The Experts below are selected from a list of 501 Experts worldwide ranked by ideXlab platform

Peter Simmonds - One of the best experts on this subject based on the ideXlab platform.

  • The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification
    Microbiome, 2018
    Co-Authors: Pakorn Aiewsakun, Peter Simmonds
    Abstract:

    Background The International Committee on Taxonomy of Viruses (ICTV) classifies Viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of Viruses detected in environmental (metagenomic) studies that lack any phenotypic data. Results The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for Viruses of all genome configurations and genome sizes. The analysis pipeline that we have called ‘Genome Relationships Applied to Virus Taxonom y ’ (GRAViTy) was highly effective at reproducing the current assignments of Viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned Viruses from Unassigned Viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic Viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy. Conclusions A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.

  • the genomic underpinnings of eukaryotic virus taxonomy creating a sequence based framework for family level virus classification
    Microbiome, 2018
    Co-Authors: Pakorn Aiewsakun, Peter Simmonds
    Abstract:

    The International Committee on Taxonomy of Viruses (ICTV) classifies Viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of Viruses detected in environmental (metagenomic) studies that lack any phenotypic data. The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for Viruses of all genome configurations and genome sizes. The analysis pipeline that we have called ‘Genome Relationships Applied to Virus Taxonomy’ (GRAViTy) was highly effective at reproducing the current assignments of Viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned Viruses from Unassigned Viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic Viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy. A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.

Pakorn Aiewsakun - One of the best experts on this subject based on the ideXlab platform.

  • The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification
    Microbiome, 2018
    Co-Authors: Pakorn Aiewsakun, Peter Simmonds
    Abstract:

    Background The International Committee on Taxonomy of Viruses (ICTV) classifies Viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of Viruses detected in environmental (metagenomic) studies that lack any phenotypic data. Results The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for Viruses of all genome configurations and genome sizes. The analysis pipeline that we have called ‘Genome Relationships Applied to Virus Taxonom y ’ (GRAViTy) was highly effective at reproducing the current assignments of Viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned Viruses from Unassigned Viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic Viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy. Conclusions A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.

  • the genomic underpinnings of eukaryotic virus taxonomy creating a sequence based framework for family level virus classification
    Microbiome, 2018
    Co-Authors: Pakorn Aiewsakun, Peter Simmonds
    Abstract:

    The International Committee on Taxonomy of Viruses (ICTV) classifies Viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of Viruses detected in environmental (metagenomic) studies that lack any phenotypic data. The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for Viruses of all genome configurations and genome sizes. The analysis pipeline that we have called ‘Genome Relationships Applied to Virus Taxonomy’ (GRAViTy) was highly effective at reproducing the current assignments of Viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned Viruses from Unassigned Viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic Viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy. A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.

R. A. A. Vlugt - One of the best experts on this subject based on the ideXlab platform.

  • Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates
    Archives of Virology, 2020
    Co-Authors: A. M. Dullemans, M.j.d. Kock, C.e. Krom, M. Botermans, J. W. Roenhorst, I. J. E. Stulemeijer, M. Verbeek, M. Westenberg, R. A. A. Vlugt
    Abstract:

    To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related Unassigned Viruses be assigned to a new genus within the family Secoviridae , named “ Stralarivirus ”. Based on the phylogenetic analysis, this genus should include at least three Viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.

A. M. Dullemans - One of the best experts on this subject based on the ideXlab platform.

  • Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates
    Archives of Virology, 2020
    Co-Authors: A. M. Dullemans, M.j.d. Kock, C.e. Krom, M. Botermans, J. W. Roenhorst, I. J. E. Stulemeijer, M. Verbeek, M. Westenberg, R. A. A. Vlugt
    Abstract:

    To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related Unassigned Viruses be assigned to a new genus within the family Secoviridae , named “ Stralarivirus ”. Based on the phylogenetic analysis, this genus should include at least three Viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.

M.j.d. Kock - One of the best experts on this subject based on the ideXlab platform.

  • Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot
    2020
    Co-Authors: Dullemans A.m., Botermans M., M.j.d. Kock, C.e. Krom, Lee, T.a.j. Van Der, Roenhorst J.w., Stulemeijer I.j.e., Verbeek M., Westenberg M., Vlugt, R.a.a. Van Der
    Abstract:

    To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related Unassigned Viruses be assigned to a new genus within the family Secoviridae, named “Stralarivirus”. Based on the phylogenetic analysis, this genus should include at least three Viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV

  • Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates
    Archives of Virology, 2020
    Co-Authors: A. M. Dullemans, M.j.d. Kock, C.e. Krom, M. Botermans, J. W. Roenhorst, I. J. E. Stulemeijer, M. Verbeek, M. Westenberg, R. A. A. Vlugt
    Abstract:

    To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related Unassigned Viruses be assigned to a new genus within the family Secoviridae , named “ Stralarivirus ”. Based on the phylogenetic analysis, this genus should include at least three Viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.