Utilization of microsatellite polymorphism for differentiating herpes simplex virus type 1 strains

Journal of Clinical Microbiology

Volumn 47, Issue 3, 2009, Pages 533-540

  Deback, C ^a,b,c   Boutolleau, D ^a,b   Depienne, C ^c   Luyt, C E ^c   Bonnafous, P ^a,b   Gautheret Dejean, A ^a,b,d   Garrigue, I ^e   Agut, H ^a,b  

^a SORBONNE UNIVERSITÉ   (France)

^b PITIÉ SALPÊTRIÈRE HOSPITAL   (France)

^c ASSISTANCE PUBLIQUE HÔPITAUX DE PARIS   (France)

^d FACULTÉ DES SCIENCES PHARMACEUTIQUES ET BIOLOGIQUES   (France)

^e University Victor Segalen   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MICROSATELLITE DNA;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DNA POLYMORPHISM; GENE IDENTIFICATION; HAPLOTYPE; HERPES SIMPLEX VIRUS 1; HUMAN; HUMAN CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VIRUS STRAIN;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CERCOPITHECUS AETHIOPS; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA, VIRAL; GENOTYPE; HAPLOTYPES; HERPESVIRUS 1, HUMAN; HUMANS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; VERO CELLS;

HUMAN HERPESVIRUS 1;

EID: 62749123509     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.01565-08     Document Type: Article

References (54)

1. Adams, G., B. H. Stover, R. A. Keenlyside, T. M. Hooton, T. G. Buchman, B. Roizman, and J. A. Stewart. 1981. Nosocomial herpetic infections in a pediatric intensive care unit. Am. J. Epidemiol. 113:126-132.
2. Baranovskaya, S., J. L. Soto, M. Perucho, and S. R. Malkhosyan. 2001. Functional significance of concomitant inactivation of hMLH1 and hMSH6 in tumor cells of the microsatellite mutator phenotype. Proc. Natl. Acad. Sci. USA 98:15107-15112.
3. Barker, D. E., and B. Roizman. 1990. Identification of three genes nonessential for growth in cell culture near the right terminus of the unique sequences of long component of herpes simplex virus 1. Virology 177:684-691.
4. Bowden, R., H. Sakaoka, P. Donnelly, and R. Ward. 2004. High recombination rate in herpes simplex virus type 1 natural populations suggests significant co-infection. Infect. Genet. Evol. 4:115-123.
5. Bowden, R., H. Sakaoka, R. Ward, and P. Donnelly. 2006. Patterns of Eurasian HSV-1 molecular diversity and inferences of human migrations. Infect. Genet. Evol. 6:63-74.
6. Buchman, T. G., B. Roizman, G. Adams, and B. H. Stover. 1978. Restriction endonuclease fingerprinting of herpes simplex virus DNA: a novel epidemiological tool applied to a nosocomial outbreak. J. Infect. Dis. 138:488-498.
7. Chaney, S. M., K. G. Warren, and J. H. Subak-Sharpe. 1983. Variable restriction endonuclease sites of herpes simplex virus type 1 isolates from encephalitic, facial and genital lesions and ganglia. J. Gen. Virol. 64(Pt 12):2717-2733.
8. Chou, J., and B. Roizman. 1990. The herpes simplex virus 1 gene for ICP34.5, which maps in inverted repeats, is conserved in several limitedpassage isolates but not in strain 17syn+. J. Virol. 64:1014-1020.
9. Davis, C. L., D. Field, D. Metzgar, R. Saiz, P. A. Morin, I. L. Smith, S. A. Spector, and C. Wills. 1999. Numerous length polymorphisms at short tandem repeats in human cytomegalovirus. J. Virol. 73:6265-6270.
10. Davison, A. J., and N. M. Wilkie. 1981. Nucleotide sequences of the joint between the L and S segments of herpes simplex virus types 1 and 2. J. Gen. Virol. 55:315-331.
11. Field, D., and C. Wills. 1996. Long, polymorphic microsatellites in simple organisms. Proc. Biol. Sci. 263:209-215.
12. Garcia-Barreno, B., T. Delgado, and J. A. Melero. 1994. Oligo(A) sequences of human respiratory syncytial virus G protein gene: assessment of their genetic stability in frameshift mutants. J. Virol. 68:5460-5468.
13. Griffiths, A., M. A. Link, C. L. Furness, and D. M. Coen. 2006. Low-level expression and reversion both contribute to reactivation of herpes simplex virus drug-resistant mutants with mutations on homopolymeric sequences in thymidine kinase. J. Virol. 80:6568-6574.
14. Gupta, R., T. Warren, and A. Wald. 2007. Genital herpes. Lancet 370:2127-2137.
15. Ham, M. F., T. Takakuwa, W. J. Luo, A. Liu, A. Horii, and K. Aozasa. 2006. Impairment of double-strand breaks repair and aberrant splicing of ATM and MRE11 in leukemia-lymphoma cell lines with microsatellite instability. Cancer Sci. 97:226-234.
16. Hammer, S. M., T. G. Buchman, L. J. D'Angelo, A. W. Karchmer, B. Roizman, and M. S. Hirsch. 1980. Temporal cluster of herpes simplex encephalitis: investigation by restriction endonuclease cleavage of viral DNA. J. Infect. Dis. 141:436-440.
17. Hayward, G. S., R. J. Jacob, S. C. Wadsworth, and B. Roizman. 1975. Anatomy of herpes simplex virus DNA: evidence for four populations of molecules that differ in the relative orientations of their long and short components. Proc. Natl. Acad. Sci. USA 72:4243-4247.
18. Jiang, C., Y. T. Hwang, J. C. Randell, D. M. Coen, and C. B. Hwang. 2007. Mutations that decrease DNA binding of the processivity factor of the herpes simplex virus DNA polymerase reduce viral yield, alter the kinetics of viral DNA replication, and decrease the fidelity of DNA replication. J. Virol. 81:3495-3502.
19. Li, Y. C., A. B. Korol, T. Fahima, and E. Nevo. 2004. Microsatellites within genes: structure, function, and evolution. Mol. Biol. Evol. 21:991-1007.
20. Lilley, C. E., C. T. Carson, A. R. Muotri, F. H. Gage, and M. D. Weitzman. 2005. DNA repair proteins affect the lifecycle of herpes simplex virus 1. Proc. Natl. Acad. Sci. USA 102:5844-5849.
21. Linnemann, C. C., Jr., T. G. Buchman, I. J. Light, and J. L. Ballard. 1978. Transmission of herpes-simplex virus type 1 in a nursery for the newborn. Identification of viral isolates by D.N.A. "fingerprinting. " Lancet i:964-966.
22. Luyt, C. E., A. Combes, C. Deback, M. H. Aubriot-Lorton, A. Nieszkowska, J. L. Trouillet, F. Capron, H. Agut, C. Gibert, and J. Chastre. 2007. Herpes simplex virus lung infection in patients undergoing prolonged mechanical ventilation. Am. J. Respir. Crit. Care Med. 175:935-942.
23. Maertzdorf, J., L. Remeijer, A. Van Der Lelij, J. Buitenwerf, H. G. Niesters, A. D. Osterhaus, and G. M. Verjans. 1999. Amplification of reiterated sequences of herpes simplex virus type 1 (HSV-1) genome to discriminate between clinical HSV-1 isolates. J. Clin. Microbiol. 37:3518-3523.
24. McGeoch, D. J., M. A. Dalrymple, A. J. Davison, A. Dolan, M. C. Frame, D. McNab, L. J. Perry, J. E. Scott, and P. Taylor. 1988. The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J. Gen. Virol. 69(Pt 7):1531-1574.
25. Mirandola, P., T. Ravaioli, and E. Cassai. 1997. PCR analysis of human telomeric repeats present on HHV-6A viral strains. Virus Genes 15:29-32.
26. Norberg, P., T. Bergstrom, and J. A. Liljeqvist. 2006. Genotyping of clinical herpes simplex virus type 1 isolates by use of restriction enzymes. J. Clin. Microbiol. 44:4511-4514.
27. Norberg, P., T. Bergstrom, E. Rekabdar, M. Lindh, and J. A. Liljeqvist. 2004. Phylogenetic analysis of clinical herpes simplex virus type 1 isolates identified three genetic groups and recombinant viruses. J. Virol. 78:10755-10764.
28. Perry, L. J., and D. J. McGeoch. 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. J. Gen. Virol. 69(Pt 11):2831-2846.
29. Picone, O., Y. Ville, J. M. Costa, C. Rouzioux, and M. Leruez-Ville. 2005. Human cytomegalovirus (HCMV) short tandem repeats analysis in congenital infection. J. Clin. Virol. 32:254-256.
30. Rekabdar, E., P. Tunback, J. A. Liljeqvist, and T. Bergstrom. 1999. Variability of the glycoprotein G gene in clinical isolates of herpes simplex virus type 1. Clin. Diagn. Lab. Immunol. 6:826-831.
31. Remeijer, L., J. Maertzdorf, J. Buitenwerf, A. D. Osterhaus, and G. M. Verjans. 2002. Corneal herpes simplex virus type 1 superinfection in patients with recrudescent herpetic keratitis. Investig. Ophthalmol. Vis. Sci. 43:358-363.
32. Remeijer, L., J. Maertzdorf, P. Doornenbal, G. M. Verjans, and A. D. Osterhaus. 2001. Herpes simplex virus 1 transmission through corneal transplantation. Lancet 357:442.
33. Rixon, F. J., M. E. Campbell, and J. B. Clements. 1984. A tandemly reiterated DNA sequence in the long repeat region of herpes simplex virus type 1 found in close proximity to immediate-early mRNA 1. J. Virol. 52:715-718.
34. Roest, R. W., W. F. Carman, J. Maertzdorf, A. Scoular, J. Harvey, M. Kant, W. I. Van Der Meijden, G. M. Verjans, and A. D. Osterhaus. 2004. Genotypic analysis of sequential genital herpes simplex virus type 1 (HSV-1) isolates of patients with recurrent HSV-1 associated genital herpes. J. Med. Virol. 73:601-604.
35. Roizman, B., D. M. Knipe, and R. Whitley. 2007. Herpes simplex viruses, p. 2501-2601. In D. M. Knipe, P. M. Howley, et al. (ed.), Fields virology, 5th ed. Lippincott Williams & Wilkins, Philadelphia, PA.
36. Roizman, B., and M. Tognon. 1983. Restriction endonuclease patterns of herpes simplex virus DNA: application to diagnosis and molecular epidemiology. Curr. Top. Microbiol. Immunol. 104:273-286.
37. Sakaoka, H., K. Kurita, Y. Iida, S. Takada, K. Umene, Y. T. Kim, C. S. Ren, and A. J. Nahmias. 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(Pt 3):513-527.
38. Sakaoka, H., Y. Saheki, K. Uzuki, T. Nakakita, H. Saito, K. Sekine, and K. Fujinaga. 1986. Two outbreaks of herpes simplex virus type 1 nosocomial infection among newborns. J. Clin. Microbiol. 24:36-40.
39. Sakaoka, H., H. Saito, K. Sekine, T. Aomori, L. Grillner, G. Wadell, and K. Fujinaga. 1987. Genomic comparison of herpes simplex virus type 1 isolates from Japan, Sweden and Kenya. J. Gen. Virol. 68(Pt 3):749-764.
40. Sasadeusz, J. J., F. Tufaro, S. Safrin, K. Schubert, M. M. Hubinette, P. K. Cheung, and S. L. Sacks. 1997. Homopolymer mutational hot spots mediate herpes simplex virus resistance to acyclovir. J. Virol. 71:3872-3878.
41. Song, L., M. Chaudhuri, C. W. Knopf, and D. S. Parris. 2004. Contribution of the 3′- to 5′-exonuclease activity of herpes simplex virus type 1 DNA polymerase to the fidelity of DNA synthesis. J. Biol. Chem. 279:18535-18543.
42. Tachida, H., and M. Iizuka. 1992. Persistence of repeated sequences that evolve by replication slippage. Genetics 131:471-478.
43. Tautz, D., and M. Renz. 1984. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res. 12:4127-4138.
44. Thi, T. N., C. Deback, I. Malet, P. Bonnafous, Z. Ait-Arkoub, and H. Agut. 2006. Rapid determination of antiviral drug susceptibility of herpes simplex virus types 1 and 2 by real-time PCR. Antivir. Res. 69:152-157.
45. Thurston, M. I., and D. Field. 2005. MsatFinder: detection and characterization of microsatellites. CEH Oxford, Oxford, United Kingdom. http//www.genomics.ceh.ac.uk/msatfinder/.
46. Tran, L. C., J. M. Kissner, L. E. Westerman, and A. E. Sears. 2000. A herpes simplex virus 1 recombinant lacking the glycoprotein G coding sequences is defective in entry through apical surfaces of polarized epithelial cells in culture and in vivo. Proc. Natl. Acad. Sci. USA 97:1818-1822.
47. Umene, K., and T. Kawana. 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.
48. Umene, K., and M. Yoshida. 1989. Reiterated sequences of herpes simplex virus type 1 (HSV-1) genome can serve as physical markers for the differentiation of HSV-1 strains. Arch. Virol. 106:281-299.
49. Vogel, J. U., B. Weber, and H. W. Doerr. 1994. Typing and strain differentiation of clinical herpes simplex virus type 1 and 2 isolates by polymerase chain reaction and subsequent restriction fragment length polymorphism analysis. Zentralbl. Bakteriol. Parasitenkd. Infektkrankh. Hyg. Abt. 1 Orig. 281:502-512.
50. Wagner, R., Jr., and M. Meselson. 1976. Repair tracts in mismatched DNA heteroduplexes. Proc. Natl. Acad. Sci. USA 73:4135-4139.
51. Walker, A., S. J. Petheram, L. Ballard, J. R. Murph, G. J. Demmler, and J. F. Bale, Jr. 2001. Characterization of human cytomegalovirus strains by analysis of short tandem repeat polymorphisms. J. Clin. Microbiol. 39:2219-2226.
52. Wilkinson, D. E., and S. K. Weller. 2004. Recruitment of cellular recombination and repair proteins to sites of herpes simplex virus type 1 DNA replication is dependent on the composition of viral proteins within prereplicative sites and correlates with the induction of the DNA damage response. J. Virol. 78:4783-4796.
53. Yoshida, M., and K. Umene. 2003. Close association of predominant genotype of herpes simplex virus type 1 with eczema herpeticum analyzed using restriction fragment length polymorphism of polymerase chain reaction. J. Virol. Methods 109:11-16.
54. Zhang, Y., and J. L. McKnight. 1993. Herpes simplex virus type 1 UL46 and UL47 deletion mutants lack VP11 and VP12 or VP13 and VP14, respectively, and exhibit altered viral thymidine kinase expression. J. Virol. 67:1482-1492.