Molecular evolution of the γ-herpesvirinae

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 356, Issue 1408, 2001, Pages 421-435

  McGeoch, Duncan J ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

Co speciation; Gene capture; Herpesviridae; Hitchhiking effect; Phylogenetic tree; Recombination

Indexed keywords

ALLELE; EPSTEIN BARR VIRUS; GAMMA HERPESVIRUS; GENETIC CONSERVATION; GENETIC DIVERGENCE; GENETIC RECOMBINATION; GENETIC RELATIONSHIP; GENETIC STRUCTURE; MOLECULAR EVOLUTION; MOUSE; PHYLOGENETIC ANALYSIS; PHYLOGENY; VIRUS GENE; VIRUS GENOME;

HERPESVIRIDAE; HERPESVIRUS 8; HUMAN HERPESVIRUS 4; HUMAN HERPESVIRUS 8; MURINAE; STAPHYLOCOCCUS PHAGE 3A;

EID: 0035967435     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2000.0775     Document Type: Review

References (75)

1. Adachi, J. & Hasegawa, M. 1994 The MOLPHY 2.2 package. Tokyo: Institute of Statistical Mathematics.
2. Agius, C. T., Nagesha, H. S. & Studdert, M. J. 1992 Equine herpesvirus 5: comparisons with EHV2 (equine cytomegalo-virus), cloning and mapping of a new equine herpesvirus with a novel genome structure. Virology 191, 176-186.
3. Albrecht, J. C. 2000 Primary structure of the herpesvirus ateles genome. J. Virol. 74, 1033-1037.
4. Albrecht, J. C. (and 10 others) 1992 Primary structure of the herpesvirus saimiri genome. J. Virol. 66, 5047-5058.
5. Alexander, L., Denekamp, L., Knapp, A., Marcy, R., Auerbach, B. D. & Desrosiers, R. C. 2000 The primary sequence of rhesus monkey rhadinovirus isolate 26-95: sequence similarities to Kaposi's sarcoma-associated herpesvirus and rhesus monkey rhadinovirus isolate 17577. J. Virol. 74, 3388-3398.
6. Baer, R. (and 11 others) 1984 DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature 310, 207-211.
7. Bhatia, K., Raj, A., Gutiérrez, M. I., Judde, J. G., Spangler, G., Venkatesh, H. & Magrath, I. T. 1996 Variation in the sequence of Epstein-Barr virus nuclear antigen 1 in normal peripheral blood lymphocytes and in Burkitt's lymphomas. Oncogene 13, 177-181.
8. Broll, H., Finsterbusch, T., Buhk, H. J. & Goltz, M. 1999 Genetic analysis of the bovine herpesvirus type 4 gene locus for the putative terminase. Virus Genes 19, 243-250.
9. r membrane antigen encoded at the left end of the Epstein-Barr virus genome. J. Virol. 61, 2063-2070.
10. Cho, Y. G., Gordadze, A. V., Ling, P. D. & Wang, F. 1999 Evolution of two types of rhesus-lymphocryptovirus similar to type 1 and type 2 Epstein-Barr virus. J. Virol. 73, 9206-9212.
11. Cook, P. M., Whitby, D., Calabro, M. L., Luppi, M., Kakoola, D. N., Hjalgrim, H., Ariyoshi, K., Ensoli, B., Davison, A. J. & Schulz, T. F. 1999 Variability and evolution of Kaposi's sarcoma-associated herpesvirus in Europe and Africa. AIDS 13, 1165-1176.
12. Dambaugh, T., Hennessy, K., Chammankit, L. & Kieff, E. 1984 U2 region of Epstein-Barr virus DNA may encode Epstein-Barr nuclear antigen 2. Proc. Natl Acad. Sci. USA 81, 7632-7636.
13. Davison, A. J. & Scott, J. E. 1986 The complete DNA sequence of varicella-zoster virus. J. Gen. Virol. 67, 1759-1816.
14. + population. Science 260, 98-100.
15. Ehlers, B., Borchers, K., Grund, C., Frölich, K., Ludwig, H. & Buhk, H. J. 1999 Detection of new DNA polymerase genes of known and potentially novel herpesviruses by PCR with degenerate and deoxyinosine-substituted primers. Virus Genes 18, 211-220.
16. Ensser, A., Pflanz, R. & Fleckenstein, B. 1997 Primary structure of the alcelaphine herpesvirus 1 genome. J. Virol. 71, 6517-6525.
17. Goltz, M., Broll, H., Mankertz, A., Weigelt, W., Ludwig, H., Buhk, H. J. & Borchers, K. 1994 Glycoprotein B of bovine herpesvirus type 4: its phylogenetic relationship to gB equivalents of the herpesviruses. Virus Genes 9, 53-59.
18. Greensill, J., Sheldon, J. A., Renwick, N. W., Beer, B. E., Norley, S., Goudsmit, J. & Schulz, T. F. 2000 Two distinct gamma-2 herpesviruses in African green monkeys: a second gamma-2 herpesvirus lineage among Old World primates. J. Virol. 74, 1572-1577.
19. Gutiérrez, M. I. (and 10 others) 1997 Sequence variations in EBNA-1 may dictate restriction of tissue distribution of Epstein-Barr virus in normal and tumour cells. J. Gen. Virol. 78, 1663-1670.
20. Habeshaw, G., Yao, Q. Y., Bell, A. I., Morton, D. & Rickinson, A. B. 1999 Epstein-Barr virus nuclear antigen 1 sequences in endemic and sporadic Burkitt's lymphoma reflect virus strains prevalent in different geographic areas. J. Virol. 73, 965-975.
21. Hayward, G. S. 1999 KSHV strains: the origins and global spread of the virus. Semin. Cancer Biol. 9, 187-199.
22. Henderson, S. A., Huen, D. & Rowe, M. 1994 Epstein-Barr virus transforming proteins. Semin. Virol. 5, 391-399.
23. Holloway, S. A., Lindquester, G. J., Studdert, M. J. & Drummer, H. E. 1999 Identification, sequence analysis and characterization of equine herpesvirus 5 glycoprotein B. Arch. Virol. 144, 287-307.
24. Honess, R. W., Gompels, U. A., Barrell, B. G., Craxton, M., Cameron, K. R., Staden, R., Chang, Y. N. & Hayward, G. S. 1989 Deviations from expected frequencies of CpG dinucleotides in herpesvirus DNAs may be diagnostic of differences in the states of their latent genomes. J. Gen. Virol. 70, 837-855.
25. Hudson, R. R. 1990 Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 7, 1-44.
26. Ishido, S., Wang, C., Lee, B. S., Cohen, G. B. & Jung, J. U. 2000a Downregulation of major histocompatibility complex class I molecules by Kaposi's sarcoma-associated herpesvirus K3 and K5 proteins. J. Virol. 74, 5300-5309.
27. Ishido, S., Choi, J.-K., Lee, B. S., Wang, C., DeMaria, M., Johnson, R. P., Cohen, G. B. & Jung, J. U. 2000b Inhibition of natural killer cell-mediated cytotoxicity by Kaposi's sarcoma-associated herpesvirus K5 protein. Immunity 13, 365-374.
28. Jones, D. T., Taylor, W. R. & Thornton, J. M. 1992 The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282.
29. Jung, J. U., Trimble, J. J., King, N. W., Biesinger, B., Fleckenstein, B. W. & Desrosiers, R. C. 1991 Identification of transforming genes of subgroup A and C strains of herpesvirus saimiri. Proc. Natl Acad. Sci. USA 88, 7051-7055.
30. Kaplan, N., Darden, T. & Hudson, R. R. 1988 The coalescent process in models with selection. Genetics 120, 819-829.
31. Kaplan, N. L., Hudson, R. R. & Langley, C. H. 1989 The 'hitchhiking effect' revisited. Genetics 123, 887-899.
32. Khanna, R., Slade, R. W., Poulsen, L., Moss, D. J., Burrows, S. R., Nicholls, J. & Burrows, J. M. 1997 Evolutionary dynamics of genetic variation in Epstein-Barr virus isolates of diverse geographical origins: evidence for immune pressure-independent genetic drift. J. Virol. 71, 8340-8346.
33. Koseki, T., Inohara, N., Chen, S., Carrio, R., Merino, J., Hottiger, M. O., Nable, G. J. & Nunez, G. 1999 CIPER, a novel NFκB-activating protein containing a caspase recruitment domain with homology to herpesvirus-2 protein E10. J. Biol. Chem. 274; 9955-9961.
34. Kumar, S. & Hedges, S. B. 1998 A molecular timescale for vertebrate evolution. Nature 392, 917-920.
35. Lacoste, V., Mauclère, P., Dubreuil, G., Lewis, J., Georges-Courbot, M.-C. & Gessain, A. 2000 KSHV-like herpesviruses in chimps and gorillas. Nature 407, 151-152.
36. Lee, S. P., Morgan, S., Skinner, J., Thomas, W. A., Jones, S. R., Sutton, J., Khanna, R., Whittle, H. C. & Rickinson, A. B. 1995 Epstein-Barr virus isolates with the major HLA B35.01-restricted cytotoxic T-lymphocyte epitope are prevalent in a highly B35.01-positive African population. Eur. J. Immunol. 25, 102-110.
37. Lee, H., Veazey, R., Williams, K., Li, M., Guo, J., Neipel, F., Fleckenstein, B., Lackner, A., Desrosiers, R. C. & Jung, J. U. 1998 Deregulation of cell growth by the K1 gene of Kaposi's sarcoma associated herpesvirus. Nature Med. 4, 435-440.
38. Lees, J. F., Arrand, J. E., De V. Pepper, S., Stewart, J. P., Mackett, M. & Arrand, J. R. 1993 The Epstein-Barr virus candidate vaccine antigen gp340/220 is highly conserved between virus types A and B. Virology 195, 578-586.
39. McGeoch, D. J. & Cook, S. 1994 Molecular phylogeny of the Alphaherpesvirinae subfamily and a proposed evolutionary timescale. J. Mol. Biol. 238, 9-22.
40. McGeoch, D. J. & Davison, A. J. 1999a The descent of human herpesvirus 8. Semin. Cancer Biol. 9, 201-209.
41. McGeoch, D. J. & Davison, A. J. 1999b The molecular evolutionary history of the herpesviruses. In Origins and evolution of viruses (ed. E. Domingo, R. Webster & J. Holland), pp. 441-465. London: Academic Press.
42. 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.
43. McGeoch, D. J., Dolan, A. & Ralph, A. C. 2000 Toward a comprehensive phylogeny for mammalian and avian herpesviruses. J. Virol. 74, 10 401-10 406.
44. MacKenzie, J., Gray, D., Pinto-Paes, R., Barrezueta, L. F. M., Armstrong, A., Alexander, F. A., McGeoch, D. J. & Jarrett, R. F. 1999 Analysis of Epstein-Barr virus (EBV) nuclear antigen 1 subtypes in EBV-associated lymphomas from Brazil and the United Kingdom. J. Gen. Virol. 80, 2741-2745.
45. Meng, Y. X. (and 11 others) 1999 Individuals from North America, Australasia and Africa are infected with four different genotypes of human herpesvirus 8. Virology 261, 106-119.
46. Midgley, R. S., Blake, N. W., Yao, Q. Y., Croom-Carter, D., Cheung, S. F., Chan, A. T. C., Johnson, P. J., Huang, D., Rickinson, A. B. & Lee, S. P. 2000 Novel intertypic recombinants of Epstein-Barr virus in the Chinese population. J. Virol. 74, 1544-1548.
47. Minson, A. C., Davison, A. J., Desrosiers, R. C., Fleckenstein, B., McGeoch, D. J., Pellett, P. E., Roizman, B. & Studdert, D. M. J. 2000 Herpesviridae. In Virus taxonomy (ed. M. H. V. van Regenmortel and 10 others), pp. 203-225, New York and San Diego, CA: Academic Press.
48. Neipel, F. & Fleckenstein, B. 1999 The role of HHV-8 in Kaposi's sarcoma. Semin. Cancer Biol. 9, 151-164.
49. Neipel, F., Albrecht, J. C. & Fleckenstein, B. 1997 Cell-homologous genes in the Kaposi's sarcoma-associated rhadinovirus human herpesvirus 8: determinants of its pathogenicity? J. Virol. 71, 4187-4192.
50. Nicholas, J. (and 11 others) 1998 Novel organizational features, captured cellular genes, and strain variability within the genome of KSHV/HHV8. Monogr. Natl Cancer Inst. 23, 79-88.
51. Parker, B. D., Bankier, A., Satchwell, S., Barrell, B. & Farrell, P. J. 1990 Sequence and transcription of Raji Epstein-Barr virus DNA spanning the B95-8 deletion. Virology 179, 339-346.
52. Peng, R. S., Gordadze, A. V., Pananá, E. M. F., Wang, F., Zong, J., Hayward, G. S., Tan, J. & Ling, P. D. 2000 Sequence and functional analysis of EBNA-LP and EBNA2 proteins from non-human primate lymphocryptoviruses. J. Virol. 74, 379-389.
53. Poole, L. J., Zong, J. C., Ciufo, D. M., Alcendor, D. J., Cannon, J. S., Ambinder, R., Orenstein, J. M., Reitz, M. S. & Hayward, G. S. 1999 Comparison of genetic variability at multiple loci across the genomes of the major subtypes of Kaposi's sarcoma associated herpesvirus reveals evidence for recombination and for two distinct types of open reading frame K15 alleles at the right-hand end. J. Virol. 73, 6646-6660.
54. Ramer, J. C., Garber, R. L., Steele, K. E., Boyson, J. F., O'Rourke, C. & Thomson, J. A. 2000 Fatal lymphoproliferative disease associated with a novel gammaherpesvirus in a captive population of common marmosets. Comp. Med. 50, 59-68.
55. Rickinson, A. B., Young, L. S. & Rowe, M. 1987 Influence of Epstein-Barr virus nuclear antigen EBNA2 on the growth phenotype of virus transformed B cells. J. Virol. 61, 1310-1317.
56. Rivailler, P., Quink, C. & Wang, F. 1999 Strong selective pressure for evolution of an Epstein-Barr virus LMP2B homologue in the rhesus lymphocryptovirus. J. Virol. 73, 8867-8872.
57. Rovnak, J., Quackenbush, S. L., Reyes, R. A., Baines, J. D., Parrish, C. R. & Casey, J. W. 1998 Detection of a novel bovine lymphotropic herpesvirus. J. Virol. 72, 4237-4242.
58. Ruf, I. K., Moghaddam, A., Wang, F. & Sample, J. 1999 Mechanisms that regulate Epstein-Barr virus EBNA-1 gene transcription during restricted latency are conserved among lymphocryptoviruses of Old World primates. J. Virol. 73, 1980-1989.
59. Russo, J. J. (and 10 others) 1996 Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8). Proc. Natl Acad. Sci. USA 93, 14 862-14 867.
60. Sample, J., Young, L., Martin, B., Chatman, T., Kieff, E., Rickinson, A. & Kieff, E. 1990 Epstein-Barr virus types 1 and 2 differ in their EBNA-3A, EBNA-3B and EBNA-3C genes. J. Virol. 64, 4084-4092.
61. Schultz, E. R., Rankin, J. G. W., Blanc, M. P., Raden, B. W., Tsai, C. C. & Rose, T. M. 2000 Characterization of two divergent lineages of macaque rhadinoviruses related to Kaposi's sarcoma-associated herpesvirus. J. Virol. 74, 4919-4928.
62. Searles, R. P., Bergquam, E. P., Axthelm, M. K. & Wong, S. W. 1999 Sequence and genomic analysis of a rhesus macaque rhadinovirus with similarity to Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8. J. Virol. 73, 3040-3053.
63. Snudden, D. K., Smith, P. R., Lai, D., Ng, M. H. & Griffin, B. E. 1995 Alterations in the structure of the EBV nuclear antigen, EBNA1, in epithelial cell tumours. Oncogene 10, 1545-1552.
64. Telford, E. A. R., Watson, M. S., Aird, H. C., Perry, J. & Davison, A. J. 1995 The DNA sequence of equine herpesvirus 2. J. Mol. Biol. 249, 520-528.
65. Thome, M., Martinon, F., Hofmann, K., Rubio, V., Steiner, V., Schneider, P., Mattmann, C. & Tschopp, J. 1999 Equine herpesvirus 2 E10 gene product, but not its cellular homologue, activates NF-κB transcription factor and c-Jun N-terminal kinase. J. Biol. Chem. 274, 9962-9968.
66. Triantos, D., Boulter, A. W., Leao, J. C., Di Alberti, L., Porter, S. R., Scully, C. M., Birnbaum, W., Johnson, N. W. & Teo, C. G. 1998 Diversity of naturally occurring Epstein-Barr virus revealed by nucleotide sequence polymorphism in hypervariable domains in the BamHI K and N subgenomic regions. J. Gen. Virol. 79, 2809-2817.
67. Ulrich, S., Goltz, M. & Ehlers, B. 1999 Characterization of the DNA polymerase loci of the novel porcine lymphotropic herpesvirus 1 and 2 in domestic and feral pigs. J. Gen. Virol. 80, 3199-3205.
68. Van Santen, V. L. 1991 Characterization of the bovine herpesvirus 4 major immediate-early transcript. J. Virol. 65, 5211-5224.
69. Vanderplasschen, A. (and 10 others) 2000 A multipotential β-1,6-N-acetylglucosaminyltransferase is encoded by bovine herpesvirus type 4. Proc. Natl Acad. Sci. USA 97, 5756-5761.
70. Virgin, H. W., Latreille, P., Wamsley, P., Hallsworth, K., Weck, K. E., Dal Canto, A. J. & Speck, S. H. 1997 Complete sequence and genomic analysis of murine gammaherpesvirus 68. J. Virol. 71, 5894-5904.
71. Wrightham, M. N., Stewart, J. P., Janjua, N. J., Pepper, S. D. V., Sample, C., Rooney, C. M. & Arrand, J. R. 1995 Antigenic and sequence variation in the C-terminal unique domain of the Epstein-Barr virus nuclear antigen EBNA-1. Virology 208, 521-530.
72. Yang, Z. 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556.
73. Yates, J. L., Camiolo, S. M., Ali, S. & Ying, A. 1996 Comparison of the EBNA1 proteins of Epstein-Barr virus and herpesvirus papio in sequence and function, Virology 222, 1-13.
74. Zimber, U. (and 10 others) 1986 Geographical prevalence of two Epstein-Barr virus types. Virology 154, 56-66.
75. Zong, J. C. (and 16 others) 1999 High-level variability in the ORF-K1 membrane protein gene at the left end of the Kaposi's sarcoma-associated herpesvirus genome defines four major virus subtypes and multiple variants or clades in different human populations. J. Virol. 73, 4156-4170.