1887

Abstract

Relationships among varicella-zoster virus (VZV; ) genome sequences were examined to evaluate descent of strains, structures of lineages and incidence of recombination events. Eighteen complete, published genome sequences were aligned and 494 single nucleotide polymorphisms (SNPs) extracted, each as two alleles. At 281 SNPs, a single sequence differed from all the others. Distributions of the remaining 213 SNPs indicated that the sequences fell into five groups, which coincided with previously recognized phylogenetic groupings, termed E1, E2, J, M1 and M2. The 213-SNP set was divisible into 104 SNPs that were specific to a single group, and 109 cross-group SNPs that defined relationships among groups. This last set was evaluated by criteria of continuities in relationships between groups and breaks in such patterns, to identify crossover points and ascribe them to lineages. For the 99 cross-group SNPs in the genome's long unique region, it was seen that the E2 and M2 groups were almost completely distinct in their SNP alleles, and the E1 group was derived from a recombinant of E2 and M2. A valid phylogenetic tree could thus be constructed for the four E2 and two M2 strains. There was no substantive evidence for recombination within the E2 group or the E1 group (ten strains). The J and M1 groups each contained only one strain, and both were interpreted as having substantial distinct histories plus possible recombinant elements from the E2 and M2 lineages. The view of VZV recombination and phylogeny reached represents a major clarification of deep relationships among VZV lineages.

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2009-04-01
2024-11-02
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References

  1. Barrett Muir W., Nichols R., Breuer J. 2002; Phylogenetic analysis of varicella-zoster virus: evidence of intercontinental spread of genotypes and recombination. J Virol 76:1971–1979 [CrossRef]
    [Google Scholar]
  2. Davison A. J. 1984; Structure of the genome termini of varicella-zoster virus. J Gen Virol 65:1969–1977 [CrossRef]
    [Google Scholar]
  3. Davison A. J., Scott J. E. 1986; The complete DNA sequence of varicella-zoster virus. J Gen Virol 67:1759–1816 [CrossRef]
    [Google Scholar]
  4. Dumas A. M., Geelen J. L. M. C., Weststrate M. W., Wertheim P., van der Noordaa J. 1981; Xba I, Pst I, and Bgl II restriction enzyme maps of the two orientations of the varicella-zoster virus genome. J Virol 39:390–400
    [Google Scholar]
  5. Felsenstein J. 2005 phylip (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences University of Washington; Seattle:
    [Google Scholar]
  6. Katoh K., Misawa K., Kuma K., Miyata T. 2002; mafft: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066 [CrossRef]
    [Google Scholar]
  7. Loparev V. N., Rubtcova E. N., Bostik V., Govil D., Birch C. J., Druce J. D., Schmid D. S., Croxson M. C. 2007; Identification of five major and two minor genotypes of varicella-zoster virus strains: a practical two-amplicon approach used to genotype clinical isolates in Australia and New Zealand. J Virol 81:12758–12765 [CrossRef]
    [Google Scholar]
  8. McGeoch D. J., Dolan A., Donald S., Brauer D. T. K. 1986; Complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1. Nucleic Acids Res 14:1727–1745 [CrossRef]
    [Google Scholar]
  9. McGeoch D. J., Davison A. J., Dolan A., Gatherer D., Sevilla-Reyes E. E. 2008; Molecular evolution of the Herpesvirales . In Origin and Evolution of Viruses , 2nd edn. pp 447–475Edited by Domingo E., Parrish C. R., Holland. London: Academic Press;
    [Google Scholar]
  10. Norberg P., Liljeqvist J. Å., Bergström, T., Sammons, S., Schmid, D. S., Loparev, V. N. 2006; Complete-genome phylogenetic approach to varicella-zoster virus evolution: genetic divergence and evidence for recombination. J Virol 80:9569–9576 [CrossRef]
    [Google Scholar]
  11. Peters G. A., Tyler S. D., Grose C., Severini A., Gray M. J., Upton C., Tipples G. A. 2006; A full-genome phylogenetic analysis of varicella-zoster virus reveals a novel origin of replication-based genotyping scheme and evidence of recombination between major circulating clades. J Virol 80:9850–9860 [CrossRef]
    [Google Scholar]
  12. Quinlivan M., Breuer J. 2006; Molecular studies of varicella-zoster virus. Rev Med Virol 16:225–250 [CrossRef]
    [Google Scholar]
  13. Quinlivan M., Hawrami K., Barrett-Muir W., Aaby P., Arvin A., Chow V. T., John T. J., Matondo P., Peiris M. other authors 2002; The molecular epidemiology of varicella-zoster virus: evidence for geographical segregation. J Infect Dis 186:888–894 [CrossRef]
    [Google Scholar]
  14. Ronquist F., Huelsenbeck J. P. 2003; MrBayes 3: Bayesian inference under mixed methods. Bioinformatics 19:1572–1574 [CrossRef]
    [Google Scholar]
  15. Sauerbrei A., Zell R., Harder M., Wutzler P. 2006; Genotyping of different varicella vaccine strains. J Clin Virol 37:109–117 [CrossRef]
    [Google Scholar]
  16. Tyler S. D., Peter G. A., Grose C., Severini A., Gray M. J., Upton U., Tipples G. A. 2007; Genomic cartography of varicella-zoster virus: a complete genome-based analysis of strain variability with implications for attenuation and phenotypic differences. Virology 359:447–458 [CrossRef]
    [Google Scholar]
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