The Experts below are selected from a list of 48 Experts worldwide ranked by ideXlab platform
Jens H Kuhn - One of the best experts on this subject based on the ideXlab platform.
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Virus Nomenclature below the species level: a standardized Nomenclature for filoVirus strains and variants rescued from cDNA
Archives of Virology, 2014Co-Authors: Jens H Kuhn, Steven Bradfute, J. Rodney Brister, Alexander A. Bukreyev, Yíngyún Caì, Yīmíng Bào, Kristina Brauburger, Stephan Becker, Sina Bavari, Kartik ChandranAbstract:Specific alterations (mutations, deletions, insertions) of Virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated Viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified Virus genomes or parts thereof. A systematic Nomenclature for such recombinant Viruses is necessary to set them apart from wild-type and laboratory-adapted Viruses, and to improve communication and collaborations among researchers who may want to use recombinant Viruses or create novel Viruses based on them. A large group of filoVirus experts has recently proposed Nomenclatures for natural and laboratory animal-adapted filoViruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include Nomenclature for filoViruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filoVirus genetic variant naming, (/)///-, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoViruses. For instance, the full-length designation of an Ebola Virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to “Ebola Virus H.sapiens-rec/COD/1995/Kikwit-abc1” (with the suffix “rec” identifying the recombinant nature of the Virus and “abc1” being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as “EBOV H.sap/COD/95/Kik-abc1”) and abbreviations (such as “EBOV/Kik-abc1”) could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
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Virus Nomenclature below the species level a standardized Nomenclature for laboratory animal adapted strains and variants of Viruses assigned to the family filoviridae
Archives of Virology, 2013Co-Authors: Jens H Kuhn, Steven Bradfute, Alexander A. Bukreyev, Yíngyún Caì, Kartik Chandran, Stephan Becker, Sina Bavari, Rodney J Brister, Yiming Bao, Robert A. DaveyAbstract:The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of Viruses into taxa, but is not responsible for the Nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of Viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and Nomenclature for filoViruses. Subsequently, and together with numerous other filoVirus experts, a consistent Nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoViruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filoVirus genetic variant naming ( / / / - ) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola Virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola Virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filoVirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
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Virus Nomenclature below the species level: a standardized Nomenclature for natural variants of Viruses assigned to the family Filoviridae
Archives of Virology, 2013Co-Authors: Jens H Kuhn, Steven Bradfute, Alexander A. Bukreyev, Kartik Chandran, Stephan Becker, Sina Bavari, J. Rodney Brister, Robert A. Davey, Olga Dolnik, Sven EnterleinAbstract:The task of international expert groups is to recommend the classification and naming of Viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and Nomenclature for filoViruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length Virus names (such as “Ebola Virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the Virus (e.g., Ebola Virus), isolation host (e.g., members of the species Homo sapiens ), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzaVirus Nomenclature and the Nomenclature recently proposed for rotaViruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this Nomenclature would increase the general understanding of filoVirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.
Kartik Chandran - One of the best experts on this subject based on the ideXlab platform.
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Virus Nomenclature below the species level: a standardized Nomenclature for filoVirus strains and variants rescued from cDNA
Archives of Virology, 2014Co-Authors: Jens H Kuhn, Steven Bradfute, J. Rodney Brister, Alexander A. Bukreyev, Yíngyún Caì, Yīmíng Bào, Kristina Brauburger, Stephan Becker, Sina Bavari, Kartik ChandranAbstract:Specific alterations (mutations, deletions, insertions) of Virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated Viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified Virus genomes or parts thereof. A systematic Nomenclature for such recombinant Viruses is necessary to set them apart from wild-type and laboratory-adapted Viruses, and to improve communication and collaborations among researchers who may want to use recombinant Viruses or create novel Viruses based on them. A large group of filoVirus experts has recently proposed Nomenclatures for natural and laboratory animal-adapted filoViruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include Nomenclature for filoViruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filoVirus genetic variant naming, (/)///-, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoViruses. For instance, the full-length designation of an Ebola Virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to “Ebola Virus H.sapiens-rec/COD/1995/Kikwit-abc1” (with the suffix “rec” identifying the recombinant nature of the Virus and “abc1” being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as “EBOV H.sap/COD/95/Kik-abc1”) and abbreviations (such as “EBOV/Kik-abc1”) could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
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Virus Nomenclature below the species level a standardized Nomenclature for laboratory animal adapted strains and variants of Viruses assigned to the family filoviridae
Archives of Virology, 2013Co-Authors: Jens H Kuhn, Steven Bradfute, Alexander A. Bukreyev, Yíngyún Caì, Kartik Chandran, Stephan Becker, Sina Bavari, Rodney J Brister, Yiming Bao, Robert A. DaveyAbstract:The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of Viruses into taxa, but is not responsible for the Nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of Viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and Nomenclature for filoViruses. Subsequently, and together with numerous other filoVirus experts, a consistent Nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoViruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filoVirus genetic variant naming ( / / / - ) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola Virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola Virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filoVirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
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Virus Nomenclature below the species level: a standardized Nomenclature for natural variants of Viruses assigned to the family Filoviridae
Archives of Virology, 2013Co-Authors: Jens H Kuhn, Steven Bradfute, Alexander A. Bukreyev, Kartik Chandran, Stephan Becker, Sina Bavari, J. Rodney Brister, Robert A. Davey, Olga Dolnik, Sven EnterleinAbstract:The task of international expert groups is to recommend the classification and naming of Viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and Nomenclature for filoViruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length Virus names (such as “Ebola Virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the Virus (e.g., Ebola Virus), isolation host (e.g., members of the species Homo sapiens ), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzaVirus Nomenclature and the Nomenclature recently proposed for rotaViruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this Nomenclature would increase the general understanding of filoVirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.
Steven Bradfute - One of the best experts on this subject based on the ideXlab platform.
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Virus Nomenclature below the species level: a standardized Nomenclature for filoVirus strains and variants rescued from cDNA
Archives of Virology, 2014Co-Authors: Jens H Kuhn, Steven Bradfute, J. Rodney Brister, Alexander A. Bukreyev, Yíngyún Caì, Yīmíng Bào, Kristina Brauburger, Stephan Becker, Sina Bavari, Kartik ChandranAbstract:Specific alterations (mutations, deletions, insertions) of Virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated Viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified Virus genomes or parts thereof. A systematic Nomenclature for such recombinant Viruses is necessary to set them apart from wild-type and laboratory-adapted Viruses, and to improve communication and collaborations among researchers who may want to use recombinant Viruses or create novel Viruses based on them. A large group of filoVirus experts has recently proposed Nomenclatures for natural and laboratory animal-adapted filoViruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include Nomenclature for filoViruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filoVirus genetic variant naming, (/)///-, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoViruses. For instance, the full-length designation of an Ebola Virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to “Ebola Virus H.sapiens-rec/COD/1995/Kikwit-abc1” (with the suffix “rec” identifying the recombinant nature of the Virus and “abc1” being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as “EBOV H.sap/COD/95/Kik-abc1”) and abbreviations (such as “EBOV/Kik-abc1”) could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
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Virus Nomenclature below the species level a standardized Nomenclature for laboratory animal adapted strains and variants of Viruses assigned to the family filoviridae
Archives of Virology, 2013Co-Authors: Jens H Kuhn, Steven Bradfute, Alexander A. Bukreyev, Yíngyún Caì, Kartik Chandran, Stephan Becker, Sina Bavari, Rodney J Brister, Yiming Bao, Robert A. DaveyAbstract:The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of Viruses into taxa, but is not responsible for the Nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of Viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and Nomenclature for filoViruses. Subsequently, and together with numerous other filoVirus experts, a consistent Nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoViruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filoVirus genetic variant naming ( / / / - ) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola Virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola Virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filoVirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
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Virus Nomenclature below the species level: a standardized Nomenclature for natural variants of Viruses assigned to the family Filoviridae
Archives of Virology, 2013Co-Authors: Jens H Kuhn, Steven Bradfute, Alexander A. Bukreyev, Kartik Chandran, Stephan Becker, Sina Bavari, J. Rodney Brister, Robert A. Davey, Olga Dolnik, Sven EnterleinAbstract:The task of international expert groups is to recommend the classification and naming of Viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and Nomenclature for filoViruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length Virus names (such as “Ebola Virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the Virus (e.g., Ebola Virus), isolation host (e.g., members of the species Homo sapiens ), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzaVirus Nomenclature and the Nomenclature recently proposed for rotaViruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this Nomenclature would increase the general understanding of filoVirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.
Sina Bavari - One of the best experts on this subject based on the ideXlab platform.
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Virus Nomenclature below the species level: a standardized Nomenclature for filoVirus strains and variants rescued from cDNA
Archives of Virology, 2014Co-Authors: Jens H Kuhn, Steven Bradfute, J. Rodney Brister, Alexander A. Bukreyev, Yíngyún Caì, Yīmíng Bào, Kristina Brauburger, Stephan Becker, Sina Bavari, Kartik ChandranAbstract:Specific alterations (mutations, deletions, insertions) of Virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated Viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified Virus genomes or parts thereof. A systematic Nomenclature for such recombinant Viruses is necessary to set them apart from wild-type and laboratory-adapted Viruses, and to improve communication and collaborations among researchers who may want to use recombinant Viruses or create novel Viruses based on them. A large group of filoVirus experts has recently proposed Nomenclatures for natural and laboratory animal-adapted filoViruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include Nomenclature for filoViruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filoVirus genetic variant naming, (/)///-, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoViruses. For instance, the full-length designation of an Ebola Virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to “Ebola Virus H.sapiens-rec/COD/1995/Kikwit-abc1” (with the suffix “rec” identifying the recombinant nature of the Virus and “abc1” being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as “EBOV H.sap/COD/95/Kik-abc1”) and abbreviations (such as “EBOV/Kik-abc1”) could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
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Virus Nomenclature below the species level a standardized Nomenclature for laboratory animal adapted strains and variants of Viruses assigned to the family filoviridae
Archives of Virology, 2013Co-Authors: Jens H Kuhn, Steven Bradfute, Alexander A. Bukreyev, Yíngyún Caì, Kartik Chandran, Stephan Becker, Sina Bavari, Rodney J Brister, Yiming Bao, Robert A. DaveyAbstract:The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of Viruses into taxa, but is not responsible for the Nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of Viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and Nomenclature for filoViruses. Subsequently, and together with numerous other filoVirus experts, a consistent Nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoViruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filoVirus genetic variant naming ( / / / - ) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola Virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola Virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filoVirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
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Virus Nomenclature below the species level: a standardized Nomenclature for natural variants of Viruses assigned to the family Filoviridae
Archives of Virology, 2013Co-Authors: Jens H Kuhn, Steven Bradfute, Alexander A. Bukreyev, Kartik Chandran, Stephan Becker, Sina Bavari, J. Rodney Brister, Robert A. Davey, Olga Dolnik, Sven EnterleinAbstract:The task of international expert groups is to recommend the classification and naming of Viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and Nomenclature for filoViruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length Virus names (such as “Ebola Virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the Virus (e.g., Ebola Virus), isolation host (e.g., members of the species Homo sapiens ), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzaVirus Nomenclature and the Nomenclature recently proposed for rotaViruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this Nomenclature would increase the general understanding of filoVirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.
Stephan Becker - One of the best experts on this subject based on the ideXlab platform.
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Virus Nomenclature below the species level: a standardized Nomenclature for filoVirus strains and variants rescued from cDNA
Archives of Virology, 2014Co-Authors: Jens H Kuhn, Steven Bradfute, J. Rodney Brister, Alexander A. Bukreyev, Yíngyún Caì, Yīmíng Bào, Kristina Brauburger, Stephan Becker, Sina Bavari, Kartik ChandranAbstract:Specific alterations (mutations, deletions, insertions) of Virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated Viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified Virus genomes or parts thereof. A systematic Nomenclature for such recombinant Viruses is necessary to set them apart from wild-type and laboratory-adapted Viruses, and to improve communication and collaborations among researchers who may want to use recombinant Viruses or create novel Viruses based on them. A large group of filoVirus experts has recently proposed Nomenclatures for natural and laboratory animal-adapted filoViruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include Nomenclature for filoViruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filoVirus genetic variant naming, (/)///-, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoViruses. For instance, the full-length designation of an Ebola Virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to “Ebola Virus H.sapiens-rec/COD/1995/Kikwit-abc1” (with the suffix “rec” identifying the recombinant nature of the Virus and “abc1” being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as “EBOV H.sap/COD/95/Kik-abc1”) and abbreviations (such as “EBOV/Kik-abc1”) could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
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Virus Nomenclature below the species level a standardized Nomenclature for laboratory animal adapted strains and variants of Viruses assigned to the family filoviridae
Archives of Virology, 2013Co-Authors: Jens H Kuhn, Steven Bradfute, Alexander A. Bukreyev, Yíngyún Caì, Kartik Chandran, Stephan Becker, Sina Bavari, Rodney J Brister, Yiming Bao, Robert A. DaveyAbstract:The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of Viruses into taxa, but is not responsible for the Nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of Viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and Nomenclature for filoViruses. Subsequently, and together with numerous other filoVirus experts, a consistent Nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoViruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filoVirus genetic variant naming ( / / / - ) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola Virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola Virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filoVirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
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Virus Nomenclature below the species level: a standardized Nomenclature for natural variants of Viruses assigned to the family Filoviridae
Archives of Virology, 2013Co-Authors: Jens H Kuhn, Steven Bradfute, Alexander A. Bukreyev, Kartik Chandran, Stephan Becker, Sina Bavari, J. Rodney Brister, Robert A. Davey, Olga Dolnik, Sven EnterleinAbstract:The task of international expert groups is to recommend the classification and naming of Viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and Nomenclature for filoViruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length Virus names (such as “Ebola Virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the Virus (e.g., Ebola Virus), isolation host (e.g., members of the species Homo sapiens ), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzaVirus Nomenclature and the Nomenclature recently proposed for rotaViruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this Nomenclature would increase the general understanding of filoVirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.
