Tempo and mode of human and simian T-lymphotropic virus (HTLV/STLV) evolution revealed by analyses of full-genome sequences

Molecular Biology and Evolution

Volumn 17, Issue 3, 2000, Pages 374-386

  Salemi, M ^a   Desmyter, J ^a   Vandamme, A M ^a  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

Author keywords

Evolutionary models; HTLV I; HTLV II; Molecular clock; STLV I; STLV II

Indexed keywords

ARTICLE; CODON; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN T CELL LEUKEMIA VIRUS 1; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RETROVIRUS; VIRUS STRAIN; VIRUS TRANSMISSION;

ANIMALIA; DNA VIRUSES; HTLV; HTLV I; HTLV II; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN T-LYMPHOTROPIC VIRUS 1; PRIMATES; RNA VIRUSES; SIMIAE; SIMIAN T-LYMPHOTROPIC VIRUS 1; SIMIAN T-LYMPHOTROPIC VIRUS 3; UNIDENTIFIED RETROVIRUS;

EID: 0034003229     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026317     Document Type: Article

References (71)

1. BASTIAN, I., J. GARDNER, D. WEBB, and I. GARDNER. 1993. Isolation of a human T-lymphotropic virus type I strain from Australian aboriginals. J. Virol. 67:843-851.
2. BIGGAR, R., M. E. TAYLOR, J. V. NEEL, B. HJELLE, P. H. LEVINE, F. BLACK, G. M. SHAW, P. M. SHARP, and B. HAHN. 1996. Genetic variants of human T-cell lymphotropic virus type II in American Indian groups. Virology 216:165-173.
3. CAVALLI-SFORZA, L. L., P. MENOZZI, and A. PIAZZA. 1994. The history and geography of human genes. Princeton University Press, Princeton, N.J.
4. CIMARELLI, A., C. A. DUCLOS, A. GESSAIN, C. CASOLI, and U. BERTAZZONI. 1996. Clonal expansion of human T-cell leukemia virus type II in patients with high proviral load. Virology 223:362-364.
5. DOMINGO, E., and J. J. HOLLAND. 1994. Mutation rates and rapid evolution of RNA viruses. Pp. 161-184 in S. S. MORSE, ed. The evolutionary biology of viruses. Raven Press, New York.
6. FA, J. A. 1989. The genus Macaca: a review of taxonomy and evolution. Mamm. Rev. 19:45-81.
7. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
8. _. 1993. PHYLIP: phylogenetic inference package. Version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle.
9. FERRER, J. F., E. ESTEBAN, S. DUBE et al. (11 co-authors). 1996. Endemic infection with human T-cell leukemia/lymphoma virus type IIB in Argentinean and Paraguayan Indians: epidemiology and molecular characterization. J. Infect. Dis. 174:944-953.
10. FUKUSHIMA, Y., M. J. LEWIS, C. MONKEN et al. (13 co-authors). 1998. Identification and molecular characterization of human T-lymphotropic virus type II infections in intravenous drug abusers in the former South Vietnam. AIDS Res. Hum. Retroviruses 14:537-540.
11. GESSAIN, A., F. BARIN, J. C. VERNANT, O. GOUT, L. MAURS, A. CALENDER, and G. DE THÉ. 1985. Antibodies to human T lymphotropic virus type-I in patients with tropical spastic paraparesis. Lancet 2:407-410.
12. GESSAIN, A., R. YANAGIHARA, G. FRANCHINI, R. M. GARRUTO, C. L. JENKINS, A. B. AJDUKIEWICZ, R. C. GALLO, and D. C. GAJDUSEK. 1991. Highly divergent molecular variants of human T-lymphotropic virus type I from isolated populations in Papua New Guinea and the Solomon Islands. Proc. Natl. Acad. Sci. USA 88:7694-7698.
13. GIRI, A., P. MARKHAM, L. DIGILIO, G. HURTEAU, R. C. GALLO, and G. FRANCHINI. 1994. Isolation of a novel simian T-cell lymphotropic virus from Pan paniscus that is distantly related to the human T-cell leukemia/lymphotropic virus types I and II. J. Virol. 68:8392-8395.
14. GOUBAU, P., J. DESMYTER, J. GHESQUIERE, and B. KASEREKA. 1992. HTLV-II among pygmies. Nature 359:201 [letter].
15. GOUBAU, P., M. VAN BRUSSEL, A.-M. VANDAMME, H. F. LIU, and J. DESMYTER. 1994. A primate T-lymphotropic virus, PTLV-L, different from human T-lymphotropic viruses types I and II, in a wild-caught baboon (Papio hamadryas). Proc. Natl. Acad. Sci. USA 91:2848-2852.
16. GRASSLY, N. C., and A. RAMBAUT. 1998. PLATO - partial likelihood assessed through optimisation. User manual. PLATO is available via anonymous ftp from evolve.zoo. ox.ac.uk in directory packages/Plato.
17. GREENBERG, J., C. TURNER, and S. ZEGURA. 1986. The settlement of the Americas: a comparison of the linguistic, dental, and genetic evidence. Curr. Anthropol. 27:477-497.
18. HAHN, B. H., G. M. SHAW, M. POPOVIC, A. LO-MONICO, R. C. GALLO, and F. STAAL-WONG. 1984. Molecular cloning and analysis of a new variant of human T-cell leukemia virus (HTLV-Ib) from an African patient with adult T-cell leukemia-lymphoma. Int. J. Cancer 34:613-618.
19. HALL, W. W., K. TAKAYUKI, S. IJICHI, H. TAKAHASHI, and S. W. ZHU. 1994. Human T cell leukemia/lymphoma virus type II (HTLV-II): emergence of an important newly recognized pathogen. Semin. Virol. 5:165-178.
20. HALL, W. W., H. TAKAHASHI, C. LIU, M. H. KAPLAN, O. SCHEEWIND, S. IJICHI, K. NAGASHIMA, and R. C. GALLO. 1992. Multiple isolates and characteristics of human T-cell leukemia virus type II. J. Virol. 66:2456-2463.
21. HASEGAWA, M., H. KISHINO, and T. YANO. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
22. HILLIS, D. M., and J. HUELSENBECK. 1992. Signal, noise, and reliability in molecular phylogenetic analysis. J. Hered. 83: 189-195.
23. HJELLE, B., S. W. ZHU, H. TAKAHASHI, S. IJICHI, and W. W. HALL. 1993. Endemic human T cell leukemia virus type II infection in southwestern US Indians involves two prototype variants of virus. J. Infect. Dis. 168:737-740.
24. HUELSENBECK, J., and B. RANNALA. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227-232.
25. IBRAHIM, F., G. DE THÉ, and A. GESSAIN. 1995. Isolation and characterization of a new simian T-cell leukemia virus type I from naturally infected Celebes macaques (Macaca tonkeana): complete nucleotide sequence and phylogenetic relationship with the Australo-Melanesian human T-cell leukemia virus type I. J. Virol. 69:6980-6993.
26. JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. MUNRO, ed. Mammalian protein metabolism. Academic Press, New York.
27. KALYANARAMAN, V. S., M. G. SARNGADHARAN, M. ROBERT-GUROFF, I. MIYOSHI, D. GOLDE, and R. C. GALLO. 1982. A new subtype of human T-cell leukemia virus (HTLV-II) associated with a T-cell variant of hairy cell leukemia. Science 218:571-573.
28. KENT, R. K. 1962. From Madagascar to the Malagasy Republic. Brittanica Encyclopedia, London.
29. KIMURA, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
30. KUMAR, S., K. TAMURA, and M. NEI. 1993. MEGA: molecular evolutionary genetic analysis. Version 1.0. Pennsylvania State University, University Park.
31. LEE, H., P. SWANSON, V. S. SHORTY, J. A. ZACK, J. D. ROSENBLATT, and I. S. Y. CHEN. 1989. High rate of HTLV-II infection in seropositive IV drug abusers in New Orleans. Science 244:471-475.
32. LI, W.-H. 1997. Molecular evolution. Sinauer, Sunderland, Mass.
33. LI, W.-H., and M. TANIMURA. 1987. The molecular clock runs more slowly in man than in apes and monkeys. Nature 326: 93-96.
34. LI, W.-H., K. H. WOLFE, J. SOURDIS, P. SHARP. 1987. Reconstruction of phylogenetic trees and estimation of divergence times under nonconstant rates of evolution. Cold Spring Harb. Symp. Quant. Biol. 52:847-856.
35. LIU, H. F., A.-M. VANDAMME, M. VAN BRUSSEL, J. DESMYTER, and P. GOUBAU. 1994. New retroviruses in human and simian T-lymphotropic viruses. Lancet 344:265-266.
36. LIU, H. F., P. GOUBAU, M. VAN BRUSSEL, K. VAN LAETHEM, Y. C. CHEN, J. DESMYTER, and A.-M. VANDAMME. 1996. The three human T-lymphotropic virus type I subtypes arose from three geographically distinct simian reservoirs. J. Gen. Virol. 77:359-368.
37. MAHIEUX, R., C. CHAPPEY, M. C. GEORGES-COUBOT, G. DEBREUIL, P. MAUCLERE, A. GEORGES, and A. GESSAIN. 1998. Simian T-lymphotropic virus type I from Mandrillus sphinx as a simian counterpart of human T-cell lymphotropic type I subtype D. J. Virol. 72:10316-10322.
38. MAHIEUX, R., F. IBRAHIM, P. MAUCLERE et al. (14 co-authors). 1997. Molecular epidemiology of 58 new African human T-cell leukemia virus type I (HTLV-I) strains: identification of a new and distinct HTLV-1 molecular subtype in Central Africa and in pygmies. J. Virol. 71:1317-1333.
39. MAHIEUX, R., J. PECON-SLATTERY, and A. GESSAIN. 1997. Molecular characterization and phylogenetic analyses of a new, highly divergent simian T-cell lymphotropic virus (STLV-1marc1) in Macaca arctoides. J. Virol. 71:6253-6258.
40. MALONEY, E. M., R. J. BIGGAR, J. V. NEEL, M. TAYLOR, B. H. HAHN, G. M. SHAW, and W. A. BLATTNER. 1992. Endemic human T cell lymphotropic virus type II infection among isolated Brazilian Amerindians. J. Infect. Dis. 166: 100-107.
41. MIURA, T., T. FUKUNAGA, and T. IGARASHI. 1994. Phylogenetic subtypes of human T-lymphotropic virus type I and their relations to the anthropological background. Proc. Natl. Acad. Sci. USA 91:1124-1127.
42. NEEL, J. V., R. J. BIGGAR, and R. I. SUZERNIK. 1994. Virologic and genetic studies relate Amerind origins to the indigenous people of the Mongolia/Manchuria/southeastern Siberia region. Proc. Natl. Acad. Sci. USA 91:10737-10741.
43. NEI, M., and T. GOJOBORI. 1986. Simple methods for estimat-ing the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
44. NIESELT-STRUVE, K. 1998. Combining likelihood-mapping and statistical geometry to a new sequence analysis tool. Pp. 13-22 in M. K. UYENOYAMA and A. VON HAESELER, eds. Prooceedings of the Trinational Workshop on Molecular Evolution. University of Munich, Munich, Germany.
45. OSAME, M., M. MATSUMOTO, K. USUKU, S. IZUMO, N. IJICHI, H. AMITANI, M. TARA, and A. IGATA. 1987. Chronic progressive myelopathy associated with elevated antibodies to human T-lymphotropic virus type I and adult T-cell leukemia like cells. Ann. Neurol. 21:117-122.
46. POIESZ, B. J., F. W. RUSCETTI, A. F. GAZDAR, P. A. BUNN, J. A. MINNA, and R. C. GALLO. 1980. Detection and isolation of type C retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma. Proc. Natl. Acad. Sci. USA 77:7415-7419.
47. ROBERTS, D., G. R. JONES, and M. A. SMITH. 1990. Report of thermoluminescence dates supporting arrival of people between 50 and 60 k. y. in southern Australia. Nature 345: 153.
48. SAKSENA, N. K., M. P. SHERMAN, R. YANAGIHARA, D. K. DUBE, and B. J. POIESZ. 1992. LTR sequence and phylogenetic analyses of a newly discovered variant of HTLV-I isolated from the Hagahai of Papua New Guinea. Virology 189:1-9.
49. SALEMI, M., M. LEWIS, J. F. EGAN, W. W. HALL, J. DESMYTER, and A.-M. VANDAMME. 1999. Different population dynamics and evolutionary rates of human T-cell lymphotropic virus type II (HTLV-II) in injecting drug users compared to in endemically infected Amerindian and Pygmy tribes. Proc. Natl. Acad. Sci. USA 69:13253-13258.
50. SALEMI, M., A.-M. VANDAMME, C. GRADOZZI, K. VAN LAETHEM, E. CATTANEO, G. TAYLOR, C. CASOLI, P. GOUBAU, J. DESMYTER, and U. BERTAZZONI. 1998a. Evolutionary rate and genetic heterogeneity of human T-cell lymphotropic virus type II (HTLV-II) using new isolates from European injecting drug users. J. Mol. Evol. 46:602-611.
51. SALEMI, M., S. VAN DOOREN, E. AUDENAERT, E. DELAPORTE, P. GOUBAU, J. DESMYTER, and A.-M. VANDAMME. 1998b. Two new human T-lymphotropic virus type I phylogenetic subtypes in seroindeterminates, a Mbuti pygmy and a Gabonese, have closest relatives among African STLV-I strains. Virology 246:277-287.
52. SARICH, V. M., and A. C. WILSON, 1967. Immunological time scale for hominid evolution. Science 158:1200-1203.
53. SONG, K. J., V. R. NERURKAR, N. SAITOU, A. LAZO, J. R. BLAKESLEE, I. MIYOSHI, and R. YANAGIHARA. 1994. Genetic analysis and molecular phylogeny of simian T-cell lymphotropic virus type I: evidence for independent virus evolution in Asia and Africa. Virology 199:56-66.
54. STRIMMER, K., and A. VON HAESELER. 1997. Likelihood mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl. Acad. Sci. USA 94:6815-6819.
55. SUZUKI, Y., and T. GOJOBORI. 1998. The origin and evolution of the human T-cell lymphotropic virus type I and II. Virus Genes 16:69-84.
56. TAMURA, K., and M. NEI. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzess. Mol. Biol. Evol. 10:512-526.
57. VAN BRUSSEL, M., P. GOUBAU, R. ROUSSEAU, J. DESMYTER, and A.-M. VANDAMME, 1997. Complete nucleotide sequence of a new simian T-lymphotropic virus, STLV-PH969 from hamadryas baboon, and unusual features of its long terminal repeats. J. Virol. 71:5464-5472.
58. VANDAMME, A.-M., H.-F. LIU, P. GOUBAU, and J. DESMYTER. 1994. Primate T-lymphotropic virus type I LTR sequence variation and its phylogenetic analysis: compatibility with an African origin of PTLV-I. Virology 202:212-223.
59. VANDAMME, A.-M., H.-F. LIU, M. VAN BRUSSEL, W. DE MEURICHY, J. DESMYTER, and P. GOLIBAU. 1996. The presence of a divergent T-lymphotropic virus in a wild-caught pygmy chimpanzee (Pan paniscus) supports and African origin for the human T-lymphotropic/simian T-lymphotropic group of viruses. J. Gen. Virol. 77:1089-1099.
60. VANDAMME, A.-M., M. SALEMI, and J. DESMYTER. 1998. The simian origins of the pathogenic human T-cell lymphotropic virus type I. Trends Microbiol. 6:477-483.
61. VANDAMME, A.-M., M. VAN BRUSSEL, H.-F. LIU, M. SALEMI, K. VAN LAETHEM, M. VAN RANST, L. MICHELS, J. DESMYTER, and P. GOUBAU. 1998. African origin of human T-lymphotropic virus type II (HTLV-II) supported by a new subtype HTLV-IId in Zairean Bambuti Efe pygmies. J. Virol. 72:4327-4340.
62. WATANABE, T., M. SEIKI, Y. HIRAYAMA, and M. YOSHIDA. 1986. Human T-cell leukemia virus type I is a member of the African subtype of simian viruses (STLV). Virology 148:385-388.
63. WATTEL, E., J.-P. VARTANIAN, C. PANNETIER, and S. WAIN-HOBSON. 1995. Clonal expansion of human T-cell leukemia virus type I - infected cells in asymptomatic and symptomatic carriers without malignancy. J. Virol. 69:2863-2868.
64. WU, C. I., and W-H. LI. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82:1741-1745.
65. XIA, X. 1999. DAMBE 3.0 (software package for data analysis in molecular biology and evolution). Department of Ecology and Biodiversity, University of Hong Kong, Hong Kong.
66. YANG, Z., 1993. Maximum likelihood estimation of the phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
67. _. 1994a. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.
68. _. 1994b. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites. J. Mol. Evol. 39:306-314.
69. _. 1997. Phylogenetic analysis by maximum-likelihood (PAML). Version 1.3b. Pennsylvania State University, Institute of Molecular Evolutionary Genetics, University Park.
70. YOSHIDA, M., I. MIYOSHI, and Y. HINUMA. 1982. Isolation and characterization of retrovirus from cell lines of human adult T-cell leukemia and its implication in the disease. Proc. Natl. Acad. Sci. USA 79:2031-2035.
71. ZELLA, D., L. MORI, M. SALA, P. FERRANTE, C. CASOLI, G. MAGNANI, G. ACHILLI, E. CATTANEO, F. LORI, and U. BERTAZZONI. 1990. HTLV-II infection in Italian drug abusers. Lancet 2:575-576.