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

Author

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

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

2. Perspective on taxonomic classification of uncultivated viruses

Author

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

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

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

Published
2021

3. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Author

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

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

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

Published
2019

4. Database resources of the National Center for Biotechnology Information in 2025.

Author

Sayers, Eric W, Beck, Jeffrey, Bolton, Evan E, Brister, J Rodney, Chan, Jessica, Connor, Ryan, Feldgarden, Michael, Fine, Anna M, Funk, Kathryn, Hoffman, Jinna, Kannan, Sivakumar, Kelly, Christopher, Klimke, William, Kim, Sunghwan, Lathrop, Stacy, Marchler-Bauer, Aron, Murphy, Terence D, O'Sullivan, Chris, Schmieder, Erin, and Skripchenko, Yuriy

Published
2025
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6. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

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

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

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

Published
2019

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

Author

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

Published
2023
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8. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author

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

Published
2021
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9. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Author

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

Published
2020

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

Author

Calisher, Charles H., Briese, Thomas, Brister, J. Rodney, Charrel, Rémi N., Dürrwald, Ralf, Ebihara, Hideki, Fulhorst, Charles F., Gāo, George Fú, Groschup, Martin H., Haddow, Andrew D., Hyndman, Timothy H., Junglen, Sandra, Klempa, Boris, Klingström, Jonas, Kropinski, Andrew M., Krupovic, Mart, LaBeaud, A. Desiree, Maes, Piet, Nowotny, Norbert, Nunes, Márcio Roberto Teixeira, Payne, Susan L., Radoshitzky, Sheli R., Rubbenstroth, Dennis, Sabanadzovic, Sead, Sasaya, Takahide, D.Stenglein, Mark, Varsani, Arvind, Wahl, Victoria, Weaver, Scott C., Zerbini, Francisco Murilo, Vasilakis, Nikos, and Kuhn, Jens H.

Published
2019

12. Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications

Author

Timme, Ruth E., primary, Karsch-Mizrachi, Ilene, additional, Waheed, Zahra, additional, Arita, Masanori, additional, MacCannell, Duncan, additional, Maguire, Finlay, additional, Petit III, Robert, additional, Page, Andrew J., additional, Mendes, Catarina Inês, additional, Nasar, Muhammad Ibtisam, additional, Oluniyi, Paul, additional, Tyler, Andrea D., additional, Raphenya, Amogelang R., additional, Guthrie, Jennifer L., additional, Olawoye, Idowu, additional, Rinck, Gabriele, additional, O’Cathail, Colman, additional, Lees, John, additional, Cochrane, Guy, additional, Cummins, Carla, additional, Brister, J. Rodney, additional, Klimke, William, additional, Feldgarden, Michael, additional, and Griffiths, Emma, additional

Published
2023
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13. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W, primary, Beck, Jeff, additional, Bolton, Evan E, additional, Brister, J Rodney, additional, Chan, Jessica, additional, Comeau, Donald C, additional, Connor, Ryan, additional, DiCuccio, Michael, additional, Farrell, Catherine M, additional, Feldgarden, Michael, additional, Fine, Anna M, additional, Funk, Kathryn, additional, Hatcher, Eneida, additional, Hoeppner, Marilu, additional, Kane, Megan, additional, Kannan, Sivakumar, additional, Katz, Kenneth S, additional, Kelly, Christopher, additional, Klimke, William, additional, Kim, Sunghwan, additional, Kimchi, Avi, additional, Landrum, Melissa, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Malheiro, Adriana, additional, Marchler-Bauer, Aron, additional, Murphy, Terence D, additional, Phan, Lon, additional, Prasad, Arjun B, additional, Pujar, Shashikant, additional, Sawyer, Amanda, additional, Schmieder, Erin, additional, Schneider, Valerie A, additional, Schoch, Conrad L, additional, Sharma, Shobha, additional, Thibaud-Nissen, Françoise, additional, Trawick, Barton W, additional, Venkatapathi, Thilakam, additional, Wang, Jiyao, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2023
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15. Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.

Author

Connor, Ryan, Shakya, Migun, Yarmosh, David A., Maier, Wolfgang, Martin, Ross, Bradford, Rebecca, Brister, J. Rodney, Chain, Patrick S. G., Copeland, Courtney A., di Iulio, Julia, Hu, Bin, Ebert, Philip, Gunti, Jonathan, Jin, Yumi, Katz, Kenneth S., Kochergin, Andrey, LaRosa, Tré, Li, Jiani, Li, Po-E, and Lo, Chien-Chi

Subjects
SARS-CoV-2, COVID-19 pandemic, SINGLE nucleotide polymorphisms, GENETIC variation, VIRAL transmission, QUALITY function deployment, WORKFLOW
Abstract

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Author

Adriaenssens, Evelien, Roux, Simon, Brister, J. Rodney, Karsch-Mizrachi, Ilene, Kuhn, Jens, Varsani, Arvind, Yigang, Tong, Reyes, Alejandro, Lood, Cédric, Lefkowitz, Elliot, Sullivan, Matthew, Edwards, Robert, Simmonds, Peter, Rubino, Luisa, Sabanadzovic, Sead, Krupovic, Mart, Dutilh, Bas, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), National Center for Biotechnology Information (NCBI), 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), Arizona State University [Tempe] (ASU), University of Cape Town, Beijing University of Chemical Technology, Universidad de los Andes [Bogota] (UNIANDES), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], University of Alabama at Birmingham [ Birmingham] (UAB), Ohio State University [Columbus] (OSU), Flinders University [Adelaide, Australia], University of Oxford, CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], 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), Utrecht University [Utrecht], E.M.A. gratefully acknowledges the support of the Biotechnology and Biological Sciences Research Council (BBSRC), and this research was funded by the BBSRC Institute Strategic Program Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. The work conducted by the US Department of Energy (DOE) Joint Genome Institute (S.R.) was supported by the Office of Science of the DOE under contract no. DE-AC02-05CH11231. Work by J.R.B. and I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), NIH. This work was supported in part through Laulima Government Solutions, LLC, prime contract with the 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. M.B.S. was supported by the US National Science Foundation Award #1759874. R.A.E. was supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the NIH under award no. RC2DK116713 and by the Australian Research Council under award no. DP220102915. C.L. was supported by a Postdoctoral Mandate from KU Leuven (PDMt2/21/038) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2051 – Project-ID 390713860. E.J.L. was supported by the NIAID, NIH, under award no. U24AI162625. P.S. was supported by a Wellcome Trust Biomedical Resource grant (WT108418AIA). S.S. acknowledges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), US Department of Agriculture (USDA)–Agricultural Research Service project 58-6066-9-033, and the National Institute of Food and Agriculture, USDA, Hatch Project, under accession USDA 1021494. B.E.D. was supported by the European Research Council (ERC) Consolidator Grant 865694: DiversiPHI, the DFG under Germany’s Excellence Strategy – EXC 2051 – Project-ID 390713860, the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt Professorship founded by German Federal Ministry of Education and Research, and the European Union’s Horizon 2020 research and innovation program, under Marie Skłodowska-Curie Actions Innovative Training Networks grant agreement no. 955974 (VIROINF).

Subjects
[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Published
2023
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17. Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification (Nature Biotechnology, (2023), 41, 7, (898-902), 10.1038/s41587-023-01844-2)

Author

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

Abstract

In the version of this article initially published, there were mistakes in Fig. 1 (ICTV-ratified species growth): in the 2022 column for the 15-rank structure, the value for “Family” was 260 instead of 264; the value for “Genus” was 2,810 instead of 2,818; and the value for “Species” was 11,265 instead of 11,273. The errors have been corrected in the HTML and PDF versions of the article.

Published
2023

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

Author

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

Abstract

This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.

Published
2023

19. Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification (Nature Biotechnology, (2023), 41, 7, (898-902), 10.1038/s41587-023-01844-2)

Author

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

Published
2023

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

Author

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

Published
2023

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

Author

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

Published
2023

22. Database resources of the National Center for Biotechnology Information.

Author

Sayers, Eric W, Beck, Jeff, Bolton, Evan E, Brister, J Rodney, Chan, Jessica, Comeau, Donald C, Connor, Ryan, DiCuccio, Michael, Farrell, Catherine M, Feldgarden, Michael, Fine, Anna M, Funk, Kathryn, Hatcher, Eneida, Hoeppner, Marilu, Kane, Megan, Kannan, Sivakumar, Katz, Kenneth S, Kelly, Christopher, Klimke, William, and Kim, Sunghwan

Published
2024
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23. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee

Author

Adriaenssens, Evelien M., Krupovic, Mart, Knezevic, Petar, Ackermann, Hans-Wolfgang, Barylski, Jakub, Brister, J. Rodney, Clokie, Martha R. C., Duffy, Siobain, Dutilh, Bas E., Edwards, Robert A., Enault, Francois, Jang, Ho Bin, Klumpp, Jochen, Kropinski, Andrew M., Lavigne, Rob, Poranen, Minna M., Prangishvili, David, Rumnieks, Janis, Sullivan, Matthew B., Wittmann, Johannes, Oksanen, Hanna M., Gillis, Annika, and Kuhn, Jens H.

Published
2017
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25. Database resources of the National Center for Biotechnology Information in 2023

Author

Sayers, Eric W, primary, Bolton, Evan E, additional, Brister, J Rodney, additional, Canese, Kathi, additional, Chan, Jessica, additional, Comeau, Donald C, additional, Farrell, Catherine M, additional, Feldgarden, Michael, additional, Fine, Anna M, additional, Funk, Kathryn, additional, Hatcher, Eneida, additional, Kannan, Sivakumar, additional, Kelly, Christopher, additional, Kim, Sunghwan, additional, Klimke, William, additional, Landrum, Melissa J, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Madden, Thomas L, additional, Malheiro, Adriana, additional, Marchler-Bauer, Aron, additional, Murphy, Terence D, additional, Phan, Lon, additional, Pujar, Shashikant, additional, Rangwala, Sanjida H, additional, Schneider, Valerie A, additional, Tse, Tony, additional, Wang, Jiyao, additional, Ye, Jian, additional, Trawick, Barton W, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2022
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26. Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

Author

Connor, Ryan, primary, Yarmosh, David A., additional, Maier, Wolfgang, additional, Shakya, Migun, additional, Martin, Ross, additional, Bradford, Rebecca, additional, Brister, J. Rodney, additional, Chain, Patrick SG, additional, Copeland, Courtney A., additional, di Iulio, Julia, additional, Hu, Bin, additional, Ebert, Philip, additional, Gunti, Jonathan, additional, Jin, Yumi, additional, Katz, Kenneth S., additional, Kochergin, Andrey, additional, LaRosa, Tré, additional, Li, Jiani, additional, Li, Po-E, additional, Lo, Chien-Chi, additional, Rashid, Sujatha, additional, Maiorova, Evguenia S., additional, Xiao, Chunlin, additional, Zalunin, Vadim, additional, and Pruitt, Kim D., additional

Published
2022
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30. Database resources of the national center for biotechnology information

Author

Sayers, Eric W, primary, Bolton, Evan E, additional, Brister, J Rodney, additional, Canese, Kathi, additional, Chan, Jessica, additional, Comeau, Donald C, additional, Connor, Ryan, additional, Funk, Kathryn, additional, Kelly, Chris, additional, Kim, Sunghwan, additional, Madej, Tom, additional, Marchler-Bauer, Aron, additional, Lanczycki, Christopher, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Thibaud-Nissen, Francoise, additional, Murphy, Terence, additional, Phan, Lon, additional, Skripchenko, Yuri, additional, Tse, Tony, additional, Wang, Jiyao, additional, Williams, Rebecca, additional, Trawick, Barton W, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2021
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31. Perspective on taxonomic classification of uncultivated viruses

Author

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

Published
2021
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32. Virus nomenclature below the species level: a standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family Filoviridae

Author

Kuhn, Jens H., Bao, Yiming, Bavari, Sina, Becker, Stephan, Bradfute, Steven, Brister, J. Rodney, Bukreyev, Alexander A., Caì, Yíngyún, Chandran, Kartik, Davey, Robert A., Dolnik, Olga, Dye, John M., Enterlein, Sven, Gonzalez, Jean-Paul, Formenty, Pierre, Freiberg, Alexander N., Hensley, Lisa E., Honko, Anna N., Ignatyev, Georgy M., Jahrling, Peter B., Johnson, Karl M., Klenk, Hans-Dieter, Kobinger, Gary, Lackemeyer, Matthew G., Leroy, Eric M., Lever, Mark S., Lofts, Loreen L., Mühlberger, Elke, Netesov, Sergey V., Olinger, Gene G., Palacios, Gustavo, Patterson, Jean L., Paweska, Janusz T., Pitt, Louise, Radoshitzky, Sheli R., Ryabchikova, Elena I., Saphire, Erica Ollmann, Shestopalov, Aleksandr M., Smither, Sophie J., Sullivan, Nancy J., Swanepoel, Robert, Takada, Ayato, Towner, Jonathan S., van der Groen, Guido, Volchkov, Viktor E., Wahl-Jensen, Victoria, Warren, Travis K., Warfield, Kelly L., Weidmann, Manfred, and Nichol, Stuart T.

Published
2013
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34. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

Author

Kuhn, Jens H., Bao, Yiming, Bavari, Sina, Becker, Stephan, Bradfute, Steven, Brister, J. Rodney, Bukreyev, Alexander A., Chandran, Kartik, Davey, Robert A., Dolnik, Olga, Dye, John M., Enterlein, Sven, Hensley, Lisa E., Honko, Anna N., Jahrling, Peter B., Johnson, Karl M., Kobinger, Gary, Leroy, Eric M., Lever, Mark S., Mühlberger, Elke, Netesov, Sergey V., Olinger, Gene G., Palacios, Gustavo, Patterson, Jean L., Paweska, Janusz T., Pitt, Louise, Radoshitzky, Sheli R., Saphire, Erica Ollmann, Smither, Sophie J., Swanepoel, Robert, Towner, Jonathan S., van der Groen, Guido, Volchkov, Viktor E., Wahl-Jensen, Victoria, Warren, Travis K., Weidmann, Manfred, and Nichol, Stuart T.

Published
2013
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35. Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG)

Author

Matthijnssens, Jelle, Ciarlet, Max, McDonald, Sarah M., Attoui, Houssam, Bányai, Krisztián, Brister, J. Rodney, Buesa, Javier, Esona, Mathew D., Estes, Mary K., Gentsch, Jon R., Iturriza-Gómara, Miren, Johne, Reimar, Kirkwood, Carl D., Martella, Vito, Mertens, Peter P. C., Nakagomi, Osamu, Parreño, Viviana, Rahman, Mustafizur, Ruggeri, Franco M., Saif, Linda J., Santos, Norma, Steyer, Andrej, Taniguchi, Koki, Patton, John T., Desselberger, Ulrich, and Van Ranst, Marc

Published
2011
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38. Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level

Author

Salimi, Vahid, primary, Viegas, Mariana, additional, Trento, Alfonsina, additional, Agoti, Charles N., additional, Anderson, Larry J., additional, Avadhanula, Vasanthi, additional, Bahl, Justin, additional, Bont, Louis, additional, Brister, J. Rodney, additional, Cane, Patricia A., additional, Galiano, Mónica, additional, Graham, Barney S., additional, Hatcher, Eneida L., additional, Hellferscee, Orienka, additional, Henke, David M., additional, Hirve, Siddhivinayak, additional, Jackson, Sandra, additional, Keyaerts, Els, additional, Kragten-Tabatabaie, Leyla, additional, Lindstrom, Stephen, additional, Nauwelaers, Inne, additional, Nokes, D. James, additional, Openshaw, Peter J., additional, Peret, Teresa C., additional, Piedra, Pedro A., additional, Ramaekers, Kaat, additional, Rector, Annabel, additional, Trovão, Nídia Sequeira, additional, von Gottberg, Anne, additional, Zambon, Maria, additional, Zhang, Wenqing, additional, Williams, Thomas C., additional, Barr, Ian G., additional, and Buchholz, Ursula J., additional

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

Author

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.

Published
2021

40. Perspective on taxonomic classification of uncultivated viruses

Author

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

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

Author

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

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

Author

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

43. Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level

Author

CTI Bont, Infectieziekten onderzoek1 (Bont), Child Health, Infection & Immunity, Salimi, Vahid, Viegas, Mariana, Trento, Alfonsina, Agoti, Charles N, Anderson, Larry J, Avadhanula, Vasanthi, Bahl, Justin, Bont, Louis, Brister, J Rodney, Cane, Patricia A, Galiano, Mónica, Graham, Barney S, Hatcher, Eneida L, Hellferscee, Orienka, Henke, David M, Hirve, Siddhivinayak, Jackson, Sandra, Keyaerts, Els, Kragten-Tabatabaie, Leyla, Lindstrom, Stephen, Nauwelaers, Inne, Nokes, D James, Openshaw, Peter J, Peret, Teresa C, Piedra, Pedro A, Ramaekers, Kaat, Rector, Annabel, Trovão, Nídia Sequeira, von Gottberg, Anne, Zambon, Maria, Zhang, Wenqing, Williams, Thomas C, Barr, Ian G, Buchholz, Ursula J, CTI Bont, Infectieziekten onderzoek1 (Bont), Child Health, Infection & Immunity, Salimi, Vahid, Viegas, Mariana, Trento, Alfonsina, Agoti, Charles N, Anderson, Larry J, Avadhanula, Vasanthi, Bahl, Justin, Bont, Louis, Brister, J Rodney, Cane, Patricia A, Galiano, Mónica, Graham, Barney S, Hatcher, Eneida L, Hellferscee, Orienka, Henke, David M, Hirve, Siddhivinayak, Jackson, Sandra, Keyaerts, Els, Kragten-Tabatabaie, Leyla, Lindstrom, Stephen, Nauwelaers, Inne, Nokes, D James, Openshaw, Peter J, Peret, Teresa C, Piedra, Pedro A, Ramaekers, Kaat, Rector, Annabel, Trovão, Nídia Sequeira, von Gottberg, Anne, Zambon, Maria, Zhang, Wenqing, Williams, Thomas C, Barr, Ian G, and Buchholz, Ursula J

Published
2021

46. Database resources of the National Center for Biotechnology Information

Author

Agarwala, Richa, Barrett, Tanya, Beck, Jeff, Benson, Dennis A, Bollin, Colleen, Bolton, Evan, Bourexis, Devon, Brister, J Rodney, Bryant, Stephen H, Canese, Kathi, Cavanaugh, Mark, Charowhas, Chad, Clark, Karen, Dondoshansky, Ilya, Feolo, Michael, Fitzpatrick, Lawrence, Funk, Kathryn, Geer, Lewis Y, Gorelenkov, Viatcheslav, Graeff, Alan, Hlavina, Wratko, Holmes, Brad, Johnson, Mark, Kattman, Brandi, Khotomlianski, Viatcheslav, Kimchi, Avi, Kimelman, Michael, Kimura, Masato, Kitts, Paul, Klimke, William, Kotliarov, Alex, Krasnov, Sergey, Kuznetsov, Anatoliy, Landrum, Melissa J, Landsman, David, Lathrop, Stacy, Lee, Jennifer M, Leubsdorf, Carl, Lu, Zhiyong, Madden, Thomas L, Marchler-Bauer, Aron, Malheiro, Adriana, Meric, Peter, Karsch-Mizrachi, Ilene, Mnev, Anatoly, Murphy, Terence, Orris, Rebecca, Ostell, James, O'Sullivan, Christopher, Palanigobu, Vasuki, Panchenko, Anna R, Phan, Lon, Pierov, Borys, Pruitt, Kim D, Rodarmer, Kurt, Sayers, Eric W, Schneider, Valerie, Schoch, Conrad L, Schuler, Gregory D, Sherry, Stephen T, Siyan, Karanjit, Soboleva, Alexandra, Soussov, Vladimir, Starchenko, Grigory, Tatusova, Tatiana A, Thibaud-Nissen, Francoise, Todorov, Kamen, Trawick, Bart W, Vakatov, Denis, Ward, Minghong, Yaschenko, Eugene, Zasypkin, Aleksandr, and Zbicz, Kerry

Subjects
0301 basic medicine, Internet, PubMed, National Library of Medicine (U.S.), 010402 general chemistry, Databases, Bibliographic, 01 natural sciences, United States, 0104 chemical sciences, 03 medical and health sciences, ComputingMethodologies_PATTERNRECOGNITION, 030104 developmental biology, Databases, Genetic, Genetics, Database Issue, Database Management Systems, Humans, Databases, Nucleic Acid, Databases, Chemical, Biotechnology
Abstract

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Data Management, RefSeq Functional Elements, genome data download, variation services API, Magic-BLAST, QuickBLASTp, and Identical Protein Groups. Resources that were updated in the past year include the genome data viewer, a human genome resources page, Gene, virus variation, OSIRIS, and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Published
2017
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47. Taxonomy of prokaryotic viruses : 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author

Adriaenssens, Evelien M, Sullivan, Matthew B., Knezevic, Petar, van Zyl, Leonardo J., Sarkar, BL, Dutilh, Bas E., Alfenas-Zerbini, Poliane, Lobocka, Malgorzata, Tong, Yigang, Brister, J. Rodney, Moreno Switt, Andrea I., Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Edwards, Rob A, Kropinski, Andrew M., Petty, Nicola K, Clokie, Martha R. C., 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, François, Turner, Dann, Poranen, Minna, Oksanen, Hanna M, Krupovic, Mart, Molecular and Integrative Biosciences Research Programme, Molecular Principles of Viruses, and Molecular and Translational Virology

Subjects
11832 Microbiology and virology, VIRION, SSDNA, PHAGE, HIS1, CLASSIFICATION
Abstract

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.

Published
2020

48. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Author

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

Published
2020

49. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Author

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

Abstract

Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order—Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods—including comparative genomics, core genome analysis, and marker gene phylogenetics—to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae—a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.

Published
2020

50. VADR: validation and annotation of virus sequence submissions to GenBank

Author

Massachusetts Institute of Technology. Department of Biology, Schäffer, Alejandro A., Hatcher, Eneida L., Yankie, Linda, Shonkwiler, Lara, Brister, J. Rodney, Karsch-Mizrachi, Ilene, Nawrocki, Eric P., Massachusetts Institute of Technology. Department of Biology, Schäffer, Alejandro A., Hatcher, Eneida L., Yankie, Linda, Shonkwiler, Lara, Brister, J. Rodney, Karsch-Mizrachi, Ilene, and Nawrocki, Eric P.

Abstract

Background GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for non-influenza viral sequence submissions. Results We developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of “alerts” that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank’s submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. Unlike the previous submission-checking system, VADR is freely available (https://github.com/nawrockie/vadr) for local installation and use. VADR has been used for Norovirus submissions since May 2018 and for Dengue virus submissions since January 2019. Since March 2020, VADR has also been used to check SARS-CoV-2 sequence submissions. Other viruses with high numbers of submissions will be added incrementally. Conclusion VADR improves the speed with which non-flu virus submissions to GenBank can be checked and improves the content and quality of the GenBank annotations. The availability and portability of the soft

Published
2020

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