1887

Abstract

Herpes simplex virus type 1 (HSV-1) is a ubiquitous human pathogen. The sequence of HSV-1 is the -acting site required for the cleavage and encapsidation of unit-length HSV-1 DNA from concatemeric forms. The consensus sequence consists of (i) DR1 (direct repeat 1), (ii) Ub, (iii) a DR2 array [a repeat of various copy numbers of DR2 elements (11 or 12 bp)], (iv) a DR4 stretch and (v) Uc. In the present study, the nucleotide sequences of the sequences of 26 HSV-1 isolates were determined and the DR4 stretches were classified into three groups. The state of a set of 20 DNA polymorphisms in the genomes of these HSV-1 isolates was determined previously. A correct classification rate of 100 % was achieved when discriminant analysis was performed between the DR4 stretch (criterion variable) and the set of 20 DNA polymorphisms (predictor variables), suggesting a close association of the DR4 stretch with HSV-1 diversification. DR2 elements of 9, 13 and 14 bp were detected in addition to those of 11 and 12 bp, and a correct classification rate of 93 % was achieved when discriminant analysis was performed between the DR2 array and the set of 20 DNA polymorphisms. Some DR2 elements of one HSV-1 isolate had the same nucleotide sequences as part of the adjacent DR4 stretch, and these variations were adequately explained by postulating recombination involving DR2 elements; hence, the DR2 array was deduced to be prone to recombination.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.83467-0
2008-04-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jgv/89/4/841.html?itemId=/content/journal/jgv/10.1099/vir.0.83467-0&mimeType=html&fmt=ahah

References

  1. Adelman K., Salmon B., Baines J. D. 2001; Herpes simplex virus DNA packaging sequences adopt novel structures that are specifically recognized by a component of the cleavage and packaging machinery. Proc Natl Acad Sci U S A 98:3086–3091 [CrossRef]
    [Google Scholar]
  2. Baines J. D., Weller S. K. 2005; Cleavage and packaging of herpes simplex virus 1 DNA. In Viral Genome Packaging Machines: Genetic, Structure, and Mechanism . pp 135–150Edited by Catalano C. E. Georgetown & New York: Landes Bioscience/Eurekah.com and Kluwer Academic/Plenum Publishers;
  3. Bowden R. J., McGeoch D. J. 2006; Evolution of herpes simplex viruses. In Herpes Simplex Viruses pp 1–34Edited by Studahl M., Cinque P., Bergström T. New York: Taylor & Francis Group;
    [Google Scholar]
  4. Bowden R., Sakaoka H., Donnelly P., Ward P. 2004; High recombination rate in herpes simplex virus type 1 natural populations suggests significant co-infection. Infect Genet Evol 4:115–123 [CrossRef]
    [Google Scholar]
  5. Bowden R., Sakaoka H., Ward P., Donnelly P. 2006; Patterns of Eurasian HSV-1 molecular diversity and inferences of human migrations. Infect Genet Evol 6:63–74 [CrossRef]
    [Google Scholar]
  6. Brown S. M., MacLean A. R. 1998 Herpes Simplex Virus Protocols Totowa: Human Press;
    [Google Scholar]
  7. Chou J., Roizman B. 1985; Isomerization of herpes simplex virus 1 genome: identification of the cis -acting and recombination sites within the domain of the a sequence. Cell 41:803–811 [CrossRef]
    [Google Scholar]
  8. Chou J., Roizman B. 1986; The terminal a sequence of the herpes simplex virus genome contains the promoter of a gene located in the repeat sequences of the L component. J Virol 57:629–637
    [Google Scholar]
  9. Davison A. J., McGeoch D. J. 1995; Herpesviridae . In Molecular Basis of Virus Evolution . pp 290–309Edited by Gibbs A. J., Calisher C. H., García-Arenal F. Cambridge: Cambridge University Press;
  10. Davison A. J., Wilkie N. M. 1981; Nucleotide sequences of the joint between the L and S segments of herpes simplex virus types 1 and 2. J Gen Virol 53:315–331
    [Google Scholar]
  11. Deiss L. P., Chou J., Frenkel N. 1986; Functional domains within the a sequence involved in the cleavage-packaging of herpes simplex virus DNA. J Virol 59:605–618
    [Google Scholar]
  12. Gentry G. A., Lowe M., Alford G., Nevins R. 1988; Sequence analyses of herpesviral enzymes suggests an ancient origin for human sexual behavior. Proc Natl Acad Sci U S A 85:2658–2661 [CrossRef]
    [Google Scholar]
  13. Hodge P. D., Stow N. D. 2001; Effects of mutations within the herpes simplex virus type 1 DNA encapsidation signal on packaging efficiency. J Virol 75:8977–8986 [CrossRef]
    [Google Scholar]
  14. Huberty C. J. 1994 Applied Discriminant Analysis New York: John Wiley & Sons Inc;
    [Google Scholar]
  15. Lehman A., O'Rourke N., Hatcher L., Stepanski E. J. 2005 JMP for Basic Univariate and Multivariate Statistics: a Step-by-Step Guide Cary: SAS Institute Inc;
    [Google Scholar]
  16. MacLean A. R., Ul-Fareed M., Robertson L., Harland J., Brown S. M. 1991; Herpes simplex virus type 1 deletion variants 1714 and 1716 pinpoint neurovirulence-related sequences in Glasgow strain 17+ between immediate early gene 1 and the ‘a’ sequence. J Gen Virol 72:631–639 [CrossRef]
    [Google Scholar]
  17. Martin D. W., Weber P. C. 1998; Role of the DR2 repeat array in the regulation of the ICP34.5 gene promoter of herpes simplex virus type 1 during productive infection. J Gen Virol 79:517–523
    [Google Scholar]
  18. Mata-Toledo R. A., Cushman P. K. 2000 Fundamentals of Relational Databases New York: McGraw-Hill;
    [Google Scholar]
  19. McGeoch D. J., Cook S. 1994; Molecular phylogeny of the Alphaherpesvirinae subfamily and a proposed evolutionary timescale. J Mol Biol 238:9–22 [CrossRef]
    [Google Scholar]
  20. McGeoch D. J., Dalrymple M. A., Davison A. J., Dolan A., Frame M. C., McNab D., Perry L. J., Scott J. E., Taylor P. 1988; The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J Gen Virol 69:1531–1574 [CrossRef]
    [Google Scholar]
  21. McGeoch D. J., Cook S., Dolan A., Jamieson F. E., Telford E. A. R. 1995; Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses. J Mol Biol 247:443–458 [CrossRef]
    [Google Scholar]
  22. Mocarski E. S., Roizman B. 1981; Site-specific inversion sequence of the herpes simplex virus genome: domain and structural features. Proc Natl Acad Sci U S A 78:7047–7051 [CrossRef]
    [Google Scholar]
  23. Mocarski E. S., Roizman B. 1982; Structure and role of the herpes simplex virus DNA termini in inversion, circularization and generation of virion DNA. Cell 31:89–97 [CrossRef]
    [Google Scholar]
  24. Mocarski E. S., Post L. E., Roizman B. 1980; Molecular engineering of the herpes simplex virus genome: insertion of a second L-S junction into the genome causes additional genome inversions. Cell 22:243–255 [CrossRef]
    [Google Scholar]
  25. Mocarski E. S., Deiss L. P., Frenkel N. 1985; Nucleotide sequence and structural features of a novel US- a junction present in a defective herpes simplex virus genome. J Virol 55:140–146
    [Google Scholar]
  26. Nahmias A. J., Lee F. K., Beckman-Nahmias S. 2006; The natural history and epidemiology of herpes simplex viruses. In Herpes Simplex Viruses pp 55–97Edited by Studahl M., Cinque P., Bergström T. New York: Taylor & Francis Group;
    [Google Scholar]
  27. Norberg, P., Bergström, T., Rekabdar, E., Lindh, M. & Liljeqvist, J. Å 2004; Phylogenetic analysis of clinical herpes simplex virus type 1 isolates identified three genetic groups and recombinant viruses. J Virol 78:10755–10764 [CrossRef]
    [Google Scholar]
  28. Norberg, P., Bergström, T. & Liljeqvist, J. Å 2006; Genotyping of clinical herpes simplex virus type 1 isolates by use of restriction enzymes. J Clin Microbiol 44:4511–4514 [CrossRef]
    [Google Scholar]
  29. Norberg, P., Olofsson, S., Tarp, M. A., Clausen, H., Bergström, T. & Liljeqvist, J. Å 2007; Glycoprotein I of herpes simplex virus type 1 contains a unique polymorphic tandem-repeated mucin region. J Gen Virol 88:1683–1688 [CrossRef]
    [Google Scholar]
  30. Sakaoka H., Kurita K., Iida Y., Takada S., Umene K., Kim Y. T., Ren C. S., Nahmias A. J. 1994; Quantitative analysis of genomic polymorphism of herpes simplex virus type 1 strains from six countries: studies of molecular evolution and molecular epidemiology of the virus. J Gen Virol 75:513–527 [CrossRef]
    [Google Scholar]
  31. Sall J., Creighton L., Lehman A. 2005 JMP Start Statistics , 3rd edn. Cary: SAS Institute Inc;
    [Google Scholar]
  32. Sambrook J., Russell D. W. 2001 Molecular Cloning: a Laboratory Manual Cold Spring Harbor: Cold Spring Harbor Laboratory Press;
    [Google Scholar]
  33. Sarisky R. T., Weber P. C. 1994; Role of anisomorphic DNA conformations in negative regulation of a herpes simplex virus type 1 promoter. Virology 204:569–579 [CrossRef]
    [Google Scholar]
  34. Sharma S. 1996 Applied Multivariate Techniques New York: John Wiley & Sons Inc;
    [Google Scholar]
  35. Smiley J. R., Fong B. S., Leung W.-C. 1981; Construction of a double-joined herpes simplex viral DNA molecule: inverted repeats are required for segment inversion, and direct repeats promote deletions. Virology 113:345–362 [CrossRef]
    [Google Scholar]
  36. Smiley J. R., Duncan J., Howes M. 1990; Sequence requirements for DNA rearrangements induced by the terminal repeat of herpes simplex virus type 1 KOS DNA. J Virol 64:5036–5050
    [Google Scholar]
  37. Umene K. 1991; Recombination of the internal direct repeat element DR2 responsible for the fluidity of the a sequence of herpes simplex virus type 1. J Virol 65:5410–5416
    [Google Scholar]
  38. Umene K. 1993; Herpes simplex virus type 1 variant a sequence generated by recombination and breakage of the a sequence in defined regions, including the one involved in recombination. J Virol 67:5685–5691
    [Google Scholar]
  39. Umene K. 1998 Herpesvirus: Genetic Variability and Recombination Fukuoka: Touka Shobo;
    [Google Scholar]
  40. Umene K. 1999; Mechanism and application of genetic recombination in herpesviruses. Rev Med Virol 9:171–182 [CrossRef]
    [Google Scholar]
  41. Umene K., Kawana T. 2003; Divergence of reiterated sequences in a series of genital isolates of herpes simplex virus type 1 from individual patients. J Gen Virol 84:917–923 [CrossRef]
    [Google Scholar]
  42. Umene K., Sakaoka H. 1997; Populations of two Eastern countries of Japan and Korea and with a related history share a predominant genotype of herpes simplex virus type 1. Arch Virol 142:1953–1961 [CrossRef]
    [Google Scholar]
  43. Umene K., Sakaoka H. 1999; Evolution of herpes simplex virus type 1 under herpseviral evolutionary processes. Arch Virol 144:637–656 [CrossRef]
    [Google Scholar]
  44. Umene K., Yoshida M. 1993; Genomic characterization of two predominant genotypes of herpes simplex virus type 1. Arch Virol 131:29–46 [CrossRef]
    [Google Scholar]
  45. Umene K., Koga C., Kameyama T. 2007; Discriminant analysis of DNA polymorphisms in herpes simplex virus type 1 strains involved in primary compared to recurrent infections. J Virol Methods 139:159–165 [CrossRef]
    [Google Scholar]
  46. Varmuza S. L., Smiley J. R. 1985; Signals for site-specific cleavage of HSV DNA: maturation involves two separate cleavage events at sites distal to the recognition sequences. Cell 41:793–802 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.83467-0
Loading
/content/journal/jgv/10.1099/vir.0.83467-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error