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51. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R, Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Databases, Genetic, Genome, Viral, Genomics, Virus Cultivation, Viruses
Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

Published
2019

58. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il-Ryong, Ciuffo, Marina, Clegg, J. Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B. H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas, Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, Martin H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy H., Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Lǐ, Jiànróng, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong-Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, and Zhou, Xueping

Published
2021
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59. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il-Ryong, Ciuffo, Marina, Clegg, J. Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B. H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas, Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, Martin H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy H., Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Lǐ, Jiànróng, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong-Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, and Zhou, Xueping

Published
2021
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60. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author

Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.

Published
2021
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63. 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

66. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)

Author

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

Published
2021
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71. Diversity, origin, and evolution of the ESCRT systems

Author

Makarova, Kira S., primary, Tobiasson, Victor, additional, Wolf, Yuri I., additional, Lu, Zhongyi, additional, Liu, Yang, additional, Zhang, Siyu, additional, Krupovic, Mart, additional, Li, Meng, additional, and Koonin, Eugene V., additional

Published
2024
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72. ICTV Virus Taxonomy Profile: Kolmioviridae 2024

Author

Kuhn, Jens H., primary, Babaian, Artem, additional, Bergner, Laura M., additional, Dény, Paul, additional, Glebe, Dieter, additional, Horie, Masayuki, additional, Koonin, Eugene V., additional, Krupovic, Mart, additional, Paraskevopoulou, Sofia, additional, de la Peña, Marcos, additional, Smura, Teemu, additional, and Hepojoki, Jussi, additional

Published
2024
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73. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Author

Barylski, Jakub, Enault, François, Dutilh, Bas E., Schuller, Margo B.P., Edwards, Robert A., Gillis, Annika, Klumpp, Jochen, Knezevic, Petar, Krupovic, Mart, Kuhn, Jens H., Lavigne, Rob, Oksanen, Hanna M., Sullivan, Matthew B., Jang, Ho Bin, Simmonds, Peter, Aiewsakun, Pakorn, Wittmann, Johannes, Tolstoy, Igor, Brister, J. Rodney, Kropinski, Andrew M., and Adriaenssens, Evelien M.

Published
2020

74. Diversity and comparative genomics of chimeric viruses in Sphagnum-dominated peatlands

Author

Quaiser, Achim, Krupovic, Mart, Dufresne, Alexis, Francez, André-Jean, and Roux, Simon

Subjects
Biotechnology, Human Genome, Genetics, Aetiology, 2.1 Biological and endogenous factors, Infection, virus ecology, viral metagenomics, virus diversity, ssDNA viruses, Evolutionary Biology, Microbiology
Abstract

A new group of viruses carrying naturally chimeric single-stranded (ss) DNA genomes that encompass genes derived from eukaryotic ssRNA and ssDNA viruses has been recently identified by metagenomic studies. The host range, genomic diversity, and abundance of these chimeric viruses, referred to as cruciviruses, remain largely unknown. In this article, we assembled and analyzed thirty-seven new crucivirus genomes from twelve peat viromes, representing twenty-four distinct genome organizations, and nearly tripling the number of available genomes for this group. All genomes possess the two characteristic genes encoding for the conserved capsid protein (CP) and a replication protein. Additional ORFs were conserved only in nearly identical genomes with no detectable similarity to known genes. Two cruciviruses possess putative introns in their replication-associated genes. Sequence and phylogenetic analyses of the replication proteins revealed intra-gene chimerism in at least eight chimeric genomes. This highlights the large extent of horizontal gene transfer and recombination events in the evolution of ssDNA viruses, as previously suggested. Read mapping analysis revealed that members of the 'Cruciviridae' group are particularly prevalent in peat viromes. Sequences matching the CP ranged from 0.6 up to 10.9 percent in the twelve peat viromes. In contrast, from sixty-nine available viromes derived from other environments, only twenty-four contained cruciviruses, which on average accounted for merely 0.2 percent of sequences. Overall, this study provides new genome information and insights into the diversity of chimeric viruses, a necessary first step in progressing toward an accurate quantification and host range identification of these new viruses.

Published
2016

75. A packing for A-form DNA in an icosahedral virus

Author

Wang, Fengbin, Liu, Ying, Su, Zhangli, Osinski, Tomasz, de Oliveira, Guilherme A. P., Conway, James F., Schouten, Stefan, Krupovic, Mart, Prangishvili, David, and Egelman, Edward H.

Published
2019

77. 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, Nunes, Márcio Roberto Teixeira, Payne, Susan L., Radoshitzky, Sheli R., Rubbenstroth, Dennis, Sabanadzovic, Sead, Sasaya, Takahide, D.Stenglein, Mark, Varsani, Arvind, Wahl, Victoria, Weaver, Scott C., Zerbini, Francisco Murilo, Vasilakis, Nikos, and Kuhn, Jens H.

Published
2019

80. Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components

Author

Duan, Changhai, Liu, Yang, Liu, Ying, Liu, Lirui, Cai, Mingwei, Zhang, Rui, Zeng, Qinglu, Koonin, Eugene V., Krupovic, Mart, Li, Meng, Duan, Changhai, Liu, Yang, Liu, Ying, Liu, Lirui, Cai, Mingwei, Zhang, Rui, Zeng, Qinglu, Koonin, Eugene V., Krupovic, Mart, and Li, Meng

Abstract

Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family “Fuxiviridae” harbor an atypical Type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family “Chiyouviridae” encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibit host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.

Published
2024

81. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Alioto, Daniela, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Anthony, Simon J., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Bartonička, Tomáš, Basler, Christopher, Bavari, Sina, Beer, Martin, Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol, Blasdell, Kim R., Bradfute, Steven B., Breyta, Rachel, Briese, Thomas, Brown, Paul A., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Buzkan, Nihal, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chamberlain, John, Chandran, Kartik, Charrel, Rémi N., Chen, Biao, Chiumenti, Michela, Choi, Il-Ryong, Clegg, J. Christopher S., Crozier, Ian, da Graça, John V., Dal Bó, Elena, Dávila, Alberto M. R., de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Di Bello, Patrick L., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolja, Valerian V., Dolnik, Olga, Drebot, Michael A., Drexler, Jan Felix, Dürrwald, Ralf, Dufkova, Lucie, Dundon, William G., Duprex, W. Paul, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Fernandes, Jorlan, Fooks, Anthony R., Formenty, Pierre B. H., Forth, Leonie F., Fouchier, Ron A. M., Freitas-Astúa, Juliana, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gbakima, Aiah, Goldstein, Tracey, Gonzalez, Jean-Paul J., Griffiths, Anthony, Groschup, Martin H., Günther, Stephan, Guterres, Alexandro, Hall, Roy A., Hammond, John, Hassan, Mohamed, Hepojoki, Jussi, Hepojoki, Satu, Hetzel, Udo, Hewson, Roger, Hoffmann, Bernd, Hongo, Seiji, Höper, Dirk, Horie, Masayuki, Hughes, Holly R., Hyndman, Timothy H., Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, Jonson, Gilda B., Junglen, Sandra, Karadağ, Serpil, Keller, Karen E., Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kurath, Gael, Kuzmin, Ivan V., Laenen, Lies, Lamb, Robert A., Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lemos, Elba R. S., Leroy, Eric M., Li, Dexin, Lǐ, Jiànróng, Liang, Mifang, Liú, Wénwén, Liú, Yàn, Lukashevich, Igor S., Maes, Piet, Marciel de Souza, William, Marklewitz, Marco, Marshall, Sergio H., Martelli, Giovanni P., Martin, Robert R., Marzano, Shin-Yi L., Massart, Sébastien, McCauley, John W., Mielke-Ehret, Nicole, Minafra, Angelantonio, Minutolo, Maria, Mirazimi, Ali, Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Nylund, Are, Økland, Arnfinn L., Oliveira, Renata C., Palacios, Gustavo, Pallas, Vicente, Pályi, Bernadett, Papa, Anna, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Pérez, Daniel R., Pfaff, Florian, Radoshitzky, Sheli R., Rahman, Aziz-ul, Ramos-González, Pedro L., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Romanowski, Víctor, Robles Luna, Gabriel, Rota, Paul, Rubbenstroth, Dennis, Runstadler, Jonathan A., Ruzek, Daniel, Sabanadzovic, Sead, Salát, Jiří, Sall, Amadou Alpha, Salvato, Maria S., Sarpkaya, Kamil, Sasaya, Takahide, Schwemmle, Martin, Shabbir, Muhammad Z., Shí, Xiǎohóng, Shí, Zhènglì, Shirako, Yukio, Simmonds, Peter, Širmarová, Jana, Sironi, Manuela, Smither, Sophie, Smura, Teemu, Song, Jin-Won, Spann, Kirsten M., Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Straková, Petra, Takada, Ayato, Tesh, Robert B., Thornburg, Natalie J., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., Turina, Massimo, Tzanetakis, Ioannis, Ulrich, Rainer G., Vaira, Anna Maria, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, Wahl, Victoria, Walker, Peter J., Wang, Hui, Wang, Jianwei, Wang, Xifeng, Wang, Lin-Fa, Wèi, Tàiyún, Wells, Heather, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wú, Zhìqiáng, Yang, Xin, Yáng, Xīnglóu, Yu, Xuejie, Yutin, Natalya, Zerbini, F. Murilo, Zhang, Tong, Zhang, Yong-Zhen, Zhou, Guohui, and Zhou, Xueping

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

Author

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

Published
2020
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86. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author

Adriaenssens, Evelien M., Sullivan, Matthew B., Knezevic, Petar, van Zyl, Leonardo J., Sarkar, B. L., Dutilh, Bas E., Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I., Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Edwards, Rob A., Kropinski, Andrew M., Petty, Nicola K., Clokie, Martha R. J., Kushkina, Alla I., Morozova, Vera V., Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M., Oksanen, Hanna M., and Krupovic, Mart

Published
2020
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88. Binomial nomenclature for virus species: a consultation

Author

Siddell, Stuart G., Walker, Peter J., Lefkowitz, Elliot J., Mushegian, Arcady R., Dutilh, Bas E., Harrach, Balázs, Harrison, Robert L., Junglen, Sandra, Knowles, Nick J., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Nibert, Max L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, and Davison, Andrew J.

Published
2020
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89. 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. [0000-0001-9016-2940], Horie, Masayuki [0000-0003-4682-7698], Hughes, Holly R.[0000-0003-1380-8263], Hyndman, Timothy [0000-0002-7047-5023], Jiāng, Dàohóng [0000-0002-3862-7461], Jonson, Gilda B.[0000-0003-0097-8634], Junglen, Sandra [0000-0002-3799-6011], Klempa, B.[0000-0002-6931-1224], Klingström, Jonas [0000-0001-9076-1441], Kondō, Hideki [0000-0001-9220-5350], Koonin, Eugene V. [0000-0003-3943-8299], Krupovic, Mart [0000-0001-5486-0098], Kurath, Gael [0000-0003-3294-560X], Laenen, Lies [0000-0001-9118-8608], Li, Jianrong [0000-0002-7130-1084], Lukashevich, Igor S.[0000-0001-6523-5116], MacDiarmid, Robin M.[0000-0002-7057-2018], Maes, Piet [0000-0002-4571-5232], Marklewitz, Marco [0000-0003-1828-8770], Marshall, Sergio H.[0000-0003-0438-8252], Marzano, Shin-Yi L. [0000-0003-0548-3761], Mühlberger, Elke [0000-0003-3547-9376], Nabeshima, Tomoyuki [0000-0002-6570-096X], Naidu, Rayapati [0000-0002-7273-5116], Natsuaki, Tomohide [0000-0003-1823-7308], Navarro, José A. [0000-0002-0536-6074], Neriya, Yutaro [0000-0002-1385-0050], Netesov, Sergey V. [0000-0002-7786-2464], Neumann, Gabriele [0000-0001-7054-1775], Nowotny, N. [0000-0002-3548-571X], Ochoa-Corona, Francisco M. [0000-0002-4112-8209], Pallás, Vicente [0000-0003-4954-989X], Papa, Anna [0000-0002-6643-3322], Paraskevopoulou, Sofia [0000-0003-2608-2596], Parrish, Colin R. [0000-0002-1836-6655], Pauvolid-Corrêa, Alex [0000-0002-6924-157X], Pawęska, Janusz T. [0000-0001-8776-7519], Pérez, Daniel R. [0000-0002-6569-5689], Pfaff, Florian [0000-0003-0178-6183], Plemper, Richard K. [0000-0003-2034-2107], Postler, Thomas S. [0000-0002-3558-9084], Rabbidge, Lee O. [0009-0001-7962-4881], Radoshitzky, Sheli R. [0000-0001-8976-8056], Ramos-González, Pedro L. [0000-0002-9640-6587], Rehanek, Marius [0000-0002-5710-5060], Resende, Renato O. [0000-0003-3852-1576], Romanowski, Víctor [0000-0001-6378-7929], Rubbenstroth, Dennis [0000-0002-8209-6274], Rubino, Luisa [0000-0002-2073-2415], Runstadler, Jonathan A. [0000-0002-6747-7765], Sabanadzovic, Sead [0000-0002-2995-2633], Salvato, Maria S. [0000-0002-3357-5391], Sasaya, Takahide [0000-0002-5020-9377], Schwemmle, Martin [0000-0002-2972-6855], Shi, Mang [0000-0002-6154-4437], Shimomoto, Yoshifumi [0000-0002-0796-7068], Kavi Sidharthan, Venkidusamy [0000-0003-1561-549X], Sironi, Manuela [0000-0002-2267-5266], Smither, Sophie [0000-0002-7835-3581], Spann, Kirsten [0000-0003-0567-8382], Spengler, Jessica R. [0000-0002-5383-0513], Stenglein, Mark D. [0000-0002-0993-813X], Takada, Ayato [0000-0003-2464-6642], Takeyama, Sawana [0009-0000-3771-5999], Tesh, Robert B. [0000-0002-9226-397X], Thornburg, Natalie J. [0000-0003-3523-3616], Tischler, Nicole D. [0000-0002-4578-4780], Tomitaka, Yasuhiro [0000-0002-6914-4016], Tomonaga, Keizō [0000-0003-0405-7103], Tordo, Noël [0000-0001-5873-059X], Tu, Changchun [0000-0002-8134-7502], Turina, Massimo [0000-0002-9659-9470], Tzanetakis, Ioannis E. [0000-0002-5970-1763], Vaira, Anna Maria [0000-0003-2526-4419], Van den Hoogen, Bernadette [0000-0003-1996-8559], Vanmechelen, Bert [0000-0002-8350-4356], Verbeek, Martin [0000-0002-8973-3803], Von Bargen, Susanne [0000-0001-8321-1572], Wada, Jiro [0000-0001-9846-0846], Wahl, Victoria [0000-0002-6588-4308], Walker, Peter J. [0000-0003-1851-642X], Waltzek, Thomas B. [0000-0001-6383-5978], Whitfield, Anna E. [0000-0002-3538-015X], Wolf, Yuri I. [0000-0002-0247-8708], Xylogianni, Evanthia [0009-0001-8768-0939], Yanagisawa, Hironobu [0000-0002-6729-466X], Ye, Gongyin [0000-0003-4937-8867], Yuan, Zhiming [0000-0002-3234-9616], Zerbini, F. Murilo [0000-0001-8617-0200], Okland, Arnfinn Lodden [0000-0003-3062-4386], Kuhn, Jens H., Abe, Junya, Adkins, Scott, Alkhovsky, Sergey V., Avsic-Zupanc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, A., Ballinger, Matthew J., Kumar Baranwal, Virendra, 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, Dal Bó, Elena, de la Torre, J. C., de Souza, William Marciel, De Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Drexler, J. Felix, Duprex, W. Paul, Dürrwald, Ralf, Easton, Andrew J., Elbeaino, Toufic, Ergünay, Koray, Feng, Guozhong, 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., Gouy de Bellocq, Joelle, Griffiths, Anthony, Groschup, M. 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, Okland, Arnfinn Lodden, 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. [0000-0001-9016-2940], Horie, Masayuki [0000-0003-4682-7698], Hughes, Holly R.[0000-0003-1380-8263], Hyndman, Timothy [0000-0002-7047-5023], Jiāng, Dàohóng [0000-0002-3862-7461], Jonson, Gilda B.[0000-0003-0097-8634], Junglen, Sandra [0000-0002-3799-6011], Klempa, B.[0000-0002-6931-1224], Klingström, Jonas [0000-0001-9076-1441], Kondō, Hideki [0000-0001-9220-5350], Koonin, Eugene V. [0000-0003-3943-8299], Krupovic, Mart [0000-0001-5486-0098], Kurath, Gael [0000-0003-3294-560X], Laenen, Lies [0000-0001-9118-8608], Li, Jianrong [0000-0002-7130-1084], Lukashevich, Igor S.[0000-0001-6523-5116], MacDiarmid, Robin M.[0000-0002-7057-2018], Maes, Piet [0000-0002-4571-5232], Marklewitz, Marco [0000-0003-1828-8770], Marshall, Sergio H.[0000-0003-0438-8252], Marzano, Shin-Yi L. [0000-0003-0548-3761], Mühlberger, Elke [0000-0003-3547-9376], Nabeshima, Tomoyuki [0000-0002-6570-096X], Naidu, Rayapati [0000-0002-7273-5116], Natsuaki, Tomohide [0000-0003-1823-7308], Navarro, José A. [0000-0002-0536-6074], Neriya, Yutaro [0000-0002-1385-0050], Netesov, Sergey V. [0000-0002-7786-2464], Neumann, Gabriele [0000-0001-7054-1775], Nowotny, N. [0000-0002-3548-571X], Ochoa-Corona, Francisco M. [0000-0002-4112-8209], Pallás, Vicente [0000-0003-4954-989X], Papa, Anna [0000-0002-6643-3322], Paraskevopoulou, Sofia [0000-0003-2608-2596], Parrish, Colin R. [0000-0002-1836-6655], Pauvolid-Corrêa, Alex [0000-0002-6924-157X], Pawęska, Janusz T. [0000-0001-8776-7519], Pérez, Daniel R. [0000-0002-6569-5689], Pfaff, Florian [0000-0003-0178-6183], Plemper, Richard K. [0000-0003-2034-2107], Postler, Thomas S. [0000-0002-3558-9084], Rabbidge, Lee O. [0009-0001-7962-4881], Radoshitzky, Sheli R. [0000-0001-8976-8056], Ramos-González, Pedro L. [0000-0002-9640-6587], Rehanek, Marius [0000-0002-5710-5060], Resende, Renato O. [0000-0003-3852-1576], Romanowski, Víctor [0000-0001-6378-7929], Rubbenstroth, Dennis [0000-0002-8209-6274], Rubino, Luisa [0000-0002-2073-2415], Runstadler, Jonathan A. 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Paul, 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., Gouy de Bellocq, Joelle, Griffiths, Anthony, Groschup, M. 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

94. Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins.

Author

Krupovic, Mart, Kuhn, Jens H., Fischer, Matthias G., and Koonin, Eugene V.

Subjects
*NATURAL history, *DNA viruses, *DNA polymerases, *STRUCTURAL frame models, *PROTEINS
Abstract

The phylum Preplasmiviricota (kingdom Bamfordvirae, realm Varidnaviria) is a broad assemblage of diverse viruses with comparatively short double-stranded DNA genomes (<50 kbp) that produce icosahedral capsids built from double jelly-roll major capsid proteins. Preplasmiviricots infect hosts from all cellular domains, testifying to their ancient origin, and, in particular, are associated with six of the seven supergroups of eukaryotes. Preplasmiviricots comprise four major groups of viruses, namely, polintons, polinton-like viruses (PLVs), virophages, and adenovirids. We used protein structure modeling and analysis to show that protein-primed DNA polymerases (pPolBs) of polintons, virophages, and cytoplasmic linear plasmids encompass an N-terminal domain homologous to the terminal proteins (TPs) of prokaryotic PRD1-like tectivirids and eukaryotic adenovirids that are involved in protein-primed replication initiation, followed by a viral ovarian tumor-like cysteine deubiquitinylase (vOTU) domain. The vOTU domain is likely responsible for the cleavage of the TP from the large pPolB polypeptide and is inactivated in adenovirids, in which TP is a separate protein. Many PLVs and transpovirons encode a distinct derivative of polinton-like pPolB that retains the TP, vOTU, and pPolB polymerization palm domains but lacks the exonuclease domain and instead contains a superfamily 1 helicase domain. Analysis of the presence/absence and inactivation of the vOTU domains and replacement of pPolB with other DNA polymerases in eukaryotic preplasmiviricots enabled us to outline a complete scenario for their origin and evolution. [ABSTRACT FROM AUTHOR]

Published
2024
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