Skip to main content
PMC home page
Journal of Virology logoLink to Journal of Virology
. 1996 Jan;70(1):78–83. doi: 10.1128/jvi.70.1.78-83.1996

Human cytomegalovirus clinical isolates carry at least 19 genes not found in laboratory strains.

T A Cha 1, E Tom 1, G W Kemble 1, G M Duke 1, E S Mocarski 1, R R Spaete 1
PMCID: PMC189790  PMID: 8523595

Abstract

Nucleotide sequence comparisons were performed on a highly heterogeneous region of three human cytomegalovirus strains, Toledo, Towne, and AD169. The low-passage, virulent Toledo genome contained a DNA segment of approximately 13 kbp that was not found in the Towne genome and a segment of approximately 15 kbp that was not found in the AD169 genome. The Towne strain contained approximately 4.7 kbp of DNA that was absent from the AD169 genome, and only about half of this segment was present, arranged in an inverted orientation, in the Toledo genome. These additional sequences were located at the unique long (UL)/b' (IRL) boundary within the L component of the viral genome. A region representing nucleotides 175082 to 178221 of the AD169 genome was conserved in all three strains; however, substantial reduction in the size of the adjacent b' sequence was found. The additional DNA segment within the Toledo genome contained 19 open reading frames not present in the AD169 genome. The additional DNA segment within the Towne genome contained four new open reading frames, only one of which shared homology with the Toledo genome. This comparison was extended to five additional clinical isolates, and the additional Toledo sequence was conserved in all. These findings reveal a dramatic level of genome sequence complexity that may explain the differences that these strains exhibit in virulence and tissue tropism. Although the additional sequences have not altered the predicted size of the viral genome (230 to 235 kbp), a total of 22 new open reading frames (denoted UL133 to UL154), many of which have sequence characteristics of glycoproteins, are now defined as cytomegalovirus specific. Our work suggests that wild-type virus carries more than 220 genes, some of which are lost by large-scale deletion and rearrangement of the UL/b' region during laboratory passage.

Full Text

The Full Text of this article is available as a PDF (295.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Bairoch A., Bucher P. PROSITE: recent developments. Nucleic Acids Res. 1994 Sep;22(17):3583–3589. [PMC free article] [PubMed] [Google Scholar]
  3. Brown J. M., Kaneshima H., Mocarski E. S. Dramatic interstrain differences in the replication of human cytomegalovirus in SCID-hu mice. J Infect Dis. 1995 Jun;171(6):1599–1603. doi: 10.1093/infdis/171.6.1599. [DOI] [PubMed] [Google Scholar]
  4. Chandler S. H., McDougall J. K. Comparison of restriction site polymorphisms among clinical isolates and laboratory strains of human cytomegalovirus. J Gen Virol. 1986 Oct;67(Pt 10):2179–2192. doi: 10.1099/0022-1317-67-10-2179. [DOI] [PubMed] [Google Scholar]
  5. Chee M. S., Bankier A. T., Beck S., Bohni R., Brown C. M., Cerny R., Horsnell T., Hutchison C. A., 3rd, Kouzarides T., Martignetti J. A. Analysis of the protein-coding content of the sequence of human cytomegalovirus strain AD169. Curr Top Microbiol Immunol. 1990;154:125–169. doi: 10.1007/978-3-642-74980-3_6. [DOI] [PubMed] [Google Scholar]
  6. Chou J., Roizman B. 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. 1986 Feb;57(2):629–637. doi: 10.1128/jvi.57.2.629-637.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chou S. Comparative analysis of sequence variation in gp116 and gp55 components of glycoprotein B of human cytomegalovirus. Virology. 1992 May;188(1):388–390. doi: 10.1016/0042-6822(92)90771-g. [DOI] [PubMed] [Google Scholar]
  8. Chou S. Molecular epidemiology of envelope glycoprotein H of human cytomegalovirus. J Infect Dis. 1992 Sep;166(3):604–607. doi: 10.1093/infdis/166.3.604. [DOI] [PubMed] [Google Scholar]
  9. Elek S. D., Stern H. Development of a vaccine against mental retardation caused by cytomegalovirus infection in utero. Lancet. 1974 Jan 5;1(7845):1–5. doi: 10.1016/s0140-6736(74)92997-3. [DOI] [PubMed] [Google Scholar]
  10. Gompels U. A., Nicholas J., Lawrence G., Jones M., Thomson B. J., Martin M. E., Efstathiou S., Craxton M., Macaulay H. A. The DNA sequence of human herpesvirus-6: structure, coding content, and genome evolution. Virology. 1995 May 10;209(1):29–51. doi: 10.1006/viro.1995.1228. [DOI] [PubMed] [Google Scholar]
  11. He Y. S., Xu L., Huang E. S. Characterization of human cytomegalovirus UL84 early gene and identification of its putative protein product. J Virol. 1992 Feb;66(2):1098–1108. doi: 10.1128/jvi.66.2.1098-1108.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hohn B., Collins J. A small cosmid for efficient cloning of large DNA fragments. Gene. 1980 Nov;11(3-4):291–298. doi: 10.1016/0378-1119(80)90069-4. [DOI] [PubMed] [Google Scholar]
  13. Huang E. S., Kilpatrick B. A., Huang Y. T., Pagano J. S. Detection of human cytomegalovirus and analysis of strain variation. Yale J Biol Med. 1976 Mar;49(1):29–43. [PMC free article] [PubMed] [Google Scholar]
  14. Kemble G. W., McCormick A. L., Pereira L., Mocarski E. S. A cytomegalovirus protein with properties of herpes simplex virus ICP8: partial purification of the polypeptide and map position of the gene. J Virol. 1987 Oct;61(10):3143–3151. doi: 10.1128/jvi.61.10.3143-3151.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kollert-Jöns A., Bogner E., Radsak K. A 15-kilobase-pair region of the human cytomegalovirus genome which includes US1 through US13 is dispensable for growth in cell culture. J Virol. 1991 Oct;65(10):5184–5189. doi: 10.1128/jvi.65.10.5184-5189.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kozak M. The scanning model for translation: an update. J Cell Biol. 1989 Feb;108(2):229–241. doi: 10.1083/jcb.108.2.229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lagenaur L. A., Manning W. C., Vieira J., Martens C. L., Mocarski E. S. Structure and function of the murine cytomegalovirus sgg1 gene: a determinant of viral growth in salivary gland acinar cells. J Virol. 1994 Dec;68(12):7717–7727. doi: 10.1128/jvi.68.12.7717-7727.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lehner R., Stamminger T., Mach M. Comparative sequence analysis of human cytomegalovirus strains. J Clin Microbiol. 1991 Nov;29(11):2494–2502. doi: 10.1128/jcm.29.11.2494-2502.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Mount S. M. A catalogue of splice junction sequences. Nucleic Acids Res. 1982 Jan 22;10(2):459–472. doi: 10.1093/nar/10.2.459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Pachl C., Probert W. S., Hermsen K. M., Masiarz F. R., Rasmussen L., Merigan T. C., Spaete R. R. The human cytomegalovirus strain Towne glycoprotein H gene encodes glycoprotein p86. Virology. 1989 Apr;169(2):418–426. doi: 10.1016/0042-6822(89)90167-0. [DOI] [PubMed] [Google Scholar]
  21. Pande H., Campo K., Tanamachi B., Zaia J. A. Human cytomegalovirus strain Towne pp65 gene: nucleotide sequence and expression in Escherichia coli. Virology. 1991 May;182(1):220–228. doi: 10.1016/0042-6822(91)90665-x. [DOI] [PubMed] [Google Scholar]
  22. Plotkin S. A., Farquhar J., Horberger E. Clinical trials of immunization with the Towne 125 strain of human cytomegalovirus. J Infect Dis. 1976 Nov;134(5):470–475. doi: 10.1093/infdis/134.5.470. [DOI] [PubMed] [Google Scholar]
  23. Plotkin S. A., Huang E. S. Cytomegalovirus vaccine virus (Towne strain) does not induce latency. J Infect Dis. 1985 Aug;152(2):395–397. doi: 10.1093/infdis/152.2.395. [DOI] [PubMed] [Google Scholar]
  24. Plotkin S. A., Smiley M. L., Friedman H. M., Starr S. E., Fleisher G. R., Wlodaver C., Dafoe D. C., Friedman A. D., Grossman R. A., Barker C. F. Towne-vaccine-induced prevention of cytomegalovirus disease after renal transplants. Lancet. 1984 Mar 10;1(8376):528–530. doi: 10.1016/s0140-6736(84)90930-9. [DOI] [PubMed] [Google Scholar]
  25. Pritchett R. F. DNA nucleotide sequence heterogeneity between the Towne and AD169 strains of cytomegalovirus. J Virol. 1980 Oct;36(1):152–161. doi: 10.1128/jvi.36.1.152-161.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Quinnan G. V., Jr, Delery M., Rook A. H., Frederick W. R., Epstein J. S., Manischewitz J. F., Jackson L., Ramsey K. M., Mittal K., Plotkin S. A. Comparative virulence and immunogenicity of the Towne strain and a nonattenuated strain of cytomegalovirus. Ann Intern Med. 1984 Oct;101(4):478–483. doi: 10.7326/0003-4819-101-4-478. [DOI] [PubMed] [Google Scholar]
  27. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  28. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Spaete R. R., Frenkel N. The herpes simplex virus amplicon: a new eucaryotic defective-virus cloning-amplifying vector. Cell. 1982 Aug;30(1):295–304. doi: 10.1016/0092-8674(82)90035-6. [DOI] [PubMed] [Google Scholar]
  30. Spaete R. R., Mocarski E. S. Regulation of cytomegalovirus gene expression: alpha and beta promoters are trans activated by viral functions in permissive human fibroblasts. J Virol. 1985 Oct;56(1):135–143. doi: 10.1128/jvi.56.1.135-143.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Spaete R. R., Mocarski E. S. The alpha sequence of the cytomegalovirus genome functions as a cleavage/packaging signal for herpes simplex virus defective genomes. J Virol. 1985 Jun;54(3):817–824. doi: 10.1128/jvi.54.3.817-824.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Spaete R. R., Thayer R. M., Probert W. S., Masiarz F. R., Chamberlain S. H., Rasmussen L., Merigan T. C., Pachl C. Human cytomegalovirus strain Towne glycoprotein B is processed by proteolytic cleavage. Virology. 1988 Nov;167(1):207–225. doi: 10.1016/0042-6822(88)90071-2. [DOI] [PubMed] [Google Scholar]
  33. Stenberg R. M., Thomsen D. R., Stinski M. F. Structural analysis of the major immediate early gene of human cytomegalovirus. J Virol. 1984 Jan;49(1):190–199. doi: 10.1128/jvi.49.1.190-199.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Takekoshi M., Ihara S., Tanaka S., Maeda-Takekoshi F., Watanabe Y. A new human cytomegalovirus isolate has an invertible subsegment within its L component producing eight genome isomers. J Gen Virol. 1987 Mar;68(Pt 3):765–776. doi: 10.1099/0022-1317-68-3-765. [DOI] [PubMed] [Google Scholar]
  35. Thompson J., Inamdar A., Jahan N., Doniger J., Rosenthal L. J. Localization and sequence analysis of morphological transforming region III within human cytomegalovirus strain Towne. Intervirology. 1993;36(3):121–127. doi: 10.1159/000150330. [DOI] [PubMed] [Google Scholar]
  36. Thomsen D. R., Stinski M. F. Cloning of the human cytomegalovirus genome as endonuclease XbaI fragments. Gene. 1981 Dec;16(1-3):207–216. doi: 10.1016/0378-1119(81)90077-9. [DOI] [PubMed] [Google Scholar]
  37. Weller T. H. The cytomegaloviruses: ubiquitous agents with protean clinical manifestations. I. N Engl J Med. 1971 Jul 22;285(4):203–214. doi: 10.1056/NEJM197107222850406. [DOI] [PubMed] [Google Scholar]
  38. Weller T. H. The cytomegaloviruses: ubiquitous agents with protean clinical manifestations. II. N Engl J Med. 1971 Jul 29;285(5):267–274. doi: 10.1056/NEJM197107292850507. [DOI] [PubMed] [Google Scholar]
  39. Weststrate M. W., Geelen J. L., Wertheim P. M., van der Noordaa J. Comparison of the physical maps of the DNAs of two cytomegalovirus strains. J Gen Virol. 1983 Jan;64(Pt 1):47–55. doi: 10.1099/0022-1317-64-1-47. [DOI] [PubMed] [Google Scholar]
  40. Weststrate M. W., Geelen J. L., van der Noordaa J. Human cytomegalovirus DNA: physical maps for restriction endonucleases BglII, hindIII and XbaI. J Gen Virol. 1980 Jul;49(1):1–21. doi: 10.1099/0022-1317-49-1-1. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES