Incongruencies in Vaccinia Virus Phylogenetic Trees
| dc.contributor.author | Smithson, Chad | |
| dc.contributor.author | Kampman, Samantha | |
| dc.contributor.author | Hetman, Benjamin M. | |
| dc.contributor.author | Upton, Chris | |
| dc.date.accessioned | 2016-06-28T19:17:28Z | |
| dc.date.available | 2016-06-28T19:17:28Z | |
| dc.date.copyright | 2014 | en_US |
| dc.date.issued | 2014-10 | |
| dc.description.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. | en_US |
| dc.description.reviewstatus | Reviewed | en_US |
| dc.description.scholarlevel | Faculty | en_US |
| dc.description.sponsorship | The authors thank the University of Victoria Computer Science Co-op students who have helped develop the Virology.ca bioinformatics tools, and especially Jeremy Ho for writing the python scripts, and Alex Purdy and Tim Van der Wekken for modifications to Base-By-Base. Funded by a Natural Sciences and Engineering Research Council Discovery Grant to Chris Upton. | en_US |
| dc.identifier.citation | Smithson, C., Kampman, S., Hetman, B.M., & Upton, C. (2014). Incongruencies in vaccinia virus phylogenetic trees. Computation, 2(4), 182-198. | en_US |
| dc.identifier.uri | http://dx.doi.org/10.3390/computation2040182 | |
| dc.identifier.uri | http://hdl.handle.net/1828/7374 | |
| dc.language.iso | en | en_US |
| dc.publisher | Computation | en_US |
| dc.rights | Attribution 2.5 Canada | * |
| dc.rights.uri | http://creativecommons.org/licenses/by/2.5/ca/ | * |
| dc.subject | poxvirus | en_US |
| dc.subject | phylogenetic tree | en_US |
| dc.subject | vaccinia virus | en_US |
| dc.subject | phylogeny | en_US |
| dc.subject | evolution | en_US |
| dc.subject | recombination | en_US |
| dc.subject | cowpox | en_US |
| dc.title | Incongruencies in Vaccinia Virus Phylogenetic Trees | en_US |
| dc.type | Article | en_US |