A phylogenomic study of the genus Alphavirus employing whole genome comparison

Aimée J. Luers, Sandra Adams, John V. Smalley, James Campanella

Research output: Contribution to journalArticleResearchpeer-review

18 Citations (Scopus)

Abstract

The phylogenetics of the genus Alphavirus have historically been characterized using partial gene, single gene or partial proteomic data. We have mined cDNA and amino acid sequences from GenBank for all fully sequenced and some partially sequenced alphaviruses and generated phylogenomic analyses of the genus Alphavirus genus, employing capsid encoding structural regions, non-structural coding regions and complete viral genomes. Our studies support the presence of the previously reported recombination event that produced the Western Equine Encephalitis clade, and confirm many of the patterns of geographic radiation and divergence of the multiple species. Our data suggest that the Salmon Pancreatic Disease Virus and Sleeping Disease Virus are sufficiently divergent to form a separate clade from the other alphaviruses. Also, unlike previously reported studies employing limited sequence data for correlation of phylogeny, our results indicate that the Barmah Forest Virus and Middelburg Virus appear to be members of the Semliki Forest clade. Additionally, our analysis indicates that the Southern Elephant Seal Virus is part of the Semliki Forest clade, although still phylogenetically distant from all known members of the genus Alphavirus. Finally, we demonstrate that the whole Rubella viral genome provides an ideal outgroup for phylogenomic studies of the genus Alphavirus.

Original languageEnglish
Pages (from-to)217-227
Number of pages11
JournalComparative and Functional Genomics
Volume6
Issue number4
DOIs
StatePublished - 1 Jun 2005

Fingerprint

Alphavirus
Genome
Viral Genome
Viruses
Western Equine Encephalomyelitis
Earless Seals
Pancreatic Diseases
Rubella
Salmon
Capsid
Nucleic Acid Databases
Virus Diseases
Phylogeny
Proteomics
Genetic Recombination
Genes
Amino Acid Sequence
Complementary DNA
Radiation

Keywords

  • Alphavirus
  • Phylogenetics
  • Phylogenomics
  • Semliki Forest Virus
  • Sindbis Virus
  • Togaviridae

Cite this

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abstract = "The phylogenetics of the genus Alphavirus have historically been characterized using partial gene, single gene or partial proteomic data. We have mined cDNA and amino acid sequences from GenBank for all fully sequenced and some partially sequenced alphaviruses and generated phylogenomic analyses of the genus Alphavirus genus, employing capsid encoding structural regions, non-structural coding regions and complete viral genomes. Our studies support the presence of the previously reported recombination event that produced the Western Equine Encephalitis clade, and confirm many of the patterns of geographic radiation and divergence of the multiple species. Our data suggest that the Salmon Pancreatic Disease Virus and Sleeping Disease Virus are sufficiently divergent to form a separate clade from the other alphaviruses. Also, unlike previously reported studies employing limited sequence data for correlation of phylogeny, our results indicate that the Barmah Forest Virus and Middelburg Virus appear to be members of the Semliki Forest clade. Additionally, our analysis indicates that the Southern Elephant Seal Virus is part of the Semliki Forest clade, although still phylogenetically distant from all known members of the genus Alphavirus. Finally, we demonstrate that the whole Rubella viral genome provides an ideal outgroup for phylogenomic studies of the genus Alphavirus.",
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A phylogenomic study of the genus Alphavirus employing whole genome comparison. / Luers, Aimée J.; Adams, Sandra; Smalley, John V.; Campanella, James.

In: Comparative and Functional Genomics, Vol. 6, No. 4, 01.06.2005, p. 217-227.

Research output: Contribution to journalArticleResearchpeer-review

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