1,399 results on '"Krupovic, Mart"'
Search Results
252. Extracellular membrane vesicles harbouring viral genomes
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Gaudin, Marie, Krupovic, Mart, Marguet, Evelyne, Gauliard, Emilie, Cvirkaite-Krupovic, Virginija, Le Cam, Eric, Oberto, Jacques, and Forterre, Patrick
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- 2014
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253. ADN polimerasas independientes de cebador y su uso para la síntesis de ADN
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Salas, Margarita [0000-0001-5939-3441], Redrejo-Rodríguez, Modesto [0000-0003-0014-4162], Krupovic, Mart [0000-0001-5486-0098], Forterre, Patrick [0000-0002-1843-7214], Salas, Margarita, Redrejo-Rodríguez, Modesto, Krupovic, Mart, Forterre, Patrick, Salas, Margarita [0000-0001-5939-3441], Redrejo-Rodríguez, Modesto [0000-0003-0014-4162], Krupovic, Mart [0000-0001-5486-0098], Forterre, Patrick [0000-0002-1843-7214], Salas, Margarita, Redrejo-Rodríguez, Modesto, Krupovic, Mart, and Forterre, Patrick
- Abstract
ADN polimerasas independientes de cebador y su uso para la síntesis de ADN. La presente invención proporciona un péptido aislado de SEQ ID NO: 1, necesario para la actividad primasa, así como nuevas enzimas ADN polimerasas replicativas, preferiblemente la de SEQ ID NO: 2, que comprenden dicho péptido. Por tanto, estas ADN polimerasas están dotadas de actividad primasa y no requieren cebadores proporcionados externamente para iniciar y realizar la amplificación de ADN. Estas polimerasas son capaces de llevar a cabo una síntesis de ADN de novo fiable y procesiva de moldes de ADN en ausencia de cebadores pre-sintetizados. Por lo tanto, estas enzimas actúan como primasas y ADN polimerasas. Asimismo, muestran capacidad de síntesis de translesión, pudiendo ser útiles no solo para la amplificación del genoma completo sino también para la amplificación de ADN dañados. La invención se refiere además a métodos para amplificar ADN moldes que usan estas enzimas
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- 2019
254. Primer-independent DNA polymerases and their use for DNA synthesis
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Salas, Margarita [0000-0001-5939-3441], Redrejo-Rodríguez, Modesto [0000-0003-0014-4162], Krupovic, Mart [0000-0001-5486-0098], Forterre, Patrick [0000-0002-1843-7214], Salas, Margarita, Redrejo-Rodríguez, Modesto, Krupovic, Mart, Forterre, Patrick, Salas, Margarita [0000-0001-5939-3441], Redrejo-Rodríguez, Modesto [0000-0003-0014-4162], Krupovic, Mart [0000-0001-5486-0098], Forterre, Patrick [0000-0002-1843-7214], Salas, Margarita, Redrejo-Rodríguez, Modesto, Krupovic, Mart, and Forterre, Patrick
- Abstract
The present invention provides an isolated peptide of SEQ ID NO: 1 needed for primase active as well as new replicative DNA polymerase enzymes, preferably that of SEQ ID NO: 2, comprising said peptide. Thus, these DNA polymerases are endowed with priming activity and do not require externally provided primers for initiating and performing DNA amplification. These polymerases are able to carry out a faithful and processive de novo DNA synthesis of DNA templates in the absence of pre-synthetized primers. Therefore, these enzymes of the invention act both as primases and DNA polymerases. Furthermore, they show translesion synthesis capacity, so that they may be useful not only for whole-genome amplification but also for the amplification of damaged DNAs. The invention further refers to methods for amplifying templates DNAs using these enzymes
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- 2019
255. Diversity of Hyperthermophilic Archaeal Viruses
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Prangishvili, David, Krupovic, Mart, Baquero, Diana, Institut Pasteur [Paris] (IP), Ivane Javakhishvili Tbilisi State University (TSU), Virologie des archées - Archaeal Virology, Sorbonne Université (SU), Bamford DH, and Zuckerman M
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Diversity ,viruses ,Morphologies ,Viruses ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Crenarchaea ,Genomics ,Virion structures ,Hyperthermophilic environments ,Archaea - Abstract
International audience; Extreme thermal environments represent a habitat for viruses with remarkable morphological diversity and unique genome contents, many of which have not been described in moderate temperature environments. Most of these viruses infect hyperthermophilic archaea of the phylum Crenarchaeota and are currently classified into 13 families. Here, we summarize the state-of-the-art knowledge on the diversity and virion structures of crenarchaeal viruses. We then highlight the genomic features of hyperthermophilic archaeal viruses and emphasize how structural and functional genomic approaches have shed light into the characterization of viral proteins. We finally discuss the origins and evolutionary relationships between crenarchaeal viruses, underpinning their distinctiveness in the global virosphere.
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- 2021
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256. Taxonomy proposal 2020 : Create one new family (Matsushitaviridae) including one renamed genus (Hukuchivirus – formerly Gammasphaerolipovirus) moved from the family Sphaerolipoviridae (Halopanivirales)
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Oksanen, Hanna M, Krupovic, Mart, Jalasvuori, Matti, Molecular and Integrative Biosciences Research Programme, and Molecular Principles of Viruses
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11832 Microbiology and virology - Published
- 2021
257. Rename the family Polydnaviridae (as Polydnaviriformidae), rename the genus Bracovirus (as Bracoviriform) and rename all polydnaviriformid species to comply with the newly ICTV-mandated binomial format
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Kuhn, Jens H., Postler, Thomas, Dolja, Valerian V., Krupovic, Mart, Adriaenssens, Evelien M, Di Serio, Francesco, Dutilh, Bas E., R. Flores, Balazs Harrach, Arcady Mushegian, B. Owens, J. Randles, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, and Koonin, Eugene V
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- 2021
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258. Modify the International Code of Virus Classification and Nomenclature (ICVCN) to prospectively mandate a uniform genus-species type virus species naming format
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Adriaenssens, Evelien M., Dutilh, Bas E., Balazs Harrach, Junglen, Sandra, Kropinski, Andrew, Krupovic, Mart, Kuhn, Jens H., Arcady Mushegian, Postler, Thomas S., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, and Murilo Zerbini
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- 2021
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259. A newly emerging alphasatellite of banana bunchy top virus affects viral replication, transcription, siRNA production and transmission by aphids
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Guyot, Valentin, Rajeswaran, Rajendran, Chu, Huong Cam, Karthikeyan, Chockalingam, Laboureau, Nathalie, Galzi, Serge, Krupovic, Mart, Kumar, P. Lava, Iskra Caruana, Marie-Line, and Pooggin, Mikhail
- Abstract
Banana bunchy top virus (BBTV) is a six-component ssDNA nanovirus transmitted by aphids, causing severe disease of monocot Musa plants, which originates from South-East Asia. Asian BBTV isolates are often associated with self-replicating alphasatellites. By Illumina sequencing analysis of banana aphids and leafs collected in Congo, we discovered an alphasatellite of previously unknown genus, phylogenetically related to alphasatellites of dicot nanoviruses. It was encapsidated by BBTV coat protein and accumulated at high levels in plants and aphids, thereby reducing helper virus loads and altering relative abundance of its genomic components (formula). Consequently, the alphasatellite reduced virus transmission efficiency and delayed symptom appearance without impacting disease severity. BBTV and alphasatellite clones caused systemic infection in Nicotiana bentamiana, followed by recovery, and BBTV replication protein Rep (but not alphasatellite Rep) induced leaf chlorosis. Illumina sequencing revealed 21, 22 and 24 nucleotide small interfering (si)RNAs covering both strands entire viral of the genome, allowed to map monodirectional Pol II transcription units for each viral mRNA and uncovered pervasive transcription of each component and alphasatellite in both polarities, likely generating double-stranded precursors of viral siRNAs. Consistent with latter hypothesis, viral DNA formulas resembled viral siRNA (but not mRNA) formulas. In summary, following African invasion, BBTV got associated with an alphasatellite, likely originating from a banana neighbour plant and having a negative impact on BBTV replication and transmission. Molecular analysis of BBTV- and alphasatelliteinfected plants revealed novel mechanistic aspects of viral DNA transcription by Pol II and siRNA production by the antiviral silencing machinery.
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- 2021
260. Expand, amend, and emend the International Code of Virus Classification and Nomenclature (ICVCN; 'the Code') and the Statutes to clearly define the remit of the ICTV
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Kuhn, Jens H., Dolja, Valerian V., Krupovic, Mart, Adriaenssens, Evelien M, Serio, Francesco Di, Dutilh, Bas E., R. Flores, Balazs Harrach, Arcady Mushegian, B. Owens, J. Randles, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, and Koonin, Eugene V
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- 2021
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261. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)
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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, Zerbini, Francisco Murilo, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Instituto de Higiene e Medicina Tropical (IHMT), Global Health and Tropical Medicine (GHTM), TB, HIV and opportunistic diseases and pathogens (THOP), University of Queensland [Brisbane], University of Bristol [Bristol], University of Alabama at Birmingham [ Birmingham] (UAB), National Science Foundation [Arlington] (NSF), Quadram Institute Biosciences, Universidade Federal de Vicosa (UFV), MRC - University of Glasgow Centre for Virus Research, Utrecht University [Utrecht], Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Invasive Insect Biocontrol and Behavior Laboratory [Beltsville, USA], USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Institute for Animal Health, the Pirbright Institute, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], 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), Centers for Disease Control and Prevention, Polish Academy of Sciences (PAN), Harvard Medical School [Boston] (HMS), University of Helsinki, Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS Torino, Mississippi State University [Mississippi], University of Oxford [Oxford], 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), E.M.A. gratefully acknowledges funding by the U.K. Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. A.J.D. is supported by the U.K. Medical Research Council (MC_UU_12014/3). B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004. B.H. is supported by the National Research, Development and Innovation Office—NKFIH (NN128309). N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (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 by funding for FINStruct and Instruct Centre FI, part of Biocenter Finland and Instruct-ERIC. D.L.R. is supported by the U.K. Medical Research Council (MC_UU_1201412). R.J.O. and D.B.S. are supported by the Wellcome Trust (WT108418AIA). S.S. acknowledges partial support from the Special Research Initiative (MAFES), Mississippi State University, and from the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period. 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 Health and Human Services, or of the institutions and companies affiliated with the authors., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), The Pirbright Institute, 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), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Oxford, and Molecular and Integrative Biosciences Research Programme
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International Cooperation ,education ,virus ,Viroids/classification ,Viruses, Unclassified/classification ,MESH: Viruses ,ICTV ,03 medical and health sciences ,SDG 17 - Partnerships for the Goals ,SDG 3 - Good Health and Well-being ,Virology ,Taverne ,SDG 14 - Life Below Water ,MESH: Phylogeny ,Phylogeny ,Taxonomy ,030304 developmental biology ,SDG 15 - Life on Land ,11832 Microbiology and virology ,0303 health sciences ,Unclassified/classification ,Code ,030306 microbiology ,Viruses/classification ,General Medicine ,Classification ,Viroids ,3. Good health ,MESH: Viroids ,MESH: Classification ,MESH: International Cooperation ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Viruses ,MESH: Viruses, Unclassified ,Viruses, Unclassified ,Classification/methods - Abstract
Funding Information: E.M.A. gratefully acknowledges funding by the U.K. Biotechnology and Biological Sciences Research Council (BBSRC); this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. A.J.D. is supported by the U.K. Medical Research Council (MC_UU_12014/3). B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004. B.H. is supported by the National Research, Development and Innovation Office—NKFIH (NN128309). N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (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 by funding for FINStruct and Instruct Centre FI, part of Biocenter Finland and Instruct-ERIC. D.L.R. is supported by the U.K. Medical Research Council (MC_UU_1201412). R.J.O. and D.B.S. are supported by the Wellcome Trust (WT108418AIA). S.S. acknowledges partial support from the Special Research Initiative (MAFES), Mississippi State University, and from the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period. 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 Health and Human Services, or of the institutions and companies affiliated with the authors. Publisher Copyright: © 2021, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply. This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2021. The entire ICTV was invited to vote on 290 taxonomic proposals approved by the ICTV Executive Committee at its meeting in October 2020, as well as on the proposed revision of the International Code of Virus Classification and Nomenclature (ICVCN). All proposals and the revision were ratified by an absolute majority of the ICTV members. Of note, ICTV mandated a uniform rule for virus species naming, which will follow the binomial 'genus-species' format with or without Latinized species epithets. The Study Groups are requested to convert all previously established species names to the new format. ICTV has also abolished the notion of a type species, i.e., a species chosen to serve as a name-bearing type of a virus genus. The remit of ICTV has been clarified through an official definition of ‘virus’ and several other types of mobile genetic elements. The ICVCN and ICTV Statutes have been amended to reflect these changes. publishersversion inpress
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- 2021
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262. Virus–Host Interactions in Archaea
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Baquero, Diana, Prangishvili, David, Krupovic, Mart, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Sorbonne Université (SU), Ivane Javakhishvili Tbilisi State University (TSU), Dennis H. Bamford, Mark Zuckerman, and Institut Pasteur [Paris]
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replication ,0303 health sciences ,DNA packaging ,defense mechanisms ,030306 microbiology ,viruses ,morphogenesis ,Archaea ,release ,03 medical and health sciences ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,entry ,transcription ,counter-defense mechanisms ,virus-host interactions ,030304 developmental biology - Abstract
International audience; Viruses infecting archaea represent a unique part of the global virosphere with their virions and genomes typically showing no relationship to those of viruses infecting bacteria or eukaryotes. In this chapter, we summarize the state-of-the-art knowledge on various aspects of virus-host interactions in archaea, including (i) host recognition and entry, (ii) mechanisms of viral genome replication, (iii) transcriptional modulation of the viral and host genes during the course of the infection, (iv) mechanisms of virion egress, and (v) defense and viral counterdefense mechanisms in archaea.
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- 2021
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263. Create one new realm (Adnaviria) for classification of filamentous archaeal viruses with linear dsDNA genomes
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Krupovic, Mart, Kuhn, Jens H., F. Wang, D. P. Baquero, E. H. Egelman, Koonin, Eugene V, and Prangishvili, David
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- 2021
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264. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
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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, Zhou, Xueping, Kuhn, Jens H., Agwanda, Bernard R., Alkhovsky, Sergey V., Amarasinghe, Gaya K., Ayllón, María A., Ballinger, Matthew J., Basler, Christopher F., Bennett, Andrew J., Bente, Dennis A., Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Borth, Wayne B., Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Calisher, Charles H., Charrel, Rémi N., Clegg, J. Christopher S., de Swart, Rik L., Dheilly, Nolwenn M., Dietzgen, Ralf G., Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dye, John M., Easton, Andrew J., Ferguson, Hugh W., Fooks, Anthony R., Formenty, Pierre B. H., Garrison, Aura R., Gonzalez, Jean-Paul J., Goldberg, Tony L., Groschup, Martin H., Hall, Roy A., Hu, John S., Hughes, Holly R., Hyndman, Timothy H., Ilyas, M., Jonson, Gilda B., Kaukinen, Karia H., Koonin, Eugene V., Lambert, Amy J., Langevin, Stanley L., Lefkowitz, Elliot J., Leroy, Eric M., Lukashevich, Igor S., Marshall, Sergio H., Marzano, Shin-Yi L., McCauley, John W., Miller, Kristina M., Ming, Tobi J., Mordecai, Gideon J., Navarro, José A., Netesov, Sergey V., Nunes, Márcio R. T., Park, Adam C., Parrish, Colin R., Patterson, David A., Pawęska, Janusz T., Pérez, Daniel R., Postler, Thomas S., Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Runstadler, Jonathan A., Salvato, Maria S., Schulze, Angela D., Siddell, Stuart G., Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Suttle, Curtis A., Tchouassi, David P., Tesh, Robert B., Thornburg, Natalie J., Towner, Jonathan S., Tzanetakis, Ioannis E., Walker, Peter J., Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Zerbini, F. Murilo, NIH - National Institute of Allergy and Infectious Diseases (NIAID) (Estados Unidos), NIH - National Cancer Institute (NCI) (Estados Unidos), National Institutes of Health (Estados Unidos), United States Department of Agriculture. National Institute of Food and Agriculture, Cancer Research UK (Reino Unido), Medical Research Council (Reino Unido), Wellcome Trust, Mississippi State University (Estados Unidos), Battelle National Biodefense Institute, National Biodefense Analysis and Countermeasures Center, Tunnell Government Services (Estados Unidos), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), U.S. Horticultural Research Laboratory ( Fort Pierce, USA), United States Department of Agriculture (USDA), Jomo Kenyatta University of Agriculture and Technology (JKUAT), National Museums of Kenya, Humboldt University Of Berlin, Ministry of Health and Social Development of Russian Federation [Moscow], Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), University of Ljubljana, Universidad Politécnica de Madrid (UPM), University of Georgia [USA], Institute of Novel and Emerging Infectious Diseases (INNT), Friedrich-Loeffler-Institut (FLI), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Stratégies antivirales, Institut Pasteur [Paris] (IP), Centre collaborateur de l'OMS Arbovirus et Fièvres Hémorragiques virales - Stratégies antivirales (CC-OMS), NIAID under Contract No. HHSN272201800013C, NCI, NIH under Contract No. 75N91019D00024, NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942, US Department of Agriculture, Hatch Project 1021494, Cancer Research UK (FC001030), UK Medical Research Council (FC001030), Wellcome Trust (FC001030), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), ARS, Medical School, University of Ljubljana, École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Virology
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Phylum ,Identification ,Alpharhabdovirinae ,Strains ,Field-collected mosquitos ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Article ,MESH: Viruses ,ICTV ,03 medical and health sciences ,Biointeractions and Plant Health ,MESH: Mononegavirales ,Taxonomy of Viruses ,Virology ,Life Science ,Humans ,Crepuscuviridae ,Myriaviridae ,ComputingMilieux_MISCELLANEOUS ,Taxonomy ,030304 developmental biology ,Bunyavirales ,2. Zero hunger ,0303 health sciences ,Virome ,030306 microbiology ,Borne virus-infectons ,Betarhabdovirinae ,Rhabdovirus ,General Medicine ,Taxonomía de Virus ,Merida virus ,3. Good health ,Negarnaviricota ,Aliusviridae ,Triniti-virus ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Viruses ,Queensland ,Mononegavirales ,Hantavirus - Abstract
In March 2021, 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 four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. Instituto de Patología Vegetal Fil: Kuhn, Jens H. National Institute of Allergy and Infectious Diseases. National Institutes of Health. Integrated Research Facility at Fort Detrick; Estados Unidos Fil: Adkins, Scott. United States Department of Agriculture. Agricultural Research Service. US Horticultural Research Laboratory; Estados Unidos Fil: Agwanda, Bernard R. National Museums of Kenya. Zoology Department; Kenia Fil: Agwanda, Bernard R. Jomo Kenyatta University of Agriculture & Technology; Kenia Fil: Kubrusli, Rim Al. Humboldt-Universität zu Berlin. Faculty of Life Sciences. Division Phytomedicine; Alemania Fil: Alkhovsky, Sergey V. D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation; Rusia Fil: Amarasinghe, Gaya K. Washington University School of Medicine. Department of Pathology and Immunology; Estados Unidos Fil: Avšič-Županc, Tatjana. University of Ljubljana. Faculty of Medicine; Eslovenia Fil: Ayllón, María A. Universidad Politécnica de Madrid—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Campus de Montegancedo. Centro de Biotecnología y Genómica de Plantas; España Fil: Ayllón, María A. Universidad Politécnica de Madrid. Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas. Departamento de Biotecnología-Biología Vegetal; España Fil: Bahl, Justin. University of Georgia. Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics; Estados Unidos Fil: Balkema-Buschmann, Anne. Institute of Novel and Emerging Infectious Diseases. Friedrich-Loeffler-Institut. Federal Research Institute for Animal Health; Alemania Fil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina Fil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina Fil: Zhou, Xueping. Chinese Academy of Agricultural Sciences. Institute of Plant Protection. State Key Laboratory for Biology of Plant Diseases and Insect Pests; China
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- 2021
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265. Create one new realm (Ribozyviria) including one new family (Kolmioviridae) including genus Deltavirus and seven new genera for a total of 15 species
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Hepojoki, Jussi, Hetzel, Udo, Paraskevopoulou, Sofia, Drosten, Christian, Balazs Harrach, Zerbini, Francisco Murilo, Koonin, Eugene V, Krupovic, Mart, Dolja, Valerian V., and Kuhn, Jens H.
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- 2021
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266. Family Genomoviridae: 2021 taxonomy update
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Varsani, Arvind, primary and Krupovic, Mart, additional
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- 2021
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267. Viruses of Asgard archaea
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Medvedeva, Sofia, primary, Sun, Jiarui, additional, Yutin, Natalya, additional, Koonin, Eugene V., additional, Nunoura, Takuro, additional, Rinke, Christian, additional, and Krupovic, Mart, additional
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- 2021
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268. New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae
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Medvedeva, Sofia, primary, Brandt, David, additional, Cvirkaite‐Krupovic, Virginija, additional, Liu, Ying, additional, Severinov, Konstantin, additional, Ishino, Sonoko, additional, Ishino, Yoshizumi, additional, Prangishvili, David, additional, Kalinowski, Jörn, additional, and Krupovic, Mart, additional
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- 2021
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269. Adnaviria : a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes
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Krupovic, Mart, primary, Kuhn, Jens H., additional, Wang, Fengbin, additional, Baquero, Diana P., additional, Dolja, Valerian V., additional, Egelman, Edward H., additional, Prangishvili, David, additional, and Koonin, Eugene V., additional
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- 2021
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270. Going to extremes – a metagenomic journey into the dark matter of life
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Aevarsson, Arnthór, primary, Kaczorowska, Anna-Karina, additional, Adalsteinsson, Björn Thor, additional, Ahlqvist, Josefin, additional, Al-Karadaghi, Salam, additional, Altenbuchner, Joseph, additional, Arsin, Hasan, additional, Átlasson, Úlfur Áugúst, additional, Brandt, David, additional, Cichowicz-Cieślak, Magdalena, additional, Cornish, Katy A S, additional, Courtin, Jérémy, additional, Dabrowski, Slawomir, additional, Dahle, Håkon, additional, Djeffane, Samia, additional, Dorawa, Sebastian, additional, Dusaucy, Julia, additional, Enault, Francois, additional, Fedøy, Anita-Elin, additional, Freitag-Pohl, Stefanie, additional, Fridjonsson, Olafur H, additional, Galiez, Clovis, additional, Glomsaker, Eirin, additional, Guérin, Mickael, additional, Gundesø, Sigurd E, additional, Gudmundsdóttir, Elisabet E, additional, Gudmundsson, Hördur, additional, Håkansson, Maria, additional, Henke, Christian, additional, Helleux, Alexandra, additional, Henriksen, Jørn Remi, additional, Hjörleifdóttir, Sigrídur, additional, Hreggvidsson, Gudmundur O, additional, Jasilionis, Andrius, additional, Jochheim, Annika, additional, Jónsdóttir, Ilmur, additional, Jónsdóttir, Lilja Björk, additional, Jurczak-Kurek, Agata, additional, Kaczorowski, Tadeusz, additional, Kalinowski, Jörn, additional, Kozlowski, Lukasz P, additional, Krupovic, Mart, additional, Kwiatkowska-Semrau, Karolina, additional, Lanes, Olav, additional, Lange, Joanna, additional, Lebrat, Julien, additional, Linares-Pastén, Javier, additional, Liu, Ying, additional, Lorentsen, Steffen A, additional, Lutterman, Tobias, additional, Mas, Thibaud, additional, Merré, William, additional, Mirdita, Milot, additional, Morzywołek, Agnieszka, additional, Ndela, Eric Olo, additional, Karlsson, Eva Nordberg, additional, Olgudóttir, Edda, additional, Pedersen, Cathrine, additional, Perler, Francine, additional, Pétursdóttir, Sólveig K, additional, Plotka, Magdalena, additional, Pohl, Ehmke, additional, Prangishvili, David, additional, Ray, Jessica L, additional, Reynisson, Birkir, additional, Róbertsdóttir, Tara, additional, Sandaa, Ruth-Anne, additional, Sczyrba, Alexander, additional, Skírnisdóttir, Sigurlaug, additional, Söding, Johannes, additional, Solstad, Terese, additional, Steen, Ida H, additional, Stefánsson, Sigmar Karl, additional, Steinegger, Martin, additional, Overå, Katrine Stange, additional, Striberny, Bernd, additional, Svensson, Anders, additional, Szadkowska, Monika, additional, Tarrant, Emma J, additional, Terzian, Paul, additional, Tourigny, Mathilde, additional, Bergh, Tom van den, additional, Vanhalst, Justine, additional, Vincent, Jonathan, additional, Vroling, Bas, additional, Walse, Björn, additional, Wang, Lei, additional, Watzlawick, Hildegard, additional, Welin, Martin, additional, Werbowy, Olesia, additional, Wons, Ewa, additional, and Zhang, Ruoshi, additional
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- 2021
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271. Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes
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Liu, Ying, primary, Demina, Tatiana A., additional, Roux, Simon, additional, Aiewsakun, Pakorn, additional, Kazlauskas, Darius, additional, Simmonds, Peter, additional, Prangishvili, David, additional, Oksanen, Hanna M., additional, and Krupovic, Mart, additional
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- 2021
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272. Genetics for Pseudoalteromonas provides tools to manipulate marine bacterial virus PM2
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Kivela, Hanna M., Madonna, Stefania, Krupovic, Mart, Tutino, M. Luisa, and Bamford, Jaana K.H.
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Genetic regulation -- Research ,Bacteriophages -- Genetic aspects ,Host-virus relationships -- Genetic aspects ,Biological sciences - Abstract
The genetic manipulation of marine double-stranded DNA (dsDNA) bacteriophage PM2 (Corticoviridae) has been limited so far. The isolation of an autonomously replicating DNA element of Pseudoalteromonas haloplanktis TACI25 and construction of a shuttle vector replicating in both Escherichia coli and Pseudoalteromonas enabled us to design a set of conjugative shuttle plasmids encoding tRNA suppressors for amber mutations. Using a host strain carrying a suppressor plasmid allows the introduction and analysis of nonsense mutations in PM2. Here, we describe the isolation and characterization of a suppressor-sensitive PM2 sus2 mutant deficient in the structural protein P10. To infect and replicate, PM2 delivers its 10-kbp genome across the cell envelopes of two gram-negative Pseudoalteromonas species. The events leading to the internalization of the circular supercoiled dsDNA are puzzling. In a poorly understood process that follows receptor recognition, the virion capsid disassembles and the internal membrane fuses with the host outer membrane. While beginning to unravel the mechanism of this process, we found that protein P10 plays an essential role in the host cell penetration.
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273. Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)
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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, Davison, Andrew J, Sub Bioinformatics, Theoretical Biology and Bioinformatics, University of Queensland [Brisbane], University of Bristol [Bristol], University of Alabama at Birmingham [ Birmingham] (UAB), Division of Molecular and Cellular Biosciences [Alexandria, USA] (MCB), National Science Foundation [Arlington] (NSF), Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Utrecht University [Utrecht], Hungarian Academy of Sciences (MTA), United States Department of Agriculture (USDA), Humboldt University Of Berlin, The Pirbright Institute, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), National Institutes of Health [Bethesda] (NIH), Harvard Medical School [Boston] (HMS), MRC - University of Glasgow Centre for Virus Research, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], University of Oxford, Arizona State University [Tempe] (ASU), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), The authors declare no conflicts of interest. 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. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. 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 Laulima Government Solutions, LLC’s prime contract with the US National Institute of Allergy and Infectious Diseases (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. N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 and European Research Council (ERC) Consolidator grant 865694: DiversiPHI. B.H. is partially supported by National Research, Development and Innovation Office – NKFIH, NN128309. S.S. acknowledges partial support from Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. E.M.A. was funded by the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. S.J. is supported by the Federal Ministry of Education and Research (BMBF) under project number 01KI1716 as part of the Research Network Zoonotic Infectious Diseases. FMZ is partially supported by CAPES (Finance Code 001). None of the work reported involved research on human participants or animals. All authors have contributed to this work and agreed to its publication. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Sub Bioinformatics, Theoretical Biology and Bioinformatics, Humboldt University of Berlin, Institute for Animal Health, the Pirbright Institute, Institut Pasteur [Paris], Consiglio Nazionale delle Ricerche (CNR), University of Oxford [Oxford], and Universidade Federal de Vicosa (UFV)
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0303 health sciences ,MESH: Terminology as Topic ,030306 microbiology ,education ,General Medicine ,Biology ,no key words ,Virology ,Executive committee ,Statute ,MESH: Viruses ,03 medical and health sciences ,MESH: Classification ,Law ,Taverne ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Classification methods ,Taxonomy (biology) ,Virus classification ,health care economics and organizations ,MESH: Virology ,030304 developmental biology - Abstract
International audience; This article reports the changes to virus classification and taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2020. The entire ICTV was invited to vote on 206 taxonomic proposals approved by the ICTV Executive Committee at its meeting in July 2019, as well as on the proposed revision of the ICTV Statutes. All proposals and the revision of the Statutes were approved by an absolute majority of the ICTV voting membership. Of note, ICTV has approved a proposal that extends the previously established realm Riboviria to encompass nearly all RNA viruses and reverse-transcribing viruses, and approved three separate proposals to establish three realms for viruses with DNA genomes.
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- 2020
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274. The first head-tailed virus, MFTV1, produced by a hyperthermophilic methanogenic deep-sea archaea
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Thiroux, Sarah, Dupont, Samuel, Nesbø, Camilla L., Bienvenu, Nadège, Krupovic, Mart, L'Haridon, Stéphane, Marie, Dominique, Forterre, Patrick, Godfroy, Anne, Geslin, Claire, Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), University of Toronto, University of Alberta, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work was financially supported by the French Ministry of Higher Education and Research and the Brittany region to ST and an ERC grant from the European Union's Seventh Framework 1243 Program, 340440 Project EVOMOBIL, to ST, CG, PF. SD received funding from IFREMER (Brest) for a post-doctoral position., European Project: 340440,EC:FP7:ERC,ERC-2013-ADG,EVOMOBIL(2014), Biologie Cellulaire des Archées (ARCHEE), Département Microbiologie (Dpt Microbio), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
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[SDV]Life Sciences [q-bio] - Abstract
Deep-sea hydrothermal vents are inhabited by complex communities of microbes and their viruses. Despite the importance of viruses in controlling the diversity, adaptation and evolution of their microbial hosts, to date, only eight bacterial and two archaeal viruses isolated from abyssal ecosystems have been described. Thus, our efforts focused on gaining new insights into viruses associated with deep-sea autotrophic archaea. Here, we provide the first evidence of an infection of a hyperthermophilic methanogenic archaea by a head-tailed virus, Methanocaldococcus fervens tailed virus 1 (MFTV1). MFTV1 has an isometric head of 50 nm in diameter and a 150 nm-long non-contractile tail. Virions are released continuously without causing a sudden drop in host growth. MFTV1 infects Methanocaldococcus species and is the first hyperthermophilic head-tailed virus described thus far. The viral genome is a double-stranded linear DNA of 31 kb. Interestingly, our results suggest potential strategies adopted by the plasmid pMEFER01, carried by M. fervens, to spread horizontally in hyperthermophilic methanogens. The data presented here opens a new window of understanding on how the abyssal mobilome interacts with hyperthermophilic marine archaea. This article is protected by copyright. All rights reserved.
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- 2020
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275. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
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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, 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, Krupovic, Mart, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Department of Civil, Environmental and Geodetic Engineering [Columbus, USA] (CEGE), Ohio State University [Columbus] (OSU), University of Novi Sad, Institute for Microbial Biotechnology and Metagenomics [Cape Town, South Africa] (IMBM), University of the Western Cape (UWC), National Institute of Cholera and Enteric Diseases, Theoretical Biology and Bioinformatics [Utrecht, The Netherlands], Utrecht University [Utrecht], Radboud University Medical Center [Nijmegen], Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Institute of Biochemistry & Biophysics, Polish Academy of Sciences (PAN), Beijing University of Chemical Technology, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Universidad Andrés Bello [Santiago] (UNAB), Institute of Food, Nutrition and Health [Zurich, Suisse] (IFNH), Department of Health Sciences and Technology [ETH Zürich] (D-HEST), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Cairo University, Adam Mickiewicz University in Poznań (UAM), Azabu University, San Diego State University (SDSU), University of Guelph, Ontario Veterinary College [Univ. Guelph, Canada], iThree Institute, University of Technology Sydney (UTS), University of Leicester, D.K. Zabolotny Institute of Microbiology and Virology [Kyiv, Ukraine], National Academy of Sciences of Ukraine (NASU), Institute of Chemical Biology and Fundamental Medicine [Novosibirsk, Russia] (ICBFM SB RAS), Siberian Branch of the Russian Academy of Sciences (SB RAS), Rutgers University [Newark], Rutgers University System (Rutgers), Imperial College London, Latvian Biomedical Research and Study Centre [Rīga], University of the Sunshine Coast (USC), George Eliava Institute of Bacteriophages, Microbiology and Virology [Tbilisi, Georgia], Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Department of Biosystems (BIOSYST), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Ivane Javakhishvili Tbilisi State University (TSU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Faculty of Health and Applied Sciences [Bristol, UK], University of the West of England [Bristol] (UWE Bristol), Faculty of Biological and Environmental Sciences [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki, This research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent project(s) BBS/E/F/000PR10353. B.E.D. was supported by the Netherlands Organization for Scientific Research (NWO), Vidi Grant 864.14.004. R.A.E was supported by Grant MCB-1330800 from the National Science Foundation. J.R.B. was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine. R.L. is a member of the PhageBiotics Research Community, supported by FWO Vlaanderen. M.M.P. was supported by the Academy of Finland (272507). H.M.O. was supported by University of Helsinki funding for Instruct-F1 research infrastructure., The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies of their organizations. E.M.A gratefully acknowledges the support of the UK Biotechnology and Biological Sciences Research Council (BBSRC)., UCL - SST/ELI/ELIM - Applied Microbiology, University of the Western Cape, Universidade Federal de Vicosa (UFV), Universidad Andrés Bello - UNAB (CHILE), Institut Pasteur [Paris], University of Helsinki, and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
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06 Biological Sciences, 07 Agricultural and Veterinary Sciences, 11 Medical and Health Sciences ,Archaeal Viruses ,0303 health sciences ,MESH: Bacteriophages/classification ,Bacteria ,030306 microbiology ,MESH: Bacteria/virology ,Coronacrisis-Taverne ,General Medicine ,Classification ,MESH: Archaeal Viruses/classification ,Archaea ,03 medical and health sciences ,All institutes and research themes of the Radboud University Medical Center ,Virology ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Bacteriophages ,MESH: Archaea/virology ,MESH: Classification/methods ,030304 developmental biology - Abstract
International audience; This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
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- 2020
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276. ICTV Virus Taxonomy Profile: Spiraviridae
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Prangishvili, David, Mochizuki, Tomohiro, Krupovic, Mart, Report Consortium, Ictv, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Ivane Javakhishvili Tbilisi State University (TSU), Earth-Life Science Institute [Tokyo] (ELSI), Tokyo Institute of Technology [Tokyo] (TITECH), Production of this summary, the online chapter, and associated resources was funded by a grant from the Wellcome Trust (WT108418AIA)., Members of the ICTV 10th Report Consortium are Stuart G. Siddell, Andrew J. Davison, Elliot J. Lefkowitz, Sead Sabanadzovic, Peter Simmonds, Donald B. Smith, Richard J. Orton and Andrew M. Kropinski., and Institut Pasteur [Paris]
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0301 basic medicine ,Prokaryotic Viruses ,Aeropyrum ,viruses ,ICTV Virus Taxonomy Profile ,030106 microbiology ,DNA, Single-Stranded ,Genome, Viral ,Biology ,Virus Replication ,Genome ,Open Reading Frames ,03 medical and health sciences ,chemistry.chemical_compound ,taxonomy ,Virology ,ICTV Report ,Virus classification ,Appendage ,Spiraviridae ,DNA Viruses ,Virion ,biology.organism_classification ,Nucleoprotein ,Nucleoproteins ,030104 developmental biology ,chemistry ,DNA, Viral ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Taxonomy (biology) ,DNA - Abstract
International audience; The family Spiraviridae includes viruses that replicate in hyperthermophilic archaea from the genus Aeropyrum. The non-enveloped, hollow, cylindrical virions are formed from a coiling fibre that consists of two intertwining halves of a single circular nucleoprotein filament. A short appendage protrudes from each end of the cylindrical virion. The genome is circular, positive-sense, single-stranded DNA of 24 893 nucleotides. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Spiraviridae, which is available at ictv.global/report/spiraviridae.
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- 2020
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277. Binomial nomenclature for virus species: a consultation
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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, Davison, Andrew J, Sub Bioinformatics, Theoretical Biology and Bioinformatics, School of Cellular and Molecular Medicine [Bristol] (CellModMed), University of Bristol [Bristol], School of Biological Sciences [Brisbane], University of Queensland [Brisbane], University of Alabama at Birmingham [ Birmingham] (UAB), Division of Molecular and Cellular Biosciences [Alexandria, USA] (MCB), National Science Foundation [Arlington] (NSF), Theoretical Biology and Bioinformatics [Utrecht, The Netherlands], Utrecht University [Utrecht], Radboud University Medical Center [Nijmegen], Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Invasive Insect Biocontrol and Behavior Laboratory [Beltsville, USA], USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Berlin Institute of Health (BIH), The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), University of Guelph, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), 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), Blavatnik Institute [Boston], Harvard Medical School [Boston] (HMS), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA] (BCH-EPP), Mississippi State University [Mississippi], Nuffield Department of Clinical Medicine [Oxford], University of Oxford, School of Life Sciences [Tempe, USA], Arizona State University [Tempe] (ASU), Departamento de Fitopatologia [Viçosa, Brazil] (BIOAGRO), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), MRC - University of Glasgow Centre for Virus Research, A.D. is supported by Medical Research Council programme Grant MC_UU_12014/3. B.E.D. is supported by the Netherlands Organization for Scientific Research (NWO) Vidi Grant 864.14.004. B.H. is supported by National Research, Development and Innovation Office–NKFIH, NN128309. N.J.K. is funded by the Department for Environment, Food and Rural Affairs (Defra), UK (Grant no. SE2944), work at the Pirbright Institute is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/E/I/00007035, BB/E/I/00007036 and BBS/E/I/00007037). J.H.K is supported through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract no. HHSN272200700016I. S.S. acknowledges partial financial support from Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University., The authors acknowledge the contribution of ICTV Life Member, Dr. Mike Adams, to previous discussions on the need for a standard binomial nomenclature for virus species., Institute for Animal Health, the Pirbright Institute, Institut Pasteur [Paris], Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), Consiglio Nazionale delle Ricerche (CNR), University of Oxford [Oxford], Universidade Federal de Vicosa (UFV), Sub Bioinformatics, and Theoretical Biology and Bioinformatics
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Library science ,Biology ,MESH: Terminology as Topic ,Binomial species names ,Executive committee ,International committee on taxonomy of viruses (ICTV) ,03 medical and health sciences ,Virology Division News ,Terminology as Topic ,Virology ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Nomenclature ,Virus classification ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Binomial nomenclature ,Virus taxonomy ,Species nomenclature ,General Medicine ,Classification ,MESH: Viruses/classification ,Viruses ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Taxonomy (biology) ,MESH: Classification/methods - Abstract
Erratum in : Correction to: Binomial nomenclature for virus species: a consultation. [Arch Virol. 2020]; International audience; The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) recognizes the need for a standardized nomenclature for virus species. This article sets out the case for establishing a binomial nomenclature and presents the advantages and disadvantages of different naming formats. The Executive Committee understands that adopting a binomial system would have major practical consequences, and invites comments from the virology community before making any decisions to change the existing nomenclature. The Executive Committee will take account of these comments in deciding whether to approve a standardized binomial system at its next meeting in October 2020. Note that this system would relate only to the formal names of virus species and not to the names of viruses.
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- 2020
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278. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021
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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., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, 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., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., 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., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, 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., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, 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.
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In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
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- 2021
279. Perspective on taxonomic classification of uncultivated viruses
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Dutilh, Bas E, Varsani, Arvind, Tong, Yigang, Simmonds, Peter, Sabanadzovic, Sead, Rubino, Luisa, Roux, Simon, Muñoz, Alejandro Reyes, Lood, Cédric, Lefkowitz, Elliot J, Kuhn, Jens H, Krupovic, Mart, Edwards, Robert A, Brister, J Rodney, Adriaenssens, Evelien M, Sullivan, Matthew B, Dutilh, Bas E, Varsani, Arvind, Tong, Yigang, Simmonds, Peter, Sabanadzovic, Sead, Rubino, Luisa, Roux, Simon, Muñoz, Alejandro Reyes, Lood, Cédric, Lefkowitz, Elliot J, Kuhn, Jens H, Krupovic, Mart, Edwards, Robert A, Brister, J Rodney, Adriaenssens, Evelien M, and Sullivan, Matthew B
- Abstract
Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on an astounding number of previously unknown viruses. As metagenomes are relatively free of biases, these data provide an unprecedented insight into the vastness of the virosphere, but to properly value the extent of this diversity it is critical that the viruses are taxonomically classified. Inclusion of uncultivated viruses has already improved the process as well as the understanding of the taxa, viruses, and their evolutionary relationships. The continuous development and testing of computational tools will be required to maintain a dynamic virus taxonomy that can accommodate the new discoveries.
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- 2021
280. The first head-tailed virus, MFTV1, infecting hyperthermophilic methanogenic deep-sea archaea
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Thiroux, Sarah, Dupont, Samuel, Nesbø, Camilla L., Bienvenu, Nadège, Krupovic, Mart, L'Haridon, Stephane, Marie, Dominique, Forterre, Patrick, Godfroy, Anne, Geslin, Claire, Thiroux, Sarah, Dupont, Samuel, Nesbø, Camilla L., Bienvenu, Nadège, Krupovic, Mart, L'Haridon, Stephane, Marie, Dominique, Forterre, Patrick, Godfroy, Anne, and Geslin, Claire
- Abstract
Deep‐sea hydrothermal vents are inhabited by complex communities of microbes and their viruses. Despite the importance of viruses in controlling the diversity, adaptation and evolution of their microbial hosts, to date, only eight bacterial and two archaeal viruses isolated from abyssal ecosystems have been described. Thus, our efforts focused on gaining new insights into viruses associated with deep‐sea autotrophic archaea. Here, we provide the first evidence of an infection of a hyperthermophilic methanogenic archaea by a head‐tailed virus, Methanocaldococcus fervens tailed virus 1 (MFTV1). MFTV1 has an isometric head of 50 nm in diameter and a 150 nm‐long non‐contractile tail. Virions are released continuously without causing a sudden drop in host growth. MFTV1 infects Methanocaldococcus species and is the first hyperthermophilic head‐tailed virus described thus far. The viral genome is a double‐stranded linear DNA of 31 kb. Interestingly, our results suggest potential strategies adopted by the plasmid pMEFER01, carried by M. fervens, to spread horizontally in hyperthermophilic methanogens. The data presented here opens a new window of understanding on how the abyssal mobilome interacts with hyperthermophilic marine archaea.
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- 2021
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281. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes.
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Liu, Ying, Liu, Ying, Demina, Tatiana A, Roux, Simon, Aiewsakun, Pakorn, Kazlauskas, Darius, Simmonds, Peter, Prangishvili, David, Oksanen, Hanna M, Krupovic, Mart, Liu, Ying, Liu, Ying, Demina, Tatiana A, Roux, Simon, Aiewsakun, Pakorn, Kazlauskas, Darius, Simmonds, Peter, Prangishvili, David, Oksanen, Hanna M, and Krupovic, Mart
- Abstract
The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments.
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- 2021
282. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, 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., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, 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., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Sub Bioinformatics, Theoretical Biology and Bioinformatics, 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., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, 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., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, 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.
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- 2021
283. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, 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, Zerbini, Francisco Murilo, Sub Bioinformatics, Theoretical Biology and Bioinformatics, 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
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- 2021
284. Perspective on taxonomic classification of uncultivated viruses
- Author
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, Dutilh, Bas E, Varsani, Arvind, Tong, Yigang, Simmonds, Peter, Sabanadzovic, Sead, Rubino, Luisa, Roux, Simon, Muñoz, Alejandro Reyes, Lood, Cédric, Lefkowitz, Elliot J, Kuhn, Jens H, Krupovic, Mart, Edwards, Robert A, Brister, J Rodney, Adriaenssens, Evelien M, Sullivan, Matthew B, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Dutilh, Bas E, Varsani, Arvind, Tong, Yigang, Simmonds, Peter, Sabanadzovic, Sead, Rubino, Luisa, Roux, Simon, Muñoz, Alejandro Reyes, Lood, Cédric, Lefkowitz, Elliot J, Kuhn, Jens H, Krupovic, Mart, Edwards, Robert A, Brister, J Rodney, Adriaenssens, Evelien M, and Sullivan, Matthew B
- Published
- 2021
285. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria : Orthornavirae), including the large orders Bunyavirales and Mononegavirales
- Author
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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, 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, and Zhang, Zhe
- Abstract
In March 2021, 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 four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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- 2021
286. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021
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UCL - SST/ELI/ELIM - Applied Microbiology, 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, Adriaenssens, Evelien M., UCL - SST/ELI/ELIM - Applied Microbiology, 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.
- Abstract
In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
- Published
- 2021
287. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
- Author
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0000-0002-7800-6045, 0000-0003-0095-8414, 0000-0003-4135-4537, 0000-0001-6913-5841, 0000-0002-0418-9707, 0000-0001-6243-0688, Ayllón, María A. [0000-0001-7893-6106], 0000-0001-7572-4300, Balkema-Buschmann, A. [0000-0001-7613-9592], 0000-0001-7453-8725, 0000-0003-4195-425X, 0000-0001-8424-5635, 0000-0002-0598-5254, 0000-0002-7851-3506, 0000-0003-1032-4781, 0000-0003-3398-8628, 0000-0001-8170-8710, 0000-0002-2803-0354, 0000-0003-2121-0376, 0000-0001-5490-3334, 0000-0001-5972-0844, 0000-0002-1985-751X, 0000-0002-9106-1014, 0000-0002-4819-8963, 0000-0002-6697-7688, 0000-0003-4669-8443, 0000-0002-2329-3198, 0000-0002-2387-9287, 0000-0002-0342-4824, 0000-0002-7238-7799, 0000-0002-2086-2594, 0000-0003-0396-262X, 0000-0003-1840-1198, 0000-0003-0232-7077, 0000-0002-7675-8251, 0000-0002-7565-8881, Chiapello, M. [0000-0001-7768-3047], 0000-0003-0422-408X, 0000-0003-2485-4011, 0000-0002-8171-8115, De Swart, Rik L. [0000-0003-3599-8969], 0000-0003-3056-3739, 0000-0002-3675-5013, 0000-0002-9694-3913, 0000-0003-2822-704X, 0000-0002-7772-2250, 0000-0001-7739-4798, Drexler, J. Felix [0000-0002-3509-0232], 0000-0002-2776-169X, 0000-0003-1716-6376, 0000-0002-3432-0438, 0000-0002-0883-5016, 0000-0002-2288-3882, 0000-0002-2576-9735, 0000-0003-2211-7907, 0000-0001-5422-1982, 0000-0002-3243-6154, 0000-0003-0101-1046, 0000-0002-9482-5411, 0000-0001-8451-1454, 0000-0002-0506-6880, 0000-0002-1084-2119, 0000-0001-6468-6943, 0000-0002-6551-1827, 0000-0003-3034-6400, 0000-0003-3063-1770, 0000-0001-5435-8364, 0000-0003-3962-4913, Groschup, M. H. [0000-0003-0215-185X], 0000-0002-6562-0230, 0000-0001-5778-1387, 0000-0001-7593-747X, 0000-0001-5699-214X, 0000-0003-2273-3152, 0000-0002-1285-4455, 0000-0003-4682-7698, 0000-0003-3003-4140, 0000-0003-1380-8263, Von Bargen, Susanne [0000-0001-8321-1572], Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avsic-Zupanc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, A., 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 B., 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, M., Choi, Il-Ryong, Ciuffo, Marina, Clegg, J Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, J. C., 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 R., Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, M. 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, Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, B., 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, Li, Jianrong, 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, N., 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, Zhou, Xueping, 0000-0002-7800-6045, 0000-0003-0095-8414, 0000-0003-4135-4537, 0000-0001-6913-5841, 0000-0002-0418-9707, 0000-0001-6243-0688, Ayllón, María A. [0000-0001-7893-6106], 0000-0001-7572-4300, Balkema-Buschmann, A. [0000-0001-7613-9592], 0000-0001-7453-8725, 0000-0003-4195-425X, 0000-0001-8424-5635, 0000-0002-0598-5254, 0000-0002-7851-3506, 0000-0003-1032-4781, 0000-0003-3398-8628, 0000-0001-8170-8710, 0000-0002-2803-0354, 0000-0003-2121-0376, 0000-0001-5490-3334, 0000-0001-5972-0844, 0000-0002-1985-751X, 0000-0002-9106-1014, 0000-0002-4819-8963, 0000-0002-6697-7688, 0000-0003-4669-8443, 0000-0002-2329-3198, 0000-0002-2387-9287, 0000-0002-0342-4824, 0000-0002-7238-7799, 0000-0002-2086-2594, 0000-0003-0396-262X, 0000-0003-1840-1198, 0000-0003-0232-7077, 0000-0002-7675-8251, 0000-0002-7565-8881, Chiapello, M. [0000-0001-7768-3047], 0000-0003-0422-408X, 0000-0003-2485-4011, 0000-0002-8171-8115, De Swart, Rik L. [0000-0003-3599-8969], 0000-0003-3056-3739, 0000-0002-3675-5013, 0000-0002-9694-3913, 0000-0003-2822-704X, 0000-0002-7772-2250, 0000-0001-7739-4798, Drexler, J. Felix [0000-0002-3509-0232], 0000-0002-2776-169X, 0000-0003-1716-6376, 0000-0002-3432-0438, 0000-0002-0883-5016, 0000-0002-2288-3882, 0000-0002-2576-9735, 0000-0003-2211-7907, 0000-0001-5422-1982, 0000-0002-3243-6154, 0000-0003-0101-1046, 0000-0002-9482-5411, 0000-0001-8451-1454, 0000-0002-0506-6880, 0000-0002-1084-2119, 0000-0001-6468-6943, 0000-0002-6551-1827, 0000-0003-3034-6400, 0000-0003-3063-1770, 0000-0001-5435-8364, 0000-0003-3962-4913, Groschup, M. H. [0000-0003-0215-185X], 0000-0002-6562-0230, 0000-0001-5778-1387, 0000-0001-7593-747X, 0000-0001-5699-214X, 0000-0003-2273-3152, 0000-0002-1285-4455, 0000-0003-4682-7698, 0000-0003-3003-4140, 0000-0003-1380-8263, Von Bargen, Susanne [0000-0001-8321-1572], Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avsic-Zupanc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, A., 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 B., 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, M., Choi, Il-Ryong, Ciuffo, Marina, Clegg, J Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, J. C., 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 R., Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, M. 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, Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, B., 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, Li, Jianrong, 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, N., 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
- Abstract
Unfortunately, the inclusion of original names (in non-Latin script) of the following authors caused problems with author name indexing in PubMed. Therefore, these original names were removed from XML data to correct the PubMed record. Mengji Cao, Yuya Chiaki, Hideki Ebihara, Jingjing Fu, George Fú Gāo, Tong Han, Jiang Hong, Ni Hong, Seiji Hongo, Masayuki Horie, Dàohóng Jiāng, Fujio Kadono, Hideki Kondō, Kenji Kubota, Shaorong Li, Longhui Li, Jiànróng Lǐ, Huazhen Liu, Tomohide Natsuaki, Sergey V. Netesov, Anna Papa, Sofia Paraskevopoulou, Liying Qi, Takahide Sasaya, Mang Shi, Xiǎohóng Shí, Zhènglì Shí, Yoshifumi Shimomoto, Jin‑Won Song, Ayato Takada, Shigeharu Takeuchi, Yasuhiro Tomitaka, Keizō Tomonaga, Shinya Tsuda, Changchun Tu, Tomio Usugi, Nikos Vasilakis, Jiro Wada, Lin‑Fa Wang, Guoping Wang, Yanxiang Wang, Yaqin Wang, Tàiyún Wèi, Shaohua Wen, Jiangxiang Wu, Lei Xu, Hironobu Yanagisawa, Caixia Yang, Zuokun Yang, Lifeng Zhai, Yong‑Zhen Zhang, Song Zhang, Jinguo Zhang, Zhe Zhang, Xueping Zhou. In addition, the publication call-out in the supplementary material was updated from issue 11 to issue 12. The original article has been corrected.
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- 2021
288. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV:update of taxonomy changes in 2021
- Author
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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, Adriaenssens, Evelien M., 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.
- Abstract
In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
- Published
- 2021
289. Reverse-transcribing viruses (Belpaoviridae, Metaviridae, and Pseudoviridae)
- Author
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Llorens, Carlos, Soriano, Beatriz, Navarrete-Muñoz, María A., Hafez, Ahmed, Arnau, Vicente, Benito, José Miguel, Gabaldón, Toni, Rallón, Norma, Pérez-Sánchez, Jaume, Krupovic, Mart, Llorens, Carlos, Soriano, Beatriz, Navarrete-Muñoz, María A., Hafez, Ahmed, Arnau, Vicente, Benito, José Miguel, Gabaldón, Toni, Rallón, Norma, Pérez-Sánchez, Jaume, and Krupovic, Mart
- Abstract
The Metaviridae, Pseudoviridae, and Belpaoviridae are the three families of eukaryotic reverse-transcribing viruses with Long Terminal Repeats (LTRs), popularly known as Ty3/Gypsy, Ty1/Copia, and Bel/Pao LTR retrotransposons, respectively. The three families are unified into the order Ortervirales together with members of the families Retroviridae and Caulimoviridae which infect vertebrates and plants, respectively. Here, we review the molecular biology and diversity of metaviruses, pseudoviruses and belpaoviruses. We explore the similarities and evolutionary relationships among them as well as with other members of the Ortervirales based on life cycle, sequence, architecture of genes and other features. Their host range and impact on the biology and evolution of eukaryotes is also discussed.
- Published
- 2021
290. Origin of programmed cell death from antiviral defense?
- Author
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Koonin, Eugene V., Krupovic, Mart, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris]
- Subjects
Programmed cell death ,[SDV]Life Sciences [q-bio] ,education ,Cell ,ENDOG ,Biology ,03 medical and health sciences ,Meiosis ,Commentaries ,Genetics ,otorhinolaryngologic diseases ,medicine ,Fragmentation (cell biology) ,health care economics and organizations ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,urogenital system ,030306 microbiology ,MESH: Antiviral Agents ,MESH: Apoptosis ,Biological Sciences ,Cell biology ,Nuclear DNA ,Multicellular organism ,medicine.anatomical_structure ,DNA fragmentation - Abstract
Viruses and other genetic parasites are ubiquitous in the biosphere, and virtually all cellular organisms evolved multiple defense mechanisms to cope with onslaughts of these parasites (1). In multicellular life forms, a major class of such mechanisms is programmed cell death (PCD), whereby an infected cell “commits altruistic suicide” to prevent infection of other cells (2). Many unicellular eukaryotes and prokaryotes also possess PCD pathways but, in this case, the function and, especially, the evolution of such self-destructing mechanisms remain controversial topics because it is not immediately clear how unicellular organisms would benefit from suicide (3⇓–5). Models have been developed to account for the origin of PCD through population-level kin selection (5⇓–7) but the controversy persists. In a PNAS article, Gao et al. (8) present observations suggesting the possibility that some forms of PCD might have evolved from antivirus defense mechanisms. The experimental system is budding yeast sporulation that involves a meiotic division resulting in the development of spores and PCD of the remains of the mother cell (9, 10). This PCD is accompanied by fragmentation of the nuclear DNA of the dying cell that is catalyzed by the NUC1 nuclease released from the mitochondria. NUC1 belongs to the EndoG family of nucleases that is highly conserved among all eukaryotes and most prokaryotes and is responsible for DNA fragmentation during PCD in animals and at least some protists (11⇓–13). Thus, this phenomenon is widely conserved in evolution and yet remains somewhat enigmatic because DNA fragmentation is not required for PCD that occurs normally … [↵][1]1To whom correspondence may be addressed. Email: koonin{at}ncbi.nlm.nih.gov or krupovic{at}pasteur.fr. [1]: #xref-corresp-1-1
- Published
- 2019
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291. Archaeal extracellular vesicles are produced in an ESCRT-dependent manner and promote gene transfer and nutrient cycling in extreme environments
- Author
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Liu, Junfeng, primary, Cvirkaite-Krupovic, Virginija, additional, Commere, Pierre-Henri, additional, Yang, Yunfeng, additional, Zhou, Fan, additional, Forterre, Patrick, additional, Shen, Yulong, additional, and Krupovic, Mart, additional
- Published
- 2021
- Full Text
- View/download PDF
292. Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins
- Author
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Marabini, Roberto, primary, Condezo, Gabriela N., additional, Krupovic, Mart, additional, Menéndez-Conejero, Rosa, additional, Gómez-Blanco, Josué, additional, and San Martín, Carmen, additional
- Published
- 2021
- Full Text
- View/download PDF
293. The healthy human virome: from virus–host symbiosis to disease
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Koonin, Eugene V, primary, Dolja, Valerian V, additional, and Krupovic, Mart, additional
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- 2021
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- View/download PDF
294. Virus-induced cell gigantism and asymmetric cell division in archaea
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Liu, Junfeng, primary, Cvirkaite-Krupovic, Virginija, additional, Baquero, Diana P., additional, Yang, Yunfeng, additional, Zhang, Qi, additional, Shen, Yulong, additional, and Krupovic, Mart, additional
- Published
- 2021
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295. Metagenome-derived virus-microbe ratios across ecosystems
- Author
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López-García, Purificación, primary, Gutiérrez-Preciado, Ana, additional, Krupovic, Mart, additional, Ciobanu, Maria, additional, Deschamps, Philippe, additional, Jardillier, Ludwig, additional, López-Pérez, Mario, additional, Rodríguez-Valera, Francisco, additional, and Moreira, David, additional
- Published
- 2021
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- View/download PDF
296. Chapter Four - Structure and assembly of archaeal viruses
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Baquero, Diana P., Liu, Ying, Wang, Fengbin, Egelman, Edward H., Prangishvili, David, and Krupovic, Mart
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- 2020
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297. Postcards from the Edge
- Author
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Krupovic, Mart, primary, White, Malcolm F., additional, Forterre, Patrick, additional, and Prangishvili, David, additional
- Published
- 2012
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298. Metagenome-derived virus-microbe ratios across ecosystems
- Author
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López-García, Purificación, Gutiérrez-Preciado, Ana, Krupovic, Mart, Ciobanu, Maria, Deschamps, Philippe, Jardillier, Ludwig, López-Pérez, Mario, Rodríguez-Valera, Francisco, and Moreira, David
- Abstract
It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa–200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2–4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.
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- 2023
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299. Primer-independent DNA polymerases and their use for DNA synthesis
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Salas, Margarita, Redrejo-Rodríguez, Modesto, Krupovic, Mart, Forterre, Patrick, Salas, Margarita [0000-0001-5939-3441], Redrejo-Rodríguez, Modesto [0000-0003-0014-4162], Krupovic, Mart [0000-0001-5486-0098], Forterre, Patrick [0000-0002-1843-7214], Salas, Margarita, Redrejo-Rodríguez, Modesto, Krupovic, Mart, and Forterre, Patrick
- Subjects
humanities - Abstract
The present invention provides an isolated peptide of SEQ ID NO: 1 needed for primase active as well as new replicative DNA polymerase enzymes, preferably that of SEQ ID NO: 2, comprising said peptide. Thus, these DNA polymerases are endowed with priming activity and do not require externally provided primers for initiating and performing DNA amplification. These polymerases are able to carry out a faithful and processive de novo DNA synthesis of DNA templates in the absence of pre-synthetized primers. Therefore, these enzymes of the invention act both as primases and DNA polymerases. Furthermore, they show translesion synthesis capacity, so that they may be useful not only for whole-genome amplification but also for the amplification of damaged DNAs. The invention further refers to methods for amplifying templates DNAs using these enzymes, Consejo Superior de Investigaciones Científicas (España), Institut Pasteur, A1 Solicitud de patente con informe sobre el estado de la técnica
- Published
- 2018
300. The logic of virus evolution.
- Author
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Koonin, Eugene V., Dolja, Valerian V., and Krupovic, Mart
- Abstract
Viruses are obligate intracellular parasites. Despite their dependence on host cells, viruses are evolutionarily autonomous, with their own genomes and evolutionary trajectories locked in arms races with the hosts. Here, we discuss a simple functional logic to explain virus macroevolution that appears to define the course of virus evolution. A small core of virus hallmark genes that are responsible for genome replication apparently descended from primordial replicators, whereas most virus genes, starting with those encoding capsid proteins, were subsequently acquired from hosts. The oldest of these acquisitions antedate the last universal cellular ancestor (LUCA). Host gene capture followed two major routes: convergent recruitment of genes with functions that directly benefit virus reproduction and exaptation when host proteins are repurposed for unique virus functions. These forms of host protein recruitment by viruses result in different levels of similarity between virus and host homologs, with the exapted ones often changing beyond easy recognition. In this perspective, Koonin, Dolja, and Krupovic examine the capture of host genes by viruses and how this process shaped virus genomes through the ∼4 billion years of virus-host coevolution. The logic of repurposing cellular proteins determines the trajectories of virus macroevolution including the emergence of new groups of viruses. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
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