Incongruencies in Vaccinia Virus Phylogenetic Trees
| Autor: | Samantha Kampman, Benjamin M. Hetman, Chris Upton, Chad Smithson |
|---|---|
| Rok vydání: | 2014 |
| Předmět: |
General Computer Science
viruses Cowpox Biology phylogeny complex mixtures Genome lcsh:QA75.5-76.95 Theoretical Computer Science chemistry.chemical_compound Phylogenetics evolution medicine phylogenetic tree Orthopoxvirus Clade Genetics Phylogenetic tree Applied Mathematics Cowpox virus virus diseases biochemical phenomena metabolism and nutrition cowpox medicine.disease biology.organism_classification vaccinia virus recombination poxvirus chemistry Modeling and Simulation lcsh:Electronic computers. Computer science Vaccinia |
| Zdroj: | Computation Volume 2 Issue 4 Pages 182-198 Computation, Vol 2, Iss 4, Pp 182-198 (2014) |
| ISSN: | 2079-3197 |
| DOI: | 10.3390/computation2040182 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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