Using genomic sequencing to explore vaccinia virus diversity, recombination and evolution

• Author / Creator

  Qin, Li

• Smallpox was eradicated using vaccinia viruses (VACV) as vaccines, including Dryvax, a calf-lymph vaccine derived from the New York City Board of Health (NYCBH) strain, and TianTan, a chicken egg cultured vaccine used exclusively in China. To take advantage of the next generation sequencing technology, this thesis examined the genetic diversity of the population of viruses present in a sample of Dryvax and TianTan stocks. In Dryvax stock, any two clones differ by approximately 570 SNPs (single nucleotide polymophism), exhibiting a patchy pattern of polymorphic sites across the whole genome due to recombination. In addition, 110 small indels (insertion and deletion) were observed in the Dryvax stock. Over 85% of indels are associated with repeats and a rare naturally attenuated virus bearing a large deletion in the right telomere (DPP17) was also identified. In contrast, there are barely any SNPs and indels detected in the TianTan clones, suggesting that this stock has been cloned previously. Two different subclones were detected; TP03 encoding large deletions in the terminal repeats that extend into both VEGF (vaccinia epithelial growth factor) genes and create a small plaque variant, and TP05 having the longest genome in all TianTan clones.
  To further study the mechanism of poxvirus recombination, I coinfected two of my sequenced viruses (TP05 and DPP17) and used the different SNPs to track the origin of progeny recombinants. My studies showed that recombinants contain a patchwork of DNA fragments, with the number of exchanges increasing with passage. Further passage also selected for TianTan DNA and correlated with increased plaque size. The recombinants produced through a single round of co-infection exhibited a bias towards the short conversion tracks (<1 kbp) and exhibited 1 exchange per 12 kbp, close to the ~1 per 8 kbp in the literature.
  Finally, I explored the possible origin of VACVs and evolutionary relationship among extant VACVs. My study showed that VACV is probably derived from a horsepox-like virus by reductive evolution. An intermediate virus has been suggested to originate from horsepox virus and serve as an ancestral strain for all other extant VACVs. A model of illegitimate recombination is proposed to help explain this evolutionary process.

• Subjects / Keywords

  • Diversity
  • Evolution
  • Vaccinia virus
  • Next generation sequencing (NGS)
  • Recombination

• Graduation date

  Fall 2014

• Type of Item

  Thesis

• Degree

  Doctor of Philosophy

• DOI

  https://doi.org/10.7939/R30C4ST2D

• License

  This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.