A1 Refereed original research article in a scientific journal
Molecular phylogenetic analysis of bovine viral diarrhoea virus: A Bayesian approach
Authors: Xia H, Liu L, Wahlberg N, Baule C, Belak S
Publisher: ELSEVIER SCIENCE BV
Publication year: 2007
Journal:: Virus Research
Journal name in source: VIRUS RESEARCH
Journal acronym: VIRUS RES
Volume: 130
Issue: 1-2
First page : 53
Last page: 62
Number of pages: 10
ISSN: 0168-1702
DOI: https://doi.org/10.1016/j.virusres.2007.05.017
Abstract
Genetic typing of bovine viral diarrhoea virus (BVDV) is important for precise classification of viruses. Traditionally, inferring BVDV phylogeny has been performed by distance-based method, i.e. neighbor-joining for single genes. In this study, 4 Bayesian approach was exploited to analyze five genetic regions of BVDV genome (5' UTR, N-pro, E2a, E2b, and NS3) for 68 taxa retrieved from GenBank. The results showed that all taxa in the consensus tree of E2a have been assigned correctly to corresponding groups, i.e. type-2 BVDV, and BVDV-1a, -lb, -1c, -le, and -1g, supported by a high posterior probability. In contrast, subgroup I a formed polytomies in the consensus trees of 5' UTR and NS3. Polytomies also appeared among the subgroup 1b in the consensus trees of N-pro and E2b. Analysis of a combined dataset produced an unambiguous, well-supported phylogenetic hypothesis. The topologies found for each genetic region separately and combined were different, but the differences were mainly weakly supported by the data. Combining the data allowed the identification of well-supported clades of strains that correspond to, some of the previously defined subgroups. Only a combined approach will allow the confident placement of new strains in the current classification of viruses into genotype and subgenotype. (c) 2007 Elsevier B.V. All rights reserved.
Genetic typing of bovine viral diarrhoea virus (BVDV) is important for precise classification of viruses. Traditionally, inferring BVDV phylogeny has been performed by distance-based method, i.e. neighbor-joining for single genes. In this study, 4 Bayesian approach was exploited to analyze five genetic regions of BVDV genome (5' UTR, N-pro, E2a, E2b, and NS3) for 68 taxa retrieved from GenBank. The results showed that all taxa in the consensus tree of E2a have been assigned correctly to corresponding groups, i.e. type-2 BVDV, and BVDV-1a, -lb, -1c, -le, and -1g, supported by a high posterior probability. In contrast, subgroup I a formed polytomies in the consensus trees of 5' UTR and NS3. Polytomies also appeared among the subgroup 1b in the consensus trees of N-pro and E2b. Analysis of a combined dataset produced an unambiguous, well-supported phylogenetic hypothesis. The topologies found for each genetic region separately and combined were different, but the differences were mainly weakly supported by the data. Combining the data allowed the identification of well-supported clades of strains that correspond to, some of the previously defined subgroups. Only a combined approach will allow the confident placement of new strains in the current classification of viruses into genotype and subgenotype. (c) 2007 Elsevier B.V. All rights reserved.
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