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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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Autores principales: 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, 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189044/
https://www.ncbi.nlm.nih.gov/pubmed/25256396
http://dx.doi.org/10.3390/v6093663
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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
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_facet 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
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 PubMed
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.
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spelling pubmed-41890442014-10-08 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 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. Viruses Letter 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. MDPI 2014-09-26 /pmc/articles/PMC4189044/ /pubmed/25256396 http://dx.doi.org/10.3390/v6093663 Text en © 2014 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Letter
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
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
topic Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189044/
https://www.ncbi.nlm.nih.gov/pubmed/25256396
http://dx.doi.org/10.3390/v6093663
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