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. 1996 Dec;34(12):2869–2874. doi: 10.1128/jcm.34.12.2869-2874.1996

Application of long PCR method of identification of variations in nucleotide sequences among varicella-zoster virus isolates.

M Takayama 1, N Takayama 1, N Inoue 1, Y Kameoka 1
PMCID: PMC229425  PMID: 8940414

Abstract

Restriction fragment length polymorphism (RFLP) analysis of whole viral DNA of varicella-zoster virus (VZV) requires the time-consuming and laborious preparation of a large amount of purified viral DNA. RFLP analysis of small DNA fragments amplified by PCR was developed as an alternative method. However, its use has been limited because of the small number of variations in VZV. To overcome these drawbacks and to identify variations in VZV, we developed an RFLP analysis method combined with the long PCR method which has recently been developed for the amplification of DNA fragments between 5 and 35 kb in length. We amplified three DNA regions ranging from 6.8 to 11.4 kb and demonstrated that RFLP analyses of these regions allowed for the classification of 40 VZV isolates in Japan into 17 groups. One-fourth of the isolates contained a nucleotide difference of C versus T, which abolished the StyI site at position 76530; this alteration was linked to the reported PstI site polymorphism at position 69349 (nucleotide positions are based on those of strain Dumas). Nucleotide sequence variation in the examined regions among VZV isolates in Japan was estimated at roughly less than 0.05%, confirming the previously proposed idea that VZV is genetically stable and not highly diversified. Our method will be useful for studies of the molecular epidemiology of VZV.

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Selected References

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  1. Adams S. G., Dohner D. E., Gelb L. D. Restriction fragment differences between the genomes of the Oka varicella vaccine virus and American wild-type varicella-zoster virus. J Med Virol. 1989 Sep;29(1):38–45. doi: 10.1002/jmv.1890290108. [DOI] [PubMed] [Google Scholar]
  2. Barnes W. M. PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates. Proc Natl Acad Sci U S A. 1994 Mar 15;91(6):2216–2220. doi: 10.1073/pnas.91.6.2216. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Buchman T. G., Roizman B., Adams G., Stover B. H. Restriction endonuclease fingerprinting of herpes simplex virus DNA: a novel epidemiological tool applied to a nosocomial outbreak. J Infect Dis. 1978 Oct;138(4):488–498. doi: 10.1093/infdis/138.4.488. [DOI] [PubMed] [Google Scholar]
  4. Cen H., Breinig M. C., Atchison R. W., Ho M., McKnight J. L. Epstein-Barr virus transmission via the donor organs in solid organ transplantation: polymerase chain reaction and restriction fragment length polymorphism analysis of IR2, IR3, and IR4. J Virol. 1991 Feb;65(2):976–980. doi: 10.1128/jvi.65.2.976-980.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cheng S., Chang S. Y., Gravitt P., Respess R. Long PCR. Nature. 1994 Jun 23;369(6482):684–685. doi: 10.1038/369684a0. [DOI] [PubMed] [Google Scholar]
  6. Cheng S., Fockler C., Barnes W. M., Higuchi R. Effective amplification of long targets from cloned inserts and human genomic DNA. Proc Natl Acad Sci U S A. 1994 Jun 7;91(12):5695–5699. doi: 10.1073/pnas.91.12.5695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chou S. W. Differentiation of cytomegalovirus strains by restriction analysis of DNA sequences amplified from clinical specimens. J Infect Dis. 1990 Sep;162(3):738–742. doi: 10.1093/infdis/162.3.738. [DOI] [PubMed] [Google Scholar]
  8. Davison A. J., Scott J. E. The complete DNA sequence of varicella-zoster virus. J Gen Virol. 1986 Sep;67(Pt 9):1759–1816. doi: 10.1099/0022-1317-67-9-1759. [DOI] [PubMed] [Google Scholar]
  9. Hayakawa Y., Torigoe S., Shiraki K., Yamanishi K., Takahashi M. Biologic and biophysical markers of a live varicella vaccine strain (Oka): identification of clinical isolates from vaccine recipients. J Infect Dis. 1984 Jun;149(6):956–963. doi: 10.1093/infdis/149.6.956. [DOI] [PubMed] [Google Scholar]
  10. Hayakawa Y., Yamamoto T., Yamanishi K., Takahashi M. Analysis of varicella-zoster virus DNAs of clinical isolates by endonuclease HpaI. J Gen Virol. 1986 Sep;67(Pt 9):1817–1829. doi: 10.1099/0022-1317-67-9-1817. [DOI] [PubMed] [Google Scholar]
  11. Her C., Weinshilboum R. M. Rapid restriction mapping by use of long PCR. Biotechniques. 1995 Oct;19(4):530–532. [PubMed] [Google Scholar]
  12. Hondo R., Yogo Y. Strain variation of R5 direct repeats in the right-hand portion of the long unique segment of varicella-zoster virus DNA. J Virol. 1988 Aug;62(8):2916–2921. doi: 10.1128/jvi.62.8.2916-2921.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hondo R., Yogo Y., Yoshida M., Fujima A., Itoh S. Distribution of varicella-zoster virus strains carrying a PstI-site-less mutation in Japan and DNA change responsible for the mutation. Jpn J Exp Med. 1989 Dec;59(6):233–237. [PubMed] [Google Scholar]
  14. Kilpatrick B. A., Huang E. S., Pagano J. S. Analysis of cytomegalovirus genomes with restriction endonucleases Hin D III and EcoR-1. J Virol. 1976 Jun;18(3):1095–1105. doi: 10.1128/jvi.18.3.1095-1105.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kinchington P. R., Remenick J., Ostrove J. M., Straus S. E., Ruyechan W. T., Hay J. Putative glycoprotein gene of varicella-zoster virus with variable copy numbers of a 42-base-pair repeat sequence has homology to herpes simplex virus glycoprotein C. J Virol. 1986 Sep;59(3):660–668. doi: 10.1128/jvi.59.3.660-668.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. LaRussa P., Lungu O., Hardy I., Gershon A., Steinberg S. P., Silverstein S. Restriction fragment length polymorphism of polymerase chain reaction products from vaccine and wild-type varicella-zoster virus isolates. J Virol. 1992 Feb;66(2):1016–1020. doi: 10.1128/jvi.66.2.1016-1020.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. McConlogue L., Brow M. A., Innis M. A. Structure-independent DNA amplification by PCR using 7-deaza-2'-deoxyguanosine. Nucleic Acids Res. 1988 Oct 25;16(20):9869–9869. doi: 10.1093/nar/16.20.9869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Pellett P. E., Lindquester G. J., Feorino P., Lopez C. Genomic heterogeneity of human herpesvirus 6 isolates. Adv Exp Med Biol. 1990;278:9–18. doi: 10.1007/978-1-4684-5853-4_2. [DOI] [PubMed] [Google Scholar]
  19. Sakaoka H., Kurita K., Iida Y., Takada S., Umene K., Kim Y. T., Ren C. S., Nahmias A. J. 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. 1994 Mar;75(Pt 3):513–527. doi: 10.1099/0022-1317-75-3-513. [DOI] [PubMed] [Google Scholar]
  20. Straus S. E., Hay J., Smith H., Owens J. Genome differences among varicella-zoster virus isolates. J Gen Virol. 1983 May;64(Pt 5):1031–1041. doi: 10.1099/0022-1317-64-5-1031. [DOI] [PubMed] [Google Scholar]
  21. Takada M., Suzutani T., Yoshida I., Matoba M., Azuma M. Identification of varicella-zoster virus strains by PCR analysis of three repeat elements and a PstI-site-less region. J Clin Microbiol. 1995 Mar;33(3):658–660. doi: 10.1128/jcm.33.3.658-660.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Takayama M., Takayama N., Kameoka Y., Hachimori K., Kaneda K., Minamitani M. Comparative restriction endonuclease analysis of varicella-zoster virus clinical isolates. Med Microbiol Immunol. 1989;178(2):61–67. doi: 10.1007/BF00203301. [DOI] [PubMed] [Google Scholar]
  23. Wyatt L. S., Frenkel N. Human herpesvirus 7 is a constitutive inhabitant of adult human saliva. J Virol. 1992 May;66(5):3206–3209. doi: 10.1128/jvi.66.5.3206-3209.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Zweerink H. J., Morton D. H., Stanton L. W., Neff B. J. Restriction endonuclease analysis of the DNA from varicella-zoster virus: stability of the DNA after passage in vitro. J Gen Virol. 1981 Jul;55(Pt 1):207–211. doi: 10.1099/0022-1317-55-1-207. [DOI] [PubMed] [Google Scholar]

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