1887

Journal of General Virology header logo

Volume 75, Issue 3

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 Free

Abstract

Using the presence or absence of 63 variable restriction endonuclease (RE) sites selected from 225 sites with six REs, genomic polymorphism of 242 herpes simplex virus type 1 (HSV-1) strains from six countries (Japan, Korea, China, Sweden, U.S.A. and Kenya) was quantitatively analysed. Twenty-five of the 63 sites were found to differ between Korean and Kenyan strains. In contrast, only three and six sites were found to differ between isolates from Sweden and the U.S.A. and between those from Korea and China, respectively, suggesting that they are closely related to each other. In this way, characterization of 63 sites enabled us to categorize 186 distinct HSV-1 genotypes from 242 individuals. Some strains from Japan, Korea and China shared the same genotypes, indicating that they are phylogenetically closely related. Many significant correlation coefficients ( | | > 0·42; <0·01) between pairs of sites were found in isolates from the three Asian countries (Japan, Korea and China) as well as in those from Sweden and the U.S.A., suggesting that HSV-1 strains from within the same ethnic groups are evolution- arily closer. The average number of nucleotide substitutions per nucleotide, as defined by nucleotide diversity (π), was estimated for HSV-1 genomes within (π or π) and between ( ) countries. On the basis of 225 sites, nucleotide diversity for Kenyan isolates was 0·0056, almost three times higher than that for Korean isolates, implying that Kenyan HSV-1 genomes are much more diverse than those from Korea. In addition, the diversity between HSV-1 isolates from different countries (π) was highest between isolates from the three Asian countries and Kenya (0·0075 to 0·0081) and lowest among those from the three Asian countries (0·0032 to 0·0040). The mutation rate (λ) for HSV-1 was estimated to be 3·5 × 10 /site/year. All these findings show that the evolution of HSV-1 may be host-dependent and very slow.

  • Received:
  • Accepted:
  • Published Online:
© The Journal of General Virology 1994
Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-75-3-513
1994-03-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/jgv/75/3/JV0750030513.html?itemId=/content/journal/jgv/10.1099/0022-1317-75-3-513&mimeType=html&fmt=ahah

References

  1. Alams T. M., Joncas J. H., Ozanne G. 1989; DNApolymorphism among isolates from multiple sites of a patient with chronic herpes simplex virus type 1 infection. Journal of Medical Virology 29:186–191
     [Google Scholar]
  2. Buchman T. G., Simpson T., Nosal C., Roizman B., Nahmias A. J. 1980; The structure of herpes simplex virus DNA and its application to molecular epidemiology. Annals of the New York Academy of Sciences 354:279–290
     [Google Scholar]
  3. Chaney S. M. J., Warren K. G., Kettyls J., Zbitnue A., Subak-Sharpe J. H. 1983a; A comparative analysis of restriction enzyme digests of the DNA of herpes simplex virus isolated from genital and facial lesions. Journal of General Virology 64:357–371
     [Google Scholar]
  4. Chaney S. M. J., Warren K. G., Subak-Sharpe J. H. 1983b; Variable restriction endonuclease sites of herpes simplex virus type 1 isolates from encephalitic, facial and genital lesions and ganglia. Journal of General Virology 64:2717–2733
     [Google Scholar]
  5. 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. Journal of General Virology 44:315–331
     [Google Scholar]
  6. Gentry G. A., Lowe M., Alford G., Nevin R. 1988; Sequence analyses of herpesviral enzymes suggest an ancient origin for human sexual behavior. Proceedings of the National Academy of Sciences, U.S.A 85:2658–2661
     [Google Scholar]
  7. Gojobori T., Moriyama E. M., Kimura M. 1990; Molecular clock of viral evolution, and neutral theory. Proceedings of the National Academy of Sciences, U.S.A 87:10015–10018
     [Google Scholar]
  8. Hammer S. M., Buchman T. G., D’Angelo L. J., Karchmer A. W., Roizman B., Hirsch M. S. 1980; Temporal cluster of herpes simplex encephalitis: investigation by restriction endonuclease cleavage of viral DNA. Journal of Infectious Diseases 141:436–440
     [Google Scholar]
  9. Hammerberg O., Watts J., Chernesky M., Luchsinger I., Rawls W. 1983; An outbreak of herpes simplex virus type 1 in an intensive care nursery. Pediatric Infectious Diseases 2:290–294
     [Google Scholar]
  10. Hondo R., Yogo Y., Yoshida M., Fujima A., Ito S. 1989; Distribution of varicella-zoster virus strains carrying a PstI-site-less mutation in Japan and DNA change responsible for the mutation. Japanese Journal of Experimental Medicine 59:233–237
     [Google Scholar]
  11. Horai S., Matsunaga E. 1986; Mitochondrial DNA polymorphism in Japanese. II. Analysis with restriction enzymes of four or five base pair recognition. Human Genetics 72:105–117
     [Google Scholar]
  12. Locker H., Frenkel N. 1979; BamI, KpnI, and SalI restriction enzyme maps of the DNAs of herpes simplex virus strains Justin and F: occurrence of heterogeneities in defined regions of the viral DNA. Journal of Virology 32:429–441
     [Google Scholar]
  13. Lonsdale D. M., Brown S. M., Subak-Sharpe J. H., Warren K. G., Koprowski H. 1979; The polypeptide and the DNA restriction enzyme profiles of spontaneous isolates of herpes simplex virus type 1 from explants of human trigeminal, superior cervical and vagus ganglia. Journal of General Virology 43:151–171
     [Google Scholar]
  14. Lonsdale D. M., Brown S. M., Lang J., Subak-Sharpe J. H., Koprowski H., Warren K. G. 1980; Variations in herpes simplex virus isolated from human ganglia and a study of clonal variation in HSV-1. Annals of the New York Academy of Science 354:291–308
     [Google Scholar]
  15. McGeoch D. J. 1989; The genomes of the human herpesviruses: contents, relationships, and evolution. Annual Review of Microbiology 43:235–265
     [Google Scholar]
  16. McGeoch D. J., Dolan A., Donald S., Rixon F. J. 1985; Sequence determination and genetic content of the short unique region in the genome of herpes simplex virus type 1. Journal of Molecular Biology 181:1–13
     [Google Scholar]
  17. McGeoch D. J., Dolan A., Donald S., Brauer D. H. K. 1986; Complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1. Nucleic Acids Research 14:1727–1745
     [Google Scholar]
  18. McGeoch D. J., Moss H. W. M., McNab D., Frame M. C. 1987; DNA sequence and genetic content of the HindIIIl region in the short unique component of the herpes simplex virus type 2 genome: identification of the gene encoding glycoprotein G, and evolutionary comparisons. Journal of General Virology 68:19–38
     [Google Scholar]
  19. 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. Journal of General Virology 69:1531–1574
     [Google Scholar]
  20. Maitland N. J., Smith I. W., Peutherer J. F., Robertson D. H. H., Jones K. W. 1982; Restriction endonuclease analysis of DNA from genital isolates of herpes simplex virus type 2. Infection and Immunity 38:834–842
     [Google Scholar]
  21. Manzella J. P., McConville J. H., Valenti W., Menegus M. A., Swierkosz E. M., Arens M. 1984; An outbreak of herpes simplex virus type 1 gingivostomatitis in a dental hygiene practice. Journal of the American Medical Association 252:2019–2022
     [Google Scholar]
  22. Mertz G. J., Coombs R. W., Ashley R., Jourdan J., Remington M., Winter C., Fahnlander A., Guinan M., Ducey H., Corey L. 1988; Transmission of genital herpes simplex in couples with one symptomatic and asymptomatic partner: a prospective study. Journal of Infectious Diseases 157:1169–1177
     [Google Scholar]
  23. Nei M. 1982; Evolution of human races at gene level. In Human Genetics part A The Unfolding Genome pp. 157–165 Bonne-Tamir B. Edited by New York: Alan R. Liss;
     [Google Scholar]
  24. Nei M. 1985; Human evolution at the molecular level. In Population Genetics and Molecular Evolution pp. 41–64 Ohta T., Aoki K. Edited by Tokyo: Japan Scientific Societies Press;
     [Google Scholar]
  25. Nei M. 1987 Molecular Evolutionary Genetics New York: Columbia University Press;
     [Google Scholar]
  26. Nei M., Li W. -H. 1979; Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, U.S.A 76:5269–5273
     [Google Scholar]
  27. Nei M., Tajima F. 1981; DNA polymorphism detectable by restriction endonucleases. Genetics 97:145–163
     [Google Scholar]
  28. Nei M., Tajima F. 1983; Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics 105:207–217
     [Google Scholar]
  29. Orito E., Mizokami M., Ina Y., Moriyama E. M., Kameshima N., Yamamoto M., Gojobori T. 1989; Host-independent evolution and genetic classification of the hepadnavirus family based on nucleotide sequences. Proceedings of the National Academy of Sciences, U.S.A 86:7059–7062
     [Google Scholar]
  30. Perry L. J., McGeoch D. J. 1988; The DNA sequences of the long repeat region and adjoining parts of the long unique region in the genome of herpes simplex virus type 1. Journal of General Virology 69:2831–2846
     [Google Scholar]
  31. Post L. E., Conley A. J., Mocarski E. S., Roizman B. 1980; Cloning of reiterated and nonreiterated herpes simplex virus 1 sequences as BamHI fragments. Proceedings of the National Academy of Sciences, U.S.A 77:4201–1205
     [Google Scholar]
  32. Roizman B. 1979; The structure and isomerization of herpes simplex virus genomes. Cell 16:481–494
     [Google Scholar]
  33. Roizman B. 1980; Genome variation and evolution among herpes viruses. Annals of the New York Academy of Science 353:472–483
     [Google Scholar]
  34. Roizman B., Buchman T. G. 1979; The molecular epidemiology of herpes simplex viruses. Hospital Practice 14:95–104
     [Google Scholar]
  35. Roizman B., Tognon M. 1983; Restriction endonuclease patterns of herpes simplex virus DNA: application to diagnosis and molecular epidemiology. Current Topics in Microbiology and Immunology 104:279–286
     [Google Scholar]
  36. Saito H., Sakaoka H., Yamashita T., Fujinaga K. 1989; A tandem repeat sequence found in a heterogeneous fragment of UL of herpes simplex virus type 1. Journal of General Virology 70:443–448
     [Google Scholar]
  37. Sakaoka H., Aomori T., Ozaki I., Ishida S., Fujinaga K. 1984; Restriction endonuclease cleavage analysis of herpes simplex virus isolates obtained from three pairs of siblings. Infection and Immunity 43:771–774
     [Google Scholar]
  38. Sakaoka H., Aomori T., Honda O., Saheki Y., Ishida S., Yamanishi S., Fujinaga K. 1985; Subtypes of herpes simplex virus type 1 in Japan: classification by restriction endonucleases and analysis of distribution. Journal of Infectious Diseases 152:190–197
     [Google Scholar]
  39. Sakaoka H., Saheki Y., Uzuki K., Nakakita T., Saito H., Sekine K., Fujinaga K. 1986; Two outbreaks of herpes simplex virus type 1 nosocomial infection among newborns. Journal of Clinical Microbiology 24:36–40
     [Google Scholar]
  40. Sakaoka H., Saito H., Sekine K., Aomori T., Grillner L., Wadell G., Fujinaga K. 1987a; Genomic comparison of herpes simplex virus type 1 isolates from Japan, Sweden and Kenya. Journal of General Virology 68:749–764
     [Google Scholar]
  41. Sakaoka H., Kawana T., Grillner L., Aomori T., Yamaguchi T., Saito H., Fujinaga K. 1987b; Genome variations in herpes simplex virus type 2 strains isolated in Japan and Sweden. Journal of General Virology 68:2105–2116
     [Google Scholar]
  42. Sanders P. G., Wilkie N. M., Davison A. J. 1982; Thymidine kinase deletion mutants of herpes simplex virus type 1. Journal of General Virology 63:277–295
     [Google Scholar]
  43. Snedecor G. W., Cochran W. G. 1980 Statistical Methods, 7th edn. Ames: Iowa State University Press;
     [Google Scholar]
  44. Soeda E., Maruyama T. 1982; Molecular evolution in papova viruses and in bacteriophages. Advances in Biophysics 15:1–17
     [Google Scholar]
  45. Southern E. M. 1975; Detection of specific sequences among DNA fragments separated by gel electrophoresis. Journal of Molecular Biology 98:503–517
     [Google Scholar]
  46. Ueno T., Suzuki N., Sakaoka H., Fujinaga K. 1982; Simple and practical methods for typing and strain differentiation. Microbiology and Immunology 26:1159–1170
     [Google Scholar]
  47. Umene K. 1987; Restriction endonucleases recognizing DNA sequences of four base pairs facilitate differentiation of herpes simplex virus type 1 strains. Archives of Virology 97:197–214
     [Google Scholar]
  48. Umene K., Sakaoka H. 1991; Flomogeneity and diversity of genome polymorphism in a set of herpes simplex virus type 1 strains classified as the same genotypic group. Archives of Virology 19:53–65
     [Google Scholar]
  49. Umene K., Yoshida M. 1989; Reiterated sequences of herpes simplex virus type 1 (HSV-1) genome can serve as physical markers for the differentiation of HSV-1 strains. Archives of Virology 106:281–299
     [Google Scholar]
  50. Umene K., Eto T., Mori R., Takagi Y., Enquist K. 1984; Herpes simplex virus type 1 restriction fragment polymorphism determined using Southern hybridization. Archives of Virology 80:275–290
     [Google Scholar]
  51. Whitley R., Lakeman A., Nahmias A., Roizman B. 1982; DNA restriction-enzyme analysis of herpes simplex virus isolates obtained from patients with encephalitis. New England Journal of Medicine 307:1060–1062
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-75-3-513
Loading
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 (1994); https://doi.org/10.1099/0022-1317-75-3-513
/content/journal/jgv/10.1099/0022-1317-75-3-513
/content/journal/jgv/10.1099/0022-1317-75-3-513
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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