Viruses classification, Terminology as Topic
Abstract: The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages.
Published: 2022
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23. PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses.

Author: Yiming Bao, Chetvernin, Vyacheslav, and Tatusova, Tatiana
Subjects: *VIRUSES, *ALGORITHMS, *GENETICS, *GENOMES, *EXTRACHROMOSOMAL DNA, *MICROORGANISMS, *GENETIC vectors
Abstract: PAirwise Sequence Comparison (PASC) is a tool that uses genome sequence similarity to help with virus classification. The PASC tool at NCBI uses two methods: local alignment based on BLAST and global alignment based on Needleman-Wunsch algorithm. It works for complete genomes of viruses of several families/groups, and for the family of Filoviridae, it currently includes 52 complete genomes available in GenBank. It has been shown that BLAST-based alignment approach works better for filoviruses, and therefore is recommended for establishing taxon demarcation criteria. When more genome sequences with high divergence become available, these demarcations will most likely become more precise. The tool can compare new genome sequences of filoviruses with the ones already in the database, and propose their taxonomic classification. [ABSTRACT FROM AUTHOR]
Published: 2012
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24. Virus Taxonomy

Author: Kuhn, Jens H.
Subjects: Virus classification, Nomenclature, viruses, Virus taxonomy, TaxoProp, International Code of Virus Classification and Nomenclature, VHG, viral hallmark gene, Classification, ICVCN, International Committee on Taxonomy of Viruses, Virus nomenclature, Article, Phylogenetics, ICTV, Taxonomy
Abstract: Virus taxonomy is the classification of viruses into categories called taxa and the development and implementation of a standardized nomenclature for taxa. Whereas virus taxonomy has been a niche subspecialty over many decades, the field has recently gained importance due to the exponentially increasing number of new viruses discovered by next-generation sequencing methods. The expanded known global virome and associated viral genome sequence space gradually morph virus taxonomy from a phenotype-based and inherently subjective process, focussing on shared or distinct, often arbitrarily chosen biophysical characteristics of virions to a significant subspecialty of systematic evolutionary biology. Indeed, current virus classification is increasingly performed using ever more complex phylogenetic approaches that move researchers closer to a rudimentary understanding of the origin, evolution, relatedness, and diversification of viruses over eons.
Published: 2020

25. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species

Author: Dennis Rubbenstroth, Thomas Briese, Victoria Wahl, Timothy H. Hyndman, Andrew D. Haddow, Sead Sabanadzovic, Arvind Varsani, Rémi N. Charrel, J. Rodney Brister, Mart Krupovic, Scott C. Weaver, Márcio Roberto Teixeira Nunes, Boris Klempa, A. Desiree LaBeaud, Takahide Sasaya, Jonas Klingström, Norbert Nowotny, Sandra Junglen, Sheli R. Radoshitzky, Susan Payne, Martin H. Groschup, Piet Maes, Ralf Dürrwald, Charles F. Fulhorst, Hideki Ebihara, Francisco Murilo Zerbini, Jens H. Kuhn, Mark D. Stenglein, Charles H. Calisher, Nikos Vasilakis, Andrew M. Kropinski, George Fú Gāo, Colorado State University [Fort Collins] (CSU), Columbia University [New York], National Institutes of Health [Bethesda] (NIH), Unité des Virus Emergents (UVE), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Robert Koch Institute [Berlin] (RKI), Mayo Clinic, The University of Texas Medical Branch (UTMB), Chinese Center for Disease Control and Prevention, Friedrich-Loeffler-Institut (FLI), United States Army (U.S. Army), Murdoch University, Humboldt State University (HSU), Slovak Academy of Science [Bratislava] (SAS), Karolinska Institutet [Stockholm], University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), University of Veterinary Medicine [Vienna] (Vetmeduni), Ministry of Health [Brasília, Brazil], Texas A&M University [College Station], Mississippi State University [Mississippi], National Agriculture and Food Research Organization (NARO), Arizona State University [Tempe] (ASU), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, Universidade Federal de Vicosa (UFV), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), This work was supported by Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K.), by US National Institutes of Health (NIH) grant R24 AI120942 (S.C.W and N.V.), and by the Intramural Research Program of the NIH, National Library of Medicine (J.R.B.). S.S. acknowledges support from Mississippi State University (MSU)—Mississippi Agricultural and Forestry Experiment Station (MAFES) Strategic Research Initiative grants. This work was also funded in part under ContractNo. HSHQDC-15-C-00064 awarded by DHS S&T for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a federally funded research and development center (V.W.), The authors thank Laura Bollinger, Integrated Research Facility, for critically editing the manuscript. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Defense or the US Army, of the US Department of Health and Human Services, the Department of Homeland Security (DHS) Science and Technology Directorate (S&T), of the International Committee on Taxonomy of Viruses, or of the institutions and companies affiliated with the authors. In no event shall any of these entities have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. The US departments do not endorse any products or commercial services mentioned in this publication, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: 0301 basic medicine, Classifica??o / m?todos, International Cooperation, viruses, [SDV]Life Sciences [q-bio], 030106 microbiology, species, virus, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, International Committee on Taxonomy of Viruses, Virus, Points of View, 03 medical and health sciences, taxonomy, Unclassified Viruses, (ICTV), Virology, Genetics, Nomenclature, Ecology, Evolution, Behavior and Systematics, Virus classification, Taxonomy, 2. Zero hunger, Species, Arbovirus, Phylum, Arbovirus / classifica??o, Classification, humanities, 3. Good health, 030104 developmental biology, Taxon, classification, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Mandate, Taxonomy (biology), nomenclature, Terminologia como Assunto
Abstract: This work was supported by Battelle Memorial Institute?s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K.), by US National Institutes of Health (NIH) grant R24 AI120942 (S.C.W and N.V.), and by the Intramural Research Program of the NIH, National Library of Medicine (J.R.B.). S.S. acknowledges support from Mississippi State University (MSU)?Mississippi Agricultural and Forestry Experiment Station (MAFES) Strategic Research Initiative grants. This work was also funded in part under ContractNo. HSHQDC-15-C-00064 awarded by DHS S&T for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a federally funded research and development center (V.W.) Colorado State University. College of Veterinary Medicine and Biomedical Sciences. Department of Microbiology, Immunology and Pathology. Arthropod-borne and Infectious Diseases Laboratory. Fort Collins, CO, USA. Columbia University. Mailman School of Public Health. Center for Infection and Immunity. Department of Epidemiology. New York, NY, USA. National Institutes of Health. National Library of Medicine. National Center for Biotechnology. Bethesda, MD, USA. Universit? Aix-Marseille. Facult? de M?decine. HU M?diterran?e Infection. Unit? des Virus Emergents. Marseille, France. Robert Koch-Institut. Department of Infectious Diseases. Berlin, Germany. Guggenheim Building. Mayo Clinic. Department of Molecular Medicine. Rochester, MN USA. University of Texas Medical Branch. Department of Pathology. Galveston, TX, USA. Chinese Center for Disease Control and Prevention. National Institute for Viral Disease Control and Prevention. Beijing, China. Friedrich-Loeffler-Institut, S?dufer. Institut f?r Virusdiagnostik. Greifswald-Insel Riems, Germany. United States Army Medical Research Institute of Infectious Diseases. Department of Virology. Frederick, MD, USA. Murdoch University. School of Veterinary and Life Sciences. College of Veterinary Medicine. Australia Australia. Humboldt-University Berlin. Berlin Institute of Health. Charit? Universit?tsmedizin Berlin. Institute of Virology. Berlin, Germany / Inhoffenstra?e 7. Deutsches Zentrum f?r Infektionsforschung. Braunschweig, Germany. Slovensk? Akad?mia Vied. Biomedic?nske centrum. Virologick? ?stav. D?bravsk?, Bratislava, Slovakia. Robert Koch-Institut. Department of Infectious Diseases. Berlin, Germany. University of Guelph. Department of Food Sciencen. Guelph, Ontario, Canada / University of Guelph. Department of Pathobiology. Guelph, Ontario, Canada. Institut Pasteur. Departement of Microbiology. Paris, France. Stanford University School of Medicine. Department of Pediatrics. Division of Infectious Diseases. Stanford, CA, USA. KU Leuven. Department of Microbiology, Immunology and Transplantation. Rega Institute. Zoonotic Infectious Diseases unit. Leuven, Belgium. University of Veterinary Medicine Vienna. Department of Pathobiology. Institute of Virology. Veterin?rplatz, Vienna, Austria / Mohammed Bin Rashid University of Medicine and Health Sciences. Department of Basic Medical Sciences. College of Medicine. Dubai, United Arab Emirates. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Texas A&M University. Veterinary Medical Sciences Building. College of Veterinary Medicine and Biomedical Sciences. Department of Veterinary Pathobiology. TX, USA. United States Army Medical Research Institute of Infectious Diseases. Molecular and Translational Sciences. Frederick, MD, USA. Friedrich-Loeffler-Institut, S?dufer. Institut f?r Virusdiagnostik. Greifswald-Insel Riems, Germany / Universit?tsklinikum Freiburg. Institut f?r Virologie. Freiburg, Germany. Mississippi State University. Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology. Mississippi State, MS, USA. National Agriculture and Food Research Organization. Department of Planning and Coordination. Ibaraki, Japan. Colorado State University. Department of Microbiology, Immunology and Pathology. Fort Collins, CO, USA. Arizona State University. School of Life Sciences, Center for Evolution and Medicine. The Biodesign Center for Fundamental and Applied Microbiomics. Tempe, AZ, USA. National Biodefense Analysis and Countermeasures Center. Frederick, MD, USA. University of Texas Medical Branch. Institute for Human Infections and Immunity. Department of Microbiology and Immunology. Galveston, TX, USA. Universidade Federal de Vi?osa. Departamento de Fitopatologia/BIOAGRO and National Institute of Science and Technology for Plant-Pest Interactions. Vi?osa, MG, Brazil. University of Texas Medical Branch. Institute for Human Infection and Immunity. Center for Tropical Diseases. Department of Pathology, Center for Biodefense and Emerging Infectious Diseases. Galveston, TX, USA. Integrated Research Facility at Fort Detrick. Frederick, MD, USA. The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV's official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology.
Published: 2019
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26. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)

Author: Peter Simmonds, Arcady Mushegian, Jens H. Kuhn, Luisa Rubino, Francisco Murilo Zerbini, Hélène Sanfaçon, Stuart G. Siddell, Michael J. Adams, Sead Sabanadzovic, Alexander E. Gorbalenya, Max L. Nibert, Andrew M. Q. King, Balázs Harrach, Nick J. Knowles, Mart Krupovic, Robert L. Harrison, Arvind Varsani, Bas E. Dutilh, Andrew J. Davison, Andrew M. Kropinski, Elliot J. Lefkowitz, Sandra Junglen, Institute for Animal Health, the Pirbright Institute, University of Alabama at Birmingham [ Birmingham] (UAB), National Science Foundation [Arlington] (NSF), Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Radboud University Medical Center [Nijmegen], Leiden University Medical Center (LUMC), Lomonosov Moscow State University (MSU), Hungarian Academy of Sciences (MTA), USDA Agricultural Research Service [Maricopa, AZ] (USDA), United States Department of Agriculture (USDA), Humboldt State University (HSU), German Centre for Infection Research (DZIF), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Harvard Medical School [Boston] (HMS), Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS Torino, Mississippi State University [Mississippi], Agriculture and Agri-Food [Ottawa] (AAFC), University of Bristol [Bristol], University of Oxford [Oxford], Arizona State University [Tempe] (ASU), Universidade Federal de Vicosa (UFV), University of Glasgow, A.J.D. is supported by the Medical Research Council (MC_UU_12014/3). B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi Grant 864.14.004. A.E.G. is partially supported by EU project EVAg 653316 and the Leids Universiteits Fonds. N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. This work was supported in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K). A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), his work on this project was supported in part by the NSF Independent Research and Development program, but the statements and opinions expressed herein are made in a personal capacity and do not imply endorsement by NSF or the government of the United States. S.S. acknowledges financial support from Mississippi State University (MSU)—Mississippi Agricultural and Forestry Experiment Station (MAFES) Strategic Research Initiative grants., The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Universiteit Leiden, Institut Pasteur [Paris] (IP), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Agriculture and Agri-Food (AAFC), University of Oxford, Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Sub Bioinformatics, and Theoretical Biology and Bioinformatics
Subjects: 0301 basic medicine, International Code of Virus Classification, viruses, [SDV]Life Sciences [q-bio], education, 030106 microbiology, Coronacrisis-Taverne, Library science, Committee Membership, virus, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, International Committee on Taxonomy of Viruses, Executive committee, taxonomy, ICTV, 03 medical and health sciences, Viral genetics, Terminology as Topic, Virology, skin and connective tissue diseases, Nomenclature, health care economics and organizations, Virus classification, Taxonomy, General Medicine, 3. Good health, International code, 030104 developmental biology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Classification methods, Taxonomy (biology), sense organs
Abstract: International audience; This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9 families and one new order were added to the taxonomy. The current totals at each taxonomic level now stand at 9 orders, 131 families, 46 subfamilies, 803 genera and 4853 species. A change was made to the International Code of Virus Classification and Nomenclature to allow the use of the names of people in taxon names under appropriate circumstances. An updated Master Species List incorporating the approved changes was released in March 2018 ( https://talk.ictvonline.org/taxonomy/ ).
Published: 2018
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27. Past, present, and future of arenavirus taxonomy

Author: Michael J. Buchmeier, Jean-Paul Gonzalez, Víctor Romanowski, Christopher S. Clegg, Anna N. Clawson, Rémi N. Charrel, Mark D. Stenglein, Joseph L. DeRisi, Maria S. Salvato, Jens H. Kuhn, Sébastien Emonet, Igor S. Lukashevich, Sheli R. Radoshitzky, Yīmíng Bào, Juan Carlos de la Torre, and Clarence J. Peters
Subjects: Otras Ciencias Biológicas, viruses, Arenaviridae, Biology, Viral hemorrhagic fever, Ciencias Biológicas, VIRAL HEMORRHAGIC FEVER, Phylogenetics, Virology, medicine, Clade, Nomenclature, Virus classification, Arenavirus, Species name, MAMMARENAVIRUS, virus diseases, General Medicine, VIRUS NOMENCLATURE, biology.organism_classification, medicine.disease, INTERNATIONAL COMMITTEE ON TAXONOMY OF VIRUSES, ARENAVIRUS, REPTARENAVIRUS, CIENCIAS NATURALES Y EXACTAS
Abstract: Until recently, members of the monogeneric family Arenaviridae (arenaviruses) have been known to infect only muroid rodents and, in one case, possibly phyllostomid bats. The paradigm of arenaviruses exclusively infecting small mammals shifted dramatically when several groups independently published the detection and isolation of a divergent group of arenaviruses in captive alethinophidian snakes. Preliminary phylogenetic analyses suggest that these reptilian arenaviruses constitute a sister clade to mammalian arenaviruses. Here, the members of the International Committee on Taxonomy of Viruses (ICTV) Arenaviridae Study Group, together with other experts, outline the taxonomic reorganization of the family Arenaviridae to accommodate reptilian arenaviruses and other recently discovered mammalian arenaviruses and to improve compliance with the Rules of the International Code of Virus Classification and Nomenclature (ICVCN). PAirwise Sequence Comparison (PASC) of arenavirus genomes and NP amino acid pairwise distances support the modification of the present classification. As a result, the current genus Arenavirus is replaced by two genera, Mammarenavirus and Reptarenavirus, which are established to accommodate mammalian and reptilian arenaviruses, respectively, in the same family. The current species landscape among mammalian arenaviruses is upheld, with two new species added for Lunk and Merino Walk viruses and minor corrections to the spelling of some names. The published snake arenaviruses are distributed among three new separate reptarenavirus species. Finally, a non-Latinized binomial species name scheme is adopted for all arenavirus species. In addition, the current virus abbreviations have been evaluated, and some changes are introduced to unequivocally identify each virus in electronic databases, manuscripts, and oral proceedings. Fil: Radoshitzky, Sheli R.. United States Army Medical Research. Institute of Infectious Diseases; Estados Unidos Fil: Bào, Yīmíng. National Institutes of Health; Estados Unidos Fil: Buchmeier, Michael J.. University of California at Irvine; Estados Unidos Fil: Charrel, Rémi N.. École des Hautes Etudes en Santé Publique; Francia. Aix Marseille Université; Francia Fil: Clawson, Anna N.. National Institutes of Health; Estados Unidos Fil: Clegg, Christopher S.. Les Mandinaux; Francia Fil: DeRisi, Joseph L.. University of California; Estados Unidos Fil: Emonet, Sébastien. Echelon Recherche de Lyon. Institut de Recherche Biomedicale de Armees. Unité de Virologie; Francia Fil: Gonzalez, Jean Paul. Metabiota Inc.; Estados Unidos Fil: Kuhn, Jens H.. National Institutes of Health; Estados Unidos Fil: Lukashevich, Igor S.. University of Louisville; Estados Unidos Fil: Peters, Clarence J.. University of Texas; Estados Unidos Fil: Romanowski, Victor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina Fil: Salvato, Maria S.. University of Maryland; Estados Unidos Fil: Stenglein, Mark D.. State University of Colorado - Fort Collins; Estados Unidos Fil: de la Torre, Juan Carlos. La Jolla Institute for Allergy and Immunology; Estados Unidos
Published: 2015
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28. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names

Author: Stephen K. Gire, Kristian G. Andersen, James Pettitt, Victoria Wahl-Jensen, Rachel Sealfon, Peter B. Jahrling, Janusz T. Paweska, Mark S. Lever, Eric M. Leroy, Nancy J. Sullivan, Louise Pitt, Erica Ollmann Saphire, Jonathan S. Towner, Olga Dolnik, Viktor E. Volchkov, Alexander N. Freiberg, Jean-Paul Gonzalez, Guido van der Groen, Lisa E. Hensley, Gary P. Kobinger, Christian T. Happi, Clarence J. Peters, Pardis C. Sabeti, Stuart T. Nichol, Kelly L. Warfield, Nicole L. Garza, Sina Bavari, Sunday Omilabu, Pierre Formenty, J. Rodney Brister, Jean L. Patterson, Stephan Becker, Aleksandr M. Shestopalov, Michael Hevey, Sophie J. Smither, Valentina A. Volchkova, Jason Kindrachuk, Yiming Bao, Kartik Chandran, Ralf G. Dietzgen, Sheli R. Radoshitzky, Elke Mühlberger, Robert F. Garry, Thomas Hoenen, Robert Swanepoel, Daniel J. Park, Steven B. Bradfute, Paul W. Fenimore, Jens H. Kuhn, Alexander A. Chepurnov, Tadeusz J. Kochel, Manfred Weidmann, Anna N. Honko, Elena I. Ryabchikova, John M. Dye, Karl M. Johnson, Nicholas H. Bergman, Gustavo Palacios, Ayato Takada, Daniel F. Lackner, Gene G. Olinger, Hans-Dieter Klenk, Olga Blinkova, Sven Enterlein, Robert A. Davey, Sergey V. Netesov, Andrew S. Herbert, Richard S. Bennett, Rekha G. Panchal, Norman A. Doggett, Georgy M. Ignatyev, Matthew G. Lackemeyer, Joshua C. Johnson, Alexander Bukreyev, Travis K. Warren, and Anthony Griffiths
Subjects: virus strain, Letter, genome annotation, marburgvirus, lcsh:QR1-502, virus nomenclature, medicine.disease_cause, lcsh:Microbiology, virus variant, Ebola virus, ICTV, Bundibugyo virus, RefSeq, Lloviu virus, cDNA clone, virus classification, Ravn virus, Marburg virus, biology, Genome project, Cuevavirus, Sudan virus, Infectious Diseases, Ebola, Reston virus, Databases, Nucleic Acid, cuevavirus, filovirus, filovirid, Computational biology, virus taxonomy, International Committee on Taxonomy of Viruses, Evolution, Molecular, Annotation, reverse genetics, Virology, medicine, Humans, virus isolate, Selection, Genetic, Virus classification, ebolavirus, Sequence (medicine), mononegavirus, mononegavirad, biology.organism_classification, Filoviridae, Mononegavirales, Taï Forest virus
Abstract: Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.
Published: 2014

29. Possibility and challenges of conversion of current virus species names to Linnaean binomials

Author: Postler, T.S. (Thomas S.), Clawson, A.N. (Anna N.), Amarasinghe, G.K. (Gaya K.), Basler, C.F. (Christopher F.), Bavari, S. (Sbina), Benko, M. (Mária), Blasdell, K.R. (Kim R.), Briese, T. (Thomas), Buchmeier, M.J. (Michael J.), Bukreyev, A. (Alexander), Calisher, C.H. (Charles H.), Chandran, K. (Kartik), Charrel, R. (Remi), Clegg, C.S. (Christopher S.), Collins, P.L. (Peter L.), De La Torre, J.C. (Juan Carlos), DeRisi, J.L. (Joseph), Dietzgen, R.G. (Ralf G.), Dolnik, O. (Olga), Dürrwald, R. (Ralf), Dye, J.M. (John M.), Easton, A.J. (Andrew J.), Emonet, S. (Sébastian), Formenty, P. (Pierre), Fouchier, R.A.M. (Ron), Ghedin, E. (Elodie), Gonzalez, J.-P. (Jean-Paul), Harrach, B. (Balázs), Hewson, R. (Roger), Horie, M. (Masayuki), Jiāng, D. (Dàohóng), Kobinger, G.P. (Gary P.), Kondo, H. (Hideki), Kropinski, A.M. (Andrew M.), Krupovic, M. (Mart), Kurath, G. (Gael), Lamb, R.A. (Robert A.), Leroy, E.M. (Eric M.), Lukashevich, I.S. (Igor S.), Maisner, A. (Andrea), Mushegian, A.R. (Arcady R.), Netesov, S.V. (Sergey V.), Nowotny, N., Patterson, J.L. (Jean L.), Payne, S.L. (Susan L.), Paweska, J.T. (Janusz T.), Peters, C.J. (Clarence J.), Radoshitzky, S.R. (Sheli R.), Rima, B.K. (Bertus K.), Romanowski, V. (Victor), Rubbenstroth, D. (Dennis), Sabanadzovic, S. (Sead), Sanfaçon, H. (Hélène), Salvato, M.S. (Maria S.), Schwemmle, M. (Martin), Smither, S.J. (Sophie J.), Stenglein, M.D. (Mark D.), Stone, D.M. (David M.), Takada, A. (Ayato), Tesh, R.B. (Robert B.), Tomonaga, K. (Keizo), Tordo, N. (Noël), Towner, J.S. (Jonathan S.), Vasilakis, N. (Nikos), Volchkov, V.E. (Viktor E.), Wahl-Jensen, V. (Victoria), Walker, P.J. (Peter J.), Wang, L.-F. (Lin-Fa), Varsani, A. (Arvind), Whitfield, A.E. (Anna E.), Murilo Zerbini, F., Kuhn, J.H. (Jens H.), Postler, T.S. (Thomas S.), Clawson, A.N. (Anna N.), Amarasinghe, G.K. (Gaya K.), Basler, C.F. (Christopher F.), Bavari, S. (Sbina), Benko, M. (Mária), Blasdell, K.R. (Kim R.), Briese, T. (Thomas), Buchmeier, M.J. (Michael J.), Bukreyev, A. (Alexander), Calisher, C.H. (Charles H.), Chandran, K. (Kartik), Charrel, R. (Remi), Clegg, C.S. (Christopher S.), Collins, P.L. (Peter L.), De La Torre, J.C. (Juan Carlos), DeRisi, J.L. (Joseph), Dietzgen, R.G. (Ralf G.), Dolnik, O. (Olga), Dürrwald, R. (Ralf), Dye, J.M. (John M.), Easton, A.J. (Andrew J.), Emonet, S. (Sébastian), Formenty, P. (Pierre), Fouchier, R.A.M. (Ron), Ghedin, E. (Elodie), Gonzalez, J.-P. (Jean-Paul), Harrach, B. (Balázs), Hewson, R. (Roger), Horie, M. (Masayuki), Jiāng, D. (Dàohóng), Kobinger, G.P. (Gary P.), Kondo, H. (Hideki), Kropinski, A.M. (Andrew M.), Krupovic, M. (Mart), Kurath, G. (Gael), Lamb, R.A. (Robert A.), Leroy, E.M. (Eric M.), Lukashevich, I.S. (Igor S.), Maisner, A. (Andrea), Mushegian, A.R. (Arcady R.), Netesov, S.V. (Sergey V.), Nowotny, N., Patterson, J.L. (Jean L.), Payne, S.L. (Susan L.), Paweska, J.T. (Janusz T.), Peters, C.J. (Clarence J.), Radoshitzky, S.R. (Sheli R.), Rima, B.K. (Bertus K.), Romanowski, V. (Victor), Rubbenstroth, D. (Dennis), Sabanadzovic, S. (Sead), Sanfaçon, H. (Hélène), Salvato, M.S. (Maria S.), Schwemmle, M. (Martin), Smither, S.J. (Sophie J.), Stenglein, M.D. (Mark D.), Stone, D.M. (David M.), Takada, A. (Ayato), Tesh, R.B. (Robert B.), Tomonaga, K. (Keizo), Tordo, N. (Noël), Towner, J.S. (Jonathan S.), Vasilakis, N. (Nikos), Volchkov, V.E. (Viktor E.), Wahl-Jensen, V. (Victoria), Walker, P.J. (Peter J.), Wang, L.-F. (Lin-Fa), Varsani, A. (Arvind), Whitfield, A.E. (Anna E.), Murilo Zerbini, F., and Kuhn, J.H. (Jens H.)
Abstract: Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted toconvert all currently official names ofspecies included in the virusfamily Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment.
Published: 2017
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30. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae

Author: Nina S. Atanasova, Julija Svirskaitė, Hanna M. Oksanen, Janne J. Ravantti, Dennis H. Bamford, Tatiana A. Demina, and Maija K. Pietilä
Subjects: Archaeal Viruses, 0301 basic medicine, viruses, 030106 microbiology, lcsh:QR1-502, halophilic archaea, Review, Alphasphaerolipovirus, International Committee on Taxonomy of Viruses, Genome, lcsh:Microbiology, Virus, 03 medical and health sciences, halovirus, Virology, Bacteriophages, Thermus, virus classification, structure-based viral lineage, Phylogeny, Virus classification, membrane virus, Adenosine Triphosphatases, biology, Virion, Sequence Analysis, DNA, archaeal virus, tailless icosahedral virus, biology.organism_classification, Archaea, Sphaerolipoviridae, Infectious Diseases, Haloarcula, Capsid, Membrane protein, Capsid Proteins
Abstract: Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1), has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV) in 2016.
Published: 2017
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31. Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis.

Author: Castrignano SB, Nagasse-Sugahara TK, Kisielius JJ, Ueda-Ito M, Brandão PE, and Curti SP
Subjects: Brazil, Circoviridae classification, Circoviridae isolation & purification, Cluster Analysis, Feces virology, Female, Humans, Microscopy, Electron, Middle Aged, Molecular Sequence Data, Open Reading Frames, Phylogeny, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Circoviridae genetics, Circoviridae ultrastructure, DNA, Viral chemistry, DNA, Viral genetics, Genome, Viral, Virion ultrastructure
Abstract: The application of viral metagenomic techniques and a series of PCRs in a human fecal sample enabled the detection of two novel circular unisense DNA viral genomes with 92% nucleotide similarity. The viruses were tentatively named circo-like virus-Brazil (CLV-BR) strains hs1 and hs2 and have genome lengths of 2526 and 2533 nucleotides, respectively. Four major open reading frames (ORFs) were identified in each of the genomes, and differences between the two genomes were primarily observed in ORF 2. Only ORF 3 showed significant amino acid similarities to a putative rolling circle replication initiator protein (Rep), although with low identity (36%). Our phylogenetic analysis, based on the Rep protein, demonstrated that the CLV-BRs do not cluster with members of the Circoviridae, Nanoviridae or Geminiviridae families and are more closely related to circo-like genomes previously identified in reclaimed water and feces of a wild rodent and of a bat. The CLV-BRs are members of a putative new family of circular Rep-encoding ssDNA viruses. Electron microscopy revealed icosahedral (~23 nm) structures, likely reflecting the novel viruses, and rod-shaped viral particles (~65-460 × 21 × 10 nm in length, diameter, and axial canal, respectively). Circo-like viruses have been detected in stool samples from humans and other mammals (bats, rodents, chimpanzees and bovines), cerebrospinal fluid and sera from humans, as well as samples from many other sources, e.g., insects, meat and the environment. Further studies are needed to classify all novel circular DNA viruses and elucidate their hosts, pathogenicity and evolutionary history., (Copyright © 2013 Elsevier B.V. All rights reserved.)
Published: 2013
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32. PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses.

Author: Bao Y, Chetvernin V, and Tatusova T
Subjects: Base Sequence, Databases, Nucleic Acid, Filoviridae chemistry, Filoviridae genetics, Molecular Sequence Data, Sequence Alignment instrumentation, Sequence Analysis, DNA, Software, Filoviridae classification, Sequence Alignment methods
Abstract: PAirwise Sequence Comparison (PASC) is a tool that uses genome sequence similarity to help with virus classification. The PASC tool at NCBI uses two methods: local alignment based on BLAST and global alignment based on Needleman-Wunsch algorithm. It works for complete genomes of viruses of several families/groups, and for the family of Filoviridae, it currently includes 52 complete genomes available in GenBank. It has been shown that BLAST-based alignment approach works better for filoviruses, and therefore is recommended for establishing taxon demarcations criteria. When more genome sequences with high divergence become available, these demarcation will most likely become more precise. The tool can compare new genome sequences of filoviruses with the ones already in the database, and propose their taxonomic classification.
Published: 2012
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33. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials

Author: Sbina Bavari, Susan Payne, Alexander Bukreyev, Arvind Varsani, Víctor Romanowski, Kartik Chandran, Ralf G. Dietzgen, Mark D. Stenglein, Anna N. Clawson, Sead Sabanadzovic, Gael Kurath, Andrea Maisner, Peter J. Walker, Ralf Dürrwald, Juan Carlos de la Torre, Eric M. Leroy, Mária Benko, Keizo Tomonaga, Gary P. Kobinger, Robert A. Lamb, Hideki Kondo, F. Murilo Zerbini, Martin Schwemmle, Robert B. Tesh, Gaya K. Amarasinghe, Andrew J. Easton, Michael J. Buchmeier, Jean-Paul Gonzalez, Anna E. Whitfield, Nikos Vasilakis, Jonathan S. Towner, Pierre Formenty, Jens H. Kuhn, Norbert Nowotny, Roger Hewson, Ayato Takada, Mart Krupovic, Igor S. Lukashevich, David M. Stone, Clarence J. Peters, Sheli R. Radoshitzky, Bertus K. Rima, Janusz T. Paweska, Masayuki Horie, Christopher S. Clegg, Victoria Wahl-Jensen, Christopher F. Basler, Sébastian Emonet, Charles H. Calisher, Lin-Fa Wang, Rémi N. Charrel, Jean L. Patterson, Elodie Ghedin, Dennis Rubbenstroth, Dàohóng Jiāng, Sergey V. Netesov, Hélène Sanfaçon, Thomas S. Postler, Ron A. M. Fouchier, Peter L. Collins, Noël Tordo, Maria S. Salvato, John M. Dye, Arcady Mushegian, Sophie J. Smither, Joseph L. DeRisi, Olga Dolnik, Kim R. Blasdell, Balázs Harrach, Viktor E. Volchkov, Thomas Briese, Andrew M. Kropinski, Columbia University College of Physicians and Surgeons, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Washington University School of Medicine (WUSM), University of Washington [Seattle], Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Institute for Soil Sciences and Agricultural Chemistry (ATK TAKI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Columbia Mailman School of Public Health, University of California [Irvine] (UCI), University of California, The University of Texas Medical Branch (UTMB), College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], Emergence des Pathologies Virales (EPV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Les Mandinaux, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Department of Immunology and Microbial Science, Scripps Research Institute, Department of Medicine [San Francisco], University of California [San Francisco] (UCSF), University of California-University of California, Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Philipps University of Marburg, IDT Biologika, School of Life Sciences, Warwick University, Unité de Virologie, Institut de Recherche Biomédicale des Armées (IRBA), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Health for Development, Public Health England [Salisbury] (PHE), Kagoshima University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Centre International de Recherches Médicales de Franceville (CIRMF), Department of Pharmacology and Toxicology, University of Louisville, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Infectious Disease, University of Texas at Austin [Austin], Novosibirsk State University (NSU), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], Texas A&M University System, National Institute for Communicable Diseases [Johannesburg] (NICD), Queen's University [Belfast] (QUB), Instituto de Biotecnología y Biología Molecular [La Plata] (IBBM), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas [La Plata], Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), University of Freiburg [Freiburg], Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA] (BCH-EPP), Mississippi State University [Mississippi], Summerland Research and Development Centre, Agriculture and Agri-Food [Ottawa] (AAFC), University of Maryland School of Medicine, University of Maryland System, Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Department of Microbiology, Immunology and Pathology, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Institute for Virus Research, Kyoto University [Kyoto], Stratégies antivirales, Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], Center for Fundamental and Applied Microbiomics, Arizona State University [Tempe] (ASU)-Biodesign Institute, Kansas State University, Departamento de Fitopatologia [Viçosa, Brazil] (BIOAGRO), Universidade Federal de Vicosa (UFV), This work was supported in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I. A subcontractor to Battelle Memorial Institute who performed this work is J.H.K., an employee of Tunnell Government Services, Inc. This work was also funded in part under National Institutes of Health (NIH) contract HHSN272201000040I/HHSN27200004/D04 and R24AI120942 (N.V., R.B.T.), and the National Science Foundation (NSF) Individual Research and Development (IR/D) program (A.R.M.)., We thank Laura Bollinger (NIH/NIAID Integrated Research Facility at Fort Detrick, Frederick, MD, USA) for critically editing the manuscript, Andrew J. Davison (MRC – University of Glasgow Centre for Virus Research, Glasgow, UK) and Michael J. Adams (Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Herts, UK) of the ICTV Executive Committee for suggestions on manuscript improvement, and Arya Ariël Kuhn for sustained vocal support and (dia)critical remarks, Albert Einstein College of Medicine, Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), Public Health England [Porton Down, Salisbury], Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Centre International de Recherches Médicales de Franceville, Texas Biomedical Research Institute [San Antonio, Texas], A&M University, National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Hokkaido University, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Duke NUS Medical School, Departamento de Fitopatologia/BIOAGRO, Virology, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Columbia University [New York], University of California [Irvine] (UC Irvine), University of California (UC), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Scripps Research Institute [La Jolla, San Diego], University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Philipps Universität Marburg = Philipps University of Marburg, University of Warwick [Coventry], Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Huazhong Agricultural University [Wuhan] (HZAU), Institut Pasteur [Paris] (IP), Agriculture and Agri-Food (AAFC), Kyoto University, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: 0301 basic medicine, MESH: Terminology as Topic, media_common.quotation_subject, Biología, 030106 microbiology, Binomials, Zoology, Biology, Points of View, 03 medical and health sciences, Genus, Terminology as Topic, Genetics, MESH: Classification, Epithet, Arenaviridae, Ecology, Evolution, Behavior and Systematics, Virus classification, media_common, Order Mononegavirales, Evolutionary Biology, Virus taxonomy, Classification, MESH: Viruses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Virus nomenclature, Genealogy, Ictv, International committee on taxonomy of viruses, 030104 developmental biology, Homo sapiens, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Mononegavirales
Abstract: Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted toconvert all currently official names ofspecies included in the viru sfamily Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment., La lista completa de autores que integran el documento puede consultarse en el archivo, Instituto de Biotecnologia y Biologia Molecular
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33 results on '"International Committee on Taxonomy of Viruses"'

1. Promotion of order Bunyavirales to class Bunyaviricetes to accommodate a rapidly increasing number of related polyploviricotine viruses.

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

3. Ambiviricota, a novel ribovirian phylum for viruses with viroidlike properties.

4. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials.

5. Bunyavirales Order

6. Guide to the Correct Use of Filoviral Nomenclature

7. Cressdnaviricota: a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes.

8. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

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

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

11. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

12. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species.

13. Guidance for creating individual and batch latinized binomial virus species names

14. Spumaretroviruses: Updated taxonomy and nomenclature.

15. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names

16. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae.

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

18. PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses

19. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae

20. Past, present, and future of arenavirus taxonomy.

21. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names.

22. Guidance for creating individual and batch latinized binomial virus species names.

23. PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses.

24. Virus Taxonomy

25. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species

26. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)

27. Past, present, and future of arenavirus taxonomy

28. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names

29. Possibility and challenges of conversion of current virus species names to Linnaean binomials

30. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae

31. Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis.

32. PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses.

33. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials

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33 results on '"International Committee on Taxonomy of Viruses"'

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