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Viruses 2017, 9(9), 253; doi:10.3390/v9090253

Re-Assembly and Analysis of an Ancient Variola Virus Genome

Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
These authors contributed equally to this work.
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Received: 22 August 2017 / Revised: 4 September 2017 / Accepted: 5 September 2017 / Published: 8 September 2017
(This article belongs to the Special Issue Smallpox and Emerging Zoonotic Orthopoxviruses: What Is Coming Next?)
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Abstract

We report a major improvement to the assembly of published short read sequencing data from an ancient variola virus (VARV) genome by the removal of contig-capping sequencing tags and manual searches for gap-spanning reads. The new assembly, together with camelpox and taterapox genomes, permitted new dates to be calculated for the last common ancestor of all VARV genomes. The analysis of recently sequenced VARV-like cowpox virus genomes showed that single nucleotide polymorphisms (SNPs) and amino acid changes in the vaccinia virus (VACV)-Cop-O1L ortholog, predicted to be associated with VARV host specificity and virulence, were introduced into the lineage before the divergence of these viruses. A comparison of the ancient and modern VARV genome sequences also revealed a measurable drift towards adenine + thymine (A + T) richness. View Full-Text
Keywords: variola virus; cowpox; orthopoxvirus; virus virulence; phylogeny; smallpox; camelpox; taterapox; poxvirus variola virus; cowpox; orthopoxvirus; virus virulence; phylogeny; smallpox; camelpox; taterapox; poxvirus
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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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Smithson, C.; Imbery, J.; Upton, C. Re-Assembly and Analysis of an Ancient Variola Virus Genome. Viruses 2017, 9, 253.

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