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Computation 2014, 2(4), 182-198; doi:10.3390/computation2040182

Incongruencies in Vaccinia Virus Phylogenetic Trees

1
Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
2
Current address: Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 30 June 2014 / Revised: 22 September 2014 / Accepted: 29 September 2014 / Published: 14 October 2014
(This article belongs to the Special Issue Genomes and Evolution: Computational Approaches)
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Abstract

Over the years, as more complete poxvirus genomes have been sequenced, phylogenetic studies of these viruses have become more prevalent. In general, the results show similar relationships between the poxvirus species; however, some inconsistencies are notable. Previous analyses of the viral genomes contained within the vaccinia virus (VACV)-Dryvax vaccine revealed that their phylogenetic relationships were sometimes clouded by low bootstrapping confidence. To analyze the VACV-Dryvax genomes in detail, a new tool-set was developed and integrated into the Base-By-Base bioinformatics software package. Analyses showed that fewer unique positions were present in each VACV-Dryvax genome than expected. A series of patterns, each containing several single nucleotide polymorphisms (SNPs) were identified that were counter to the results of the phylogenetic analysis. The VACV genomes were found to contain short DNA sequence blocks that matched more distantly related clades. Additionally, similar non-conforming SNP patterns were observed in (1) the variola virus clade; (2) some cowpox clades; and (3) VACV-CVA, the direct ancestor of VACV-MVA. Thus, traces of past recombination events are common in the various orthopoxvirus clades, including those associated with smallpox and cowpox viruses. View Full-Text
Keywords: poxvirus; phylogenetic tree; vaccinia virus; phylogeny; evolution; recombination; cowpox poxvirus; phylogenetic tree; vaccinia virus; phylogeny; evolution; recombination; cowpox
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Smithson, C.; Kampman, S.; Hetman, B.M.; Upton, C. Incongruencies in Vaccinia Virus Phylogenetic Trees. Computation 2014, 2, 182-198.

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