Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names
Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-ex...
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| Format: | Article |
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MDPI AG
2019
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| Online Access: | https://hdl.handle.net/1721.1/121454 |
| _version_ | 1826193019434434560 |
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| author | Kuhn, Jens H. Andersen, Kristian G. Bào, Yīmíng Bavari, Sina Becker, Stephan Bennett, Richard S. Bergman, Nicholas H. Blinkova, Olga Bradfute, Steven Brister, J. Rodney Bukreyev, Alexander Chandran, Kartik Chepurnov, Alexander A. Davey, Robert A. Dietzgen, Ralf G. Doggett, Norman A. Dolnik, Olga Dye, John M. Enterlein, Sven Fenimore, Paul W. Formenty, Pierre Freiberg, Alexander N. Garry, Robert F. Garza, Nicole L. Gire, Stephen K. Gonzalez, Jean-Paul Griffiths, Anthony Happi, Christian T. Hensley, Lisa E. Herbert, Andrew S. Hevey, Michael C. Hoenen, Thomas Honko, Anna N. Ignatyev, Georgy M. Jahrling, Peter B. Johnson, Joshua C. Johnson, Karl M. Kindrachuk, Jason Klenk, Hans-Dieter Kobinger, Gary Kochel, Tadeusz J. Lackemeyer, Matthew G. Lackner, Daniel F. Leroy, Eric M. Lever, Mark S. Mühlberger, Elke Netesov, Sergey V. Olinger, Gene G. Omilabu, Sunday A. Palacios, Gustavo Panchal, Rekha G. Park, Daniel J. Patterson, Jean L. Paweska, Janusz T. Peters, Clarence J. Pettitt, James Pitt, Louise Radoshitzky, Sheli R. Ryabchikova, Elena I. Saphire, Erica Ollmann Sabeti, Pardis C. Sealfon, Rachel Sima Shestopalov, Aleksandr M. Smither, Sophie J. Sullivan, Nancy J. Swanepoel, Robert Takada, Ayato Towner, Jonathan S. Van der Groen, Guido Volchkov, Viktor E. Volchkova, Valentina A. Wahl-Jensen, Victoria Warren, Travis K. Warfield, Kelly L. Weidmann, Manfred Nichol, Stuart T. |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Kuhn, Jens H. Andersen, Kristian G. Bào, Yīmíng Bavari, Sina Becker, Stephan Bennett, Richard S. Bergman, Nicholas H. Blinkova, Olga Bradfute, Steven Brister, J. Rodney Bukreyev, Alexander Chandran, Kartik Chepurnov, Alexander A. Davey, Robert A. Dietzgen, Ralf G. Doggett, Norman A. Dolnik, Olga Dye, John M. Enterlein, Sven Fenimore, Paul W. Formenty, Pierre Freiberg, Alexander N. Garry, Robert F. Garza, Nicole L. Gire, Stephen K. Gonzalez, Jean-Paul Griffiths, Anthony Happi, Christian T. Hensley, Lisa E. Herbert, Andrew S. Hevey, Michael C. Hoenen, Thomas Honko, Anna N. Ignatyev, Georgy M. Jahrling, Peter B. Johnson, Joshua C. Johnson, Karl M. Kindrachuk, Jason Klenk, Hans-Dieter Kobinger, Gary Kochel, Tadeusz J. Lackemeyer, Matthew G. Lackner, Daniel F. Leroy, Eric M. Lever, Mark S. Mühlberger, Elke Netesov, Sergey V. Olinger, Gene G. Omilabu, Sunday A. Palacios, Gustavo Panchal, Rekha G. Park, Daniel J. Patterson, Jean L. Paweska, Janusz T. Peters, Clarence J. Pettitt, James Pitt, Louise Radoshitzky, Sheli R. Ryabchikova, Elena I. Saphire, Erica Ollmann Sabeti, Pardis C. Sealfon, Rachel Sima Shestopalov, Aleksandr M. Smither, Sophie J. Sullivan, Nancy J. Swanepoel, Robert Takada, Ayato Towner, Jonathan S. Van der Groen, Guido Volchkov, Viktor E. Volchkova, Valentina A. Wahl-Jensen, Victoria Warren, Travis K. Warfield, Kelly L. Weidmann, Manfred Nichol, Stuart T. |
| author_sort | Kuhn, Jens H. |
| collection | MIT |
| description | Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [<virus name> (<strain>)/<;isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences. Keywords: Bundibugyo virus; cDNA clone; cuevavirus; Ebola; Ebola virus; ebolavirus; filovirid; Filoviridae; filovirus; genome annotation; ICTV; International Committee on Taxonomy of Viruses; Lloviu virus; Marburg virus; marburgvirus; mononegavirad; Mononegavirales; mononegavirus; Ravn virus; RefSeq; Reston virus; reverse genetics; Sudan virus; Taï Forest virus; virus classification; virus isolate; virus nomenclature; virus strain; virus taxonomy; virus variant |
| first_indexed | 2024-09-23T09:32:23Z |
| format | Article |
| id | mit-1721.1/121454 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T09:32:23Z |
| publishDate | 2019 |
| publisher | MDPI AG |
| record_format | dspace |
| spelling | mit-1721.1/1214542022-09-30T15:11:47Z Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names Kuhn, Jens H. Andersen, Kristian G. Bào, Yīmíng Bavari, Sina Becker, Stephan Bennett, Richard S. Bergman, Nicholas H. Blinkova, Olga Bradfute, Steven Brister, J. Rodney Bukreyev, Alexander Chandran, Kartik Chepurnov, Alexander A. Davey, Robert A. Dietzgen, Ralf G. Doggett, Norman A. Dolnik, Olga Dye, John M. Enterlein, Sven Fenimore, Paul W. Formenty, Pierre Freiberg, Alexander N. Garry, Robert F. Garza, Nicole L. Gire, Stephen K. Gonzalez, Jean-Paul Griffiths, Anthony Happi, Christian T. Hensley, Lisa E. Herbert, Andrew S. Hevey, Michael C. Hoenen, Thomas Honko, Anna N. Ignatyev, Georgy M. Jahrling, Peter B. Johnson, Joshua C. Johnson, Karl M. Kindrachuk, Jason Klenk, Hans-Dieter Kobinger, Gary Kochel, Tadeusz J. Lackemeyer, Matthew G. Lackner, Daniel F. Leroy, Eric M. Lever, Mark S. Mühlberger, Elke Netesov, Sergey V. Olinger, Gene G. Omilabu, Sunday A. Palacios, Gustavo Panchal, Rekha G. Park, Daniel J. Patterson, Jean L. Paweska, Janusz T. Peters, Clarence J. Pettitt, James Pitt, Louise Radoshitzky, Sheli R. Ryabchikova, Elena I. Saphire, Erica Ollmann Sabeti, Pardis C. Sealfon, Rachel Sima Shestopalov, Aleksandr M. Smither, Sophie J. Sullivan, Nancy J. Swanepoel, Robert Takada, Ayato Towner, Jonathan S. Van der Groen, Guido Volchkov, Viktor E. Volchkova, Valentina A. Wahl-Jensen, Victoria Warren, Travis K. Warfield, Kelly L. Weidmann, Manfred Nichol, Stuart T. Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [<virus name> (<strain>)/<;isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences. Keywords: Bundibugyo virus; cDNA clone; cuevavirus; Ebola; Ebola virus; ebolavirus; filovirid; Filoviridae; filovirus; genome annotation; ICTV; International Committee on Taxonomy of Viruses; Lloviu virus; Marburg virus; marburgvirus; mononegavirad; Mononegavirales; mononegavirus; Ravn virus; RefSeq; Reston virus; reverse genetics; Sudan virus; Taï Forest virus; virus classification; virus isolate; virus nomenclature; virus strain; virus taxonomy; virus variant 2019-06-28T16:17:38Z 2019-06-28T16:17:38Z 2014-09-26 2014-09 2019-03-29T19:39:42Z Article http://purl.org/eprint/type/JournalArticle 1999-4915 https://hdl.handle.net/1721.1/121454 Kuhn, Jens H. et al. "Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names." Viruses 6, 9(September 2014): 3663-3682 © 2014 The Authors http://dx.doi.org/10.3390/v6093663 Viruses Creative Commons Attribution 3.0 unported license https://creativecommons.org/licenses/by/3.0/ application/pdf MDPI AG Multidisciplinary Digital Publishing Institute |
| spellingShingle | Kuhn, Jens H. Andersen, Kristian G. Bào, Yīmíng Bavari, Sina Becker, Stephan Bennett, Richard S. Bergman, Nicholas H. Blinkova, Olga Bradfute, Steven Brister, J. Rodney Bukreyev, Alexander Chandran, Kartik Chepurnov, Alexander A. Davey, Robert A. Dietzgen, Ralf G. Doggett, Norman A. Dolnik, Olga Dye, John M. Enterlein, Sven Fenimore, Paul W. Formenty, Pierre Freiberg, Alexander N. Garry, Robert F. Garza, Nicole L. Gire, Stephen K. Gonzalez, Jean-Paul Griffiths, Anthony Happi, Christian T. Hensley, Lisa E. Herbert, Andrew S. Hevey, Michael C. Hoenen, Thomas Honko, Anna N. Ignatyev, Georgy M. Jahrling, Peter B. Johnson, Joshua C. Johnson, Karl M. Kindrachuk, Jason Klenk, Hans-Dieter Kobinger, Gary Kochel, Tadeusz J. Lackemeyer, Matthew G. Lackner, Daniel F. Leroy, Eric M. Lever, Mark S. Mühlberger, Elke Netesov, Sergey V. Olinger, Gene G. Omilabu, Sunday A. Palacios, Gustavo Panchal, Rekha G. Park, Daniel J. Patterson, Jean L. Paweska, Janusz T. Peters, Clarence J. Pettitt, James Pitt, Louise Radoshitzky, Sheli R. Ryabchikova, Elena I. Saphire, Erica Ollmann Sabeti, Pardis C. Sealfon, Rachel Sima Shestopalov, Aleksandr M. Smither, Sophie J. Sullivan, Nancy J. Swanepoel, Robert Takada, Ayato Towner, Jonathan S. Van der Groen, Guido Volchkov, Viktor E. Volchkova, Valentina A. Wahl-Jensen, Victoria Warren, Travis K. Warfield, Kelly L. Weidmann, Manfred Nichol, Stuart T. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title | Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title_full | Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title_fullStr | Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title_full_unstemmed | Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title_short | Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title_sort | filovirus refseq entries evaluation and selection of filovirus type variants type sequences and names |
| url | https://hdl.handle.net/1721.1/121454 |
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