The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin

Journal of Virology

Volumn 70, Issue 10, 1996, Pages 7013-7029

  Gao, Feng ^a   Robertson, David L ^c   Morrison, Sandra G ^a   Hui, Huxiong ^a   Craig, Stevenson ^a   Decker, Julie ^a   Fultz, Patricia N ^b   Girard, Marc ^d   Shaw, George M ^a,b   Hahn, Beatrice H ^a,b   Sharp, Paul M ^c  

^a University of Alabama at Birmingham   (United States)

^b University of Alabama at Birmingham   (United States)

^c UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^d INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; ENVELOPE GENE; GENETIC POLYMORPHISM; HETEROSEXUALITY; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NONHUMAN; PRIORITY JOURNAL; SEXUAL TRANSMISSION; STRAIN DIFFERENCE; THAILAND; VIRUS GENE; VIRUS STRAIN; VIRUS TRANSMISSION;

EID: 9544220664     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.70.10.7013-7029.1996     Document Type: Article

References (115)

1. Alizon, M., S. Wain-Hobson, L. Montagnier, and P. Sonigo. 1986. Genetic variability of the AIDS virus: nucleotide sequence analysis of two isolates from African patients. Cell 46:63-74.
2. Artenstein, A. W., J. Coppola, A. E. Brown, J. K. Carr, E. Sanders-Buell, E. Galbarini, J. R. Mascola, T. C. VanCott, P. Schonbrood, and F. E. McCutchan. 1995. Multiple introductions of HIV-1 subtype E into the western hemisphere. Lancet 346:1197-1198.
3. Ausubel, F. M., R. Brent, R. E. Kinston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl, (ed.), 1987. Current protocols in molecular biology. John Wiley & Sons, New York.
4. Barre-Sinoussi, F., M.-C. Georges-Courbot, P. N. Fultz, E. Muchmore, E. van der Ryst, S. Saragosti, G. Dubreuil, A. Georges, and M. Girard. Characterization and titration of an HIV-1 clade E chimpanzee challenge stock. Submitted for publication.
5. Berkhout, B. 1992. Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis. Nucleic Acids Res. 20: 27-31.
6. Bobkov, A., R. Cheingsong-Popov, M. Garaev, A. Rzhaninova, P. Kaleebu, S. Beddows, M. H. Bachmann, J. I. Mullins, J. Louwagie, W. Janssens, G. van der Groen, F. McCutchan, and J. Weber. 1994. Identification of an env G subtype and heterogeneity of HIV-1 strains in the Russian Federation and Belarus. AIDS 8:1649-1655.
7. Bolognesi, D. P., L. Corey, S. H. Vermund, and D. F. Hoth. 1994. HIV vaccine development: a progress report. Ann. Intern. Med. 8:603-611.
8. Brodine, S. K., J. R. Mascola, P. J. Weiss, S. I. Ito, K. R. Porter, A. W. Artenstein, F. C. Garland, F. E. McCutchan, and D. S. Burke. 1995. Detection of diverse HIV-1 genetic subtypes in the USA. Lancet 346:1198-1199.
9. Carr, J. K., M. O. Salminen, C. Koch, D. Gotte, A. W. Artenstein, P. A. Hegerich, D. St. Louis, D. S. Burke, and F. E. McCutchan. 1996. Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand. J. Virol. 70:5935-5943.
10. Chakrabarti, R., F. M. Hofman, R. Pandep, L. E. Mathes, and P. Roy-Burman. 1994. Recombination between feline exogenous and endogenous retroviral sequence generates tropism for cerebral endothelial cells. Am. J. Pathol. 144:348-358.
11. Coffin, J. M. 1979. Structure, replication, and recombination of retrovirus genomes: some unifying hypotheses. J. Gen. Virol. 42:1-26.
12. Coffin, J. M. 1990. Retroviridae and their replication, p. 1437-1500. In B. N. Fields and D. M. Knipe (ed.), Fields virology. Raven Press, New York.
13. Coffin, J. M. 1995. HIV population dynamics in vivo: implifications for genetic variation, pathogenesis and therapy. Science 267:483-489.
14. Cohen, J. 1995. Thailand weighs AIDS vaccine tests. Science 270:904-907.
15. Delassus, S., R. Cheynier, and S. Wain-Hobson. 1991. Evolution of human immunodeficiency virus type 1 nef and long terminal repeat sequence over 4 years in vivo and in vitro. J. Virol. 65:225-231.
16. Diaz, R. S., E. C. Sabino, A. Mayer, J. W. Mosley, M. P. Busch, and The Transfusion Safety Study Group. 1995. Dual human immunodeficiency virus type 1 infection and recombination in a dually exposed transfusion recipient. J. Virol. 69:3273-3281.
17. Douglas, N. W., A. I. Knight, A. Hayhurst, W. Y. Barrett, M. J. Kevany, and R. S. Daniels. 1996. An efficient method for the rescue and analysis of functional HIV-1 env genes: evidence for recombination in the vicinity of the tat/rev splice site. AIDS 10:39-46.
18. Faulkner, D. M., and J. Jurka. 1988. Multiple aligned sequence editor (MASE). Trends Biochem. Sci. 13:321-322.
19. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
20. Felsenstein, J. 1992. PHYLIP (Phylogeny Inference Package), 3.5c ed. Department of Genetics, University of Washington, Seattle, Wash.
21. Feng, S., and E. C. Holland. 1988. HIV-1 tat trans-activation requires the loop sequence within tar. Nature (London) 334:165-167.
22. Fenrick, R., M. H. Malim, J. Hauber, S.-Y. Le, J. Maizel, and B. R. Cullen. 1989. Functional analysis of the Tat trans-activator of human immunodeficiency virus type 2. J. Virol. 63:5006-5012.
23. Fultz, P. N. Personal communication.
24. Fultz, P. N., Q. Wei, J. Stallworth, F. Barre-Sinoussi, A. Deslandres, and M. Girard. 1995. Superinfection of chimpanzees with HIV-1 strains representing the same or different subtypes, p. 257-262. In M. Girard and B. Dodet (ed.), Retroviruses of human AIDS and related animal diseases. Dixieme Colloque des Cent Gardes. Pasteur Mérieux, Marnes-la-coquette, France.
25. Gao, F., and B. H. Hahn. Unpublished data.
26. Gao, F., S. G. Morrison, D. L. Robertson, C. L. Thornton, S. Craig, G. Karlsson, J. Sodroski, M. Morgado, B. Galvao-Castro, H. von Briesen, S. Beddows, J. Weber, P. M. Sharp, G. M. Shaw, B. H. Hahn, and WHO and NIAID Networks for HIV Isolation and Characterization. 1996. Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. J. Virol. 70:1651-1667.
27. Gao, F., L. Yue, S. Craig, C. L. Thornton, D. L. Robertson, F. E. McCutchan, J. A. Bradac, P. M. Sharp, and B. H. Hahn. 1994. Genetic variation of HIV type 1 in four World Health Organization-sponsored vaccine evaluation sites: generation of functional envelope (glycoprotein 160) clones representative of sequence subtypes A, B, C, and E. AIDS Res. Hum. Retroviruses 10:1359-1368.
28. Gao, F., L. Yue, A. T. White, P. G. Pappas, J. Barchue, A. P. Hanson, B. M. Greene, P. M. Sharp, G. M. Shaw, and B. H. Hahn. 1992. Human infection by genetically diverse SIV related HIV-2 in West Africa. Nature (London) 358:495-499.
29. Gaynor, R. 1992. Cellular transcription factors involved in the regulation of HIV-1 gene expression. AIDS 6:347-363.
30. Ghosh, S. K., P. N. Fultz, E. Keddie, M. S. Saag, P. M. Sharp, B. H. Hahn, and G. M. Shaw. 1993. A molecular clone of HIV-1 tropic and cytopathic for human and chimpanzee lymphocytes. Virology 194:858-864.
31. Golovkina, T. V., A. B. Jaffe, and S. R. Ross. 1994. Coexpression of exogenous and endogenous mouse mammary tumor virus RNA in vivo results in viral recombination and broadens the virus host range. J. Virol. 68:5019-5026.
32. Goodrich, D. W., and P. H. Duesberg. 1990, Retroviral recombination during reverse transcription. Proc. Natl. Acad. Sci. USA 87:2052-2056.
33. Graham, B. S., and P. F. Wright. 1995. Candidate AIDS vaccines. N. Engl. J. Med. 333:1331-1339.
34. Groenink, M., A. C. Andeweg, R. A. M. Fouchier, S. Broersen, R. C. M. van der Jagt, H. Schuitemaker, R. E. Y. de Goede, M. L. Bosch, H. G. Huisman, and M. Tersmette. 1992. Phenotype-associated env gene variation among eight related human immunodeficiency virus type 1 clones: evidence for in vivo recombination and determinants of cytotropism outside the V3 domain. J. Virol. 66:6175-6180.
35. Hahn, B. H., D. L. Robertson, and P. M. Sharp. 1995. Intersubtype recombination in HIV-1 and HIV-2, p. III-22-III-29. In G. Myers, B. Korber, S. Wain-Hobson. K.-T. Jeang, L. E. Henderson. and G. N. Pavlakis (ed.), Human retroviruses and AIDS 1995: a compilation and analysis of nucleic acid and amino acid sequences. Los Alamos National Laboratory. Los Alamos. N.Mex.
36. Hahn, B. H., G. M. Shaw, S. K. Arya, M. Popovic, R. C. Gallo, and F. Wong-Staal. 1984. Molecular cloning and characterization of the HTLV-III virus associated with AIDS. Nature (London) 321:166-169.
37. Harrich, D., C. Ulich, and R. B. Gaynor. 1996. A critical role for the TAR element in promoting efficient human immunodeficiency virus type 1 reverse transcription. J. Virol. 70:4017-4027.
38. Higgins, D. G., and P. M. Sharp. 1989. Fast and sensitive multiple sequence alignments on a microcomputer. Comput. Appl. Biosci. 5:151-153.
39. Ho, D. D., A. U. Neumann, A. S. Perelson, W. Chen, J. M. Leonard, and M. Markowitz. 1995. Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature (London) 373:123-126.
40. Howell, R. M., J. E. Fitzgibbon, M. Noe, Z. Ren, D. J. Gocke, T. A. Schwartzer, and D. T. Dubin. 1991. In vivo sequence variation of the human immunodeficiency virus type 1 env gene: evidence for recombination among variants found in a single individual. AIDS Res. Hum. Retroviruses 7:869-876.
41. Hu, W.-S., and H. M. Temin. 1990. Retroviral recombination and reverse transcription. Science 250:1227-1233.
42. Hu, W.-S., and H. M. Temin. 1990. Genetic consequences of packaging two RNA genomes in one retroviral particle: pseudodiploidy and high rate of genetic recombination. Proc. Natl. Acad. Sci. USA 87:1556-1560.
43. Jameel, S., M. Zafrullah, M. Ahmad, G. S. Kapoor, and S. Sehgal. 1995. A genetic analysis of HIV-1 from Punjab, India reveals the presence of multiple variants. AIDS 9:685-690.
44. Jin, M. J., H. Hui, D. L. Robertson, M. C. Muller, F. Barre-Sinoussi, V. M. Hirsch, J. S. Allan, G. M. Shaw, P. M. Sharp, and B. H. Hahn. 1994. Mosaic genome structure of simian immunodeficiency virus from West African green monkeys. EMBO J. 13:2935-2947.
45. Jones, K. A., and B. M. Peterlin. 1994. Control of RNA initiation and elongation at the HIV-1 promoter. Annu. Rev. Biochem. 63:717-743.
46. Kaleebu, P., A. Bobkov, R. Cheingsong-Popov, P. Bieniasz, M. Garaev, and J. Weber. 1995. Identification of HIV-1 subtype G from Uganda. AIDS Res. Hum. Retroviruses 11:657-659.
47. Kalish, M. L., A. Baldwin, S. Raktham, C. Wasi, C.-C. Luo, G. Schochetman. T. D. Mastro, N. Young, S. Vanichseni, H. Rubsamen-Waigmann, H. von Briesen, J. I. Mullins, E. Delwart, B. Herring, J. Esparza, W. L. Heyward, and S. Osmanov. 1995. The evolving molecular epidemiology of HIV-1 envelope subtypes in injecting drug users in Bangkok, Thailand: implications for HIV vaccine trials. AIDS 9:851-857.
48. Katz, R. A., and A. M. Skalka. 1990. Generation of diversity in retroviruses. Annu. Rev. Genet. 24:409-445.
49. Kellam, P., and B. A. Larder. 1995. Retroviral recombination can lead to linkage of reverse transcriptase mutations that confer increased zidovudine resistance. J. Virol. 69:669-674.
50. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparitive studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
51. Korber, B. T. M., S. Osmanov, J. Esparza, G. Myers, and WHO Network for HIV Isolation and Characterization. 1994. The World Health Organization Global Programme on AIDS Proposal for Standardization of HIV Sequence Nomenclature. AIDS Res. Hum. Retroviruses 10:1355-1358.
52. Kostrikis, L. G., E. Bagdades, Y. Cao, L. Zhang, D. Dimitriou, and D. D. Ho. 1995. Genetic analysis of human immunodeficiency virus type 1 strains from patients in Cyprus: identification of a new subtype designated subtype I. J. Virol. 69:6122-6130.
53. Kunanusont, C., H. M. Foy, J. K. Kreiss, S. Rerks-Ngarm, P. Phanuphak, S. Raktham, C.-P. Pau, and N. L. Young. 1995. HIV-1 subtypes and male-to-female transmission in Thailand. Lancet 345:1078-1083.
54. Kusumi, K., B. Conway, S. Cunningham, A. Berson, C. Evans, A. K. N. Iversen, D. Colvin, M. V. Gallo, S. Coutre, E. G. Shpaer, D. V. Faulkner, A. deRonde, S. Volkman, C. Williams, M. S. Hirsch, and J. I. Mullins. 1992. Human immunodeficiency virus type 1 envelope gene structure and diversity in vivo and after cocultivation in vitro. J. Virol. 66:875-885.
55. Larder, B. A., P. Kellam, and S. D. Kemp. 1993. Convergent combination therapy can select viable multidrug-resistant HIV-1 in vitro. Nature (London) 365:451-453.
56. Leitner, T., A. Alaeus, S. Marquina, E. Lilja, K. Lidman, and J. Albert. 1995. Yet another subtype of HIV type 1? AIDS Res. Hum. Retroviruses 11:995-997.
57. Leitner, T., D. Escanilla, S. Marquina, J. Wahlberg, C. Brotstrom, H. B. Hansson, M. Uhlen, and J. Albert. 1995. Biological and molecular characterization of subtype D, G, and A/D recombinant HIV-1 transmissions in Sweden. Virology 209:136-146.
58. Li, W.-H. 1993. Unbiased estimation of the rates of synonymous and non-synonymous substitution. J. Mol. Evol. 36:96-99.
59. Li, W.-H., M. Tanimura, and P. M. Sharp. 1988. Rates and dates of divergence between AIDS virus nucleotide sequences. Mol. Biol. Evol. 5:313-330.
60. Li, Y., J. C. Kappes, J. A. Conway, R. W. Price, G. M. Shaw, and B. H. Hahn. 1991. Molecular characterization of human immunodeficiency virus type 1 cloned directly from uncultured human brain tissue: identification of replication-competent and -defective viral genomes. J. Virol. 65:3973-3985.
61. Liu, H., K. X. Wu, M. Newman, G. M. Shaw, B. H. Hahn, and J. C. Kappes. 1995. The Vif protein of human and simian immunodeficiency viruses is packaged into virions and associates with viral core structures. J. Virol. 69:7630-7638.
62. Loussert-Ajaka, I., M.-L. Chaic, B. T. M. Korber, F. Letournearu, E. Gomas, E. Alien, T.-D. Ly, F. Brun-Vezinet, F. Simon, and S. Saragosti. 1995. Variability of human immunodeficiency virus type 1 group O strains isolated from Cameroonian patients living in France. J. Virol. 69:5640-5649.
63. Louwagie, J., F. E. McCutchan, M. Peeters, T. P. Brennan, E. Sanders-Buell, G. A. Eddy, G. van der Groen, K. Fransen, G.-M. Gershy-Damet, R. Deleys, and D. S. Burke. 1993. Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes. AIDS 7:769-780.
64. Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning: a laboratory manual, p. 269-295. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
65. Mansky, L. M., and H. M. Temin. 1995. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J. Virol. 69:5087-5094.
66. Martin-Gallardo, A., J. Lamerdin, and A. Carrano. 1994. Shotgun sequencing, p. 37-41. In M. D. Adams, C. Fields, and J. C. Venter (ed.), Automated DNA sequencing and analysis. Academic Press, London.
67. Mastro, T. D., G. A. Saiten, T. Nobkesorn, S. Sangkharomya, and I. M. Longini, Jr. 1994. Probability of female-male transmission of HIV-1 in Thailand. Lancet 343:204-207.
68. McCutchan, F. E., P. A. Hegerich, T. P. Brennan, P. Phanuphak, P. Singharaj, A. Jugsudee, P. W. Berman, A. M. Gray, A. K. Fowler, and D. S. Burke. 1992. Genetic variants of HIV-1 in Thailand. AIDS Res. Hum. Retroviruses 8:1887-1895.
69. Miyamoto, S., and I. M. Verma. 1995. Rel/NF-κB/IκB story. Adv. Cancer Res. 66:255-292.
70. Moore, J., and R. Anderson. 1994. The WHO and why of HIV vaccine trials. Nature (London) 372:313-314.
71. Moore, J. P., and D. D. Ho. 1995. HIV-1 neutralization: the consequences of viral adaptation to growth on transformed T cells. AIDS 9:S117-S136.
72. Muesing, M., D. H. Smith, C. Cabradilla, C. Benton, L. Lasky, and D. Capon. 1985. Nucleic acid structure and expression of human AIDS retrovirus. Nature (London) 313:450-458.
73. Murphy, E., B. Korber, M.-C. Georges-Courbot, B. You, A. Pinter, D. Cook, M.-P. Kieny, A. Georges, C. Mathiot. F. Barre-Sinoussi, and M. Girard. 1993. Diversity of V3 region sequences of human immunodeficiency viruses type 1 from the Central African Republic. AIDS Res. Hum. Retroviruses 9:997-1007.
74. Myers, G. 1994. HIV: between past and future. AIDS Res. Hum. Retroviruses 10:1317-1324.
75. Myers, G., B. Korber, J. A. Berzofsky, R. F. Smith, and G. N. Pavlakis. 1992. Human retroviruses and AIDS: a compilation and analysis of nucleic acid and amino acid sequences. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, N.Mex.
76. Myers, G., B. Korber, B. H. Hahn, K.-T. Jeang, J. W. Mellors, F. E. McCutchan, L. E. Henderson, and G. N. Pavlakis. 1995. Human retroviruses and AIDS 1995: a compilation and analysis of nucleic acid and amino acid sequences. Los Alamos National Laboratory. Los Alamos, N.Mex.
77. Najera, I., D. D. Richman, I. Olivares, J. M. Rojas, M. A. Peinado, M. Perucho, R. Najera, and C. Lopez-Galindez. 1994 Natural occurrence of drug resistance mutations in the1 reverse transcriptase of human immunodeficiency virus type 1 isolates. AIDS Res. Hum. Retroviruses 10:1479-1488.
78. Nelson, K. E., D. D. Celentano, S. Suprasert, N. Wright, S. Eiumtrakul, S. Tulvatana, A. Matanasarawoot, P. Akarasewi, S. Kontolbutra, S. Romyen, N. Sirisopana, and C. Theetranont. 1993. Risk factors for HIV infection among young adult men in Northern Thailand. JAMA 270:955-960.
79. Nkengasong, J. N., W. Janssens, L. Heyndrickx, K. Fransen, P. M. Ndumbe, J. Motte, A. Leonaers, M. Ngolle, J. Ayuk, P. Piot, and G. van der Groen. 1994. Genetic subtypes of HIV-1 in Cameroon. AIDS 8:1405-1412.
80. Nopkesorn, T., T. D. Mastro, S. Sangkharomya, M. Sweat, P. Singharaj, K. Limpakarnjanarat, H. D. Gayle, and B. G. Weniger. 1993. HIV-1 infection in young men in northern Thailand. AIDS 7:1233-1239.
81. Ou, C.-Y., Y. Takebe, C.-C. Luo, M. Kalish, W. Auwanit, C. Bandea, N. de la Torre, J. L. Moore, G. Schochetman, S. Yamazaki, H. D. Gayle, N. L. Young, and B. G. Weniger. 1992. Wide distribution of two subtypes of HIV-1 in Thailand. AIDS Res. Hum. Retroviruses 8:1471-1472.
82. Ou, C.-Y., Y. Takebe, B. G. Weniger, C.-C. Luo, M. L. Kalish, W. Auwanit, S. Yamazaki, H. D. Gayle, N. L. Young, and G. Schochetman. 1993. Independent introductions of two major HIV-1 genotypes into distinct high-risk populations in Thailand. Lancet 341:1171-1174.
83. Pau, C. P., S. Lee-Thomas, W. Auwanit, J. R. George, C.-Y. Ou, B. S. Parekh, T. C. Granade, D. L. Holloman, S. Phillips, G. Schochetman, K. Limpakarnjanarat, N. L. Young, Y. Takebe, H. D. Gayle, and B. G. Weniger. 1992. Highly specific V3 peptide enzyme immunoassay for serotyping HIV-1 specimens from Thailand. AIDS 7:337-340.
84. Perelson, A. S., A. U. Neumann, M. Markowitz, J. M. Leonard, and D. D. Ho. 1996. HIV-1 dynamics in vivo: virion clearance rate, infected cell lifespan, and viral generation time. Science 271:1582-1586.
85. Richman, D. D. 1995. Protease uninhibited. Nature (London) 374:494.
86. Robertson, D. L., B. H. Hahn, and P. M. Sharp. 1995. Recombination in AIDS viruses. J. Mol. Evol. 40:249-259.
87. Robertson, D. L., P. M. Sharp, F. E. McCutchan, and B. H. Hahn. 1995. Recombination in HIV-1. Nature (London) 374:124-126.
88. Roy, S., U. Delling, C.-H. Chen, C. A. Rosen, and N. Sonenberg. 1990. A bulge structure in HIV-1 TAR RNA is required for Tat binding and Tatmediated trans-activation. Genes Dev. 4:1364-1373.
89. Sabino, E. C., E. G. Shpaer, M. G. Morgado, B. T. M. Korber, R. S. Diaz, V. Bongertz, S. Cavalcante, B. Gãlvao-Castro, J. I. Mullins, and A. Mayer. 1994. Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals from Brazil. J. Virol. 68:6340-6346.
90. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
91. Sala, M., E. Pelletier, and S. Wain-Hobson. 1995. HIV-1 gp120 sequences from a doubly infected drug user. AIDS Res. Hum. Retroviruses 11:653-655.
92. Salminen, M. O., J. K. Carr, D. S. Burke, and F. E. McCutchan. 1995. Genotyping of HIV-1, p. III-30-III-34. In G. Myers, B. Korber, S. Wain-Hobson, K.-T. Jeang, L. E. Henderson, and G. N. Pavlakis (ed.), Human retroviruses and AIDS 1995: a compilation and analysis of nucleic acid and amino acid sequences. Los Alamos National Laboratory, Los Alamos, N.Mex.
93. Salminen, M. O., J. K. Carr, D. S. Burke, and F. E. McCutchan. 1995. Identification of breakpoints in intergenotypic recombinants of HIV-1 by bootscanning. AIDS Res. Hum. Retroviruses 11:1423-1425.
94. Salminen, M. O., J. K. Carr, D. L. Robertson, P. Hegerich, D. Gotte, C. Koch, E. Sanders-Buel, F. Gao, P. M. Sharp, B. H. Hahn, D. S. Burke, and F. E. McCutchan. Unpublished data.
95. Salminen, M. O., C. Koch, E. Sanders-Buell, P. K. Ehrenberg, N. L. Michael, J. K. Carr, D. S. Burke, and F. E. McCutchan. 1995. Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction. Virology 213:80-86.
96. Shafer, R. W., and T. C. Merigan. 1995. Editorial: new virologic tools for the design and analysis of clinical trials. J. Infect. Dis. 171:1325-1328.
97. Sharp, P. M., D. L. Robertson, F. Gao, and B. H. Hahn. 1994. Origins and diversity of human immunodeficiency viruses. AIDS 8:S27-S42.
98. Sharp, P. M., D. L. Robertson, and B. H. Hahn. 1995. Cross-species transmission and recombination of AIDS viruses. Philos. Trans. R. Soc. London Ser. B 349:41-47.
99. Shaw, G. M., B. H. Hahn, S. K. Arya, J. E. Groopman, R. C. Gallo, and F. Wong-Staal. 1984. Molecular characterization of human T-cell leukemia (lymphotropic) virus type III in the acquired immune deficiency syndrome. Science 226:1165-1171.
100. Siepel, A. C., and B. T. Korber. 1995. Scanning the database for recombinant HIV-1 genomes, p. III-35-III-60. In G. Myers, B. Korber, S. Wain-Hobson, K.-T. Jeang, L. E. Henderson, and G. N. Pavlakis (ed.), Human retroviruses and AIDS 1995: a compilation and analysis of nucleic acid and amino acid sequences. Los Alamos National Laboratory, Los Alamos, N.Mex.
101. Sittitrai, W., and T. Brown. 1994. Risk factors for HIV infection in Thailand. AIDS 8(suppl. 2):S143-S153.
102. Smith, R. F., and T. F. Smith. 1990. Automatic generation of primary sequence patterns from sets of related protein sequences. Proc. Natl. Acad. Sci. USA 87:118-122.
103. Smith, R. F., and T. F. Smith. 1992. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modeling. Protein Eng. 5:35-41.
104. Soto-Ramirez, L. E., B. Renjifo, M. F. McLane, R. Marlink, C. O'Hara, R. Sutthent. C. Wasi, P. Vithayasai, V. Vithayasai, C. Apichartpiyakul, P. Auewarakul, V. Pena Cruz, D.-S. Chui, R. Osathanondh, K. Mayer, T.-H. Lee, and M. Essex. 1996. HIV-1 langerhans' cell tropism associated with heterosexual transmission of HIV. Science 271:1291-1293.
105. Spira, A. I., P. A. Marx, B. K. Patterson, J. Mahoney, R. A. Koup, S. M. Wolinsky, and D. D. Ho. 1996. Cellular targets of infection and route of viral dissemination after an intravaginal inoculation of simian immunodeficiency virus into rhesus macaques. J. Exp. Med. 183:215-225.
106. Stuhlmann, H., and P. Berg. 1992. Homologous recombination of copackaged retrovirus RNAs during reverse transcription. J. Virol. 66:2378-2388.
107. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
108. Tumas, K. M., J. M. Poszgay, N. Avidan, S. J. Ksiazek, B. Overmoyer, K. J. Blank, and M. B. Prystowsky. 1993. Loss of antigenic epitopes as the result of env gene recombination in retrovirus-induced leukemia in immunocompetent mice. Virology 192:587-595.
109. Vartanian, J.-P., A. Meyerhans, B. Asjo, and S. Wain-Hobson. 1991. Selection, recombination, and G→A hypermutation of human immunodeficiency virus type 1 genomes. J. Virol. 65:1779-1788.
110. Wasi, C., B. Herring, S. Raktham, S. Vanichseni, T. D. Mastro, N. L. Young, H. Rübsamen-Waigmann, H. von Briesen, M. L. Kalish, C.-C. Luo, C.-P. Pau, A. Baldwin, J. I. Mullins, E. L. Delwart, J. Esparza, W. L. Heyward, and S. Osmanov. 1995. Determination of HIV-1 subtypes in injecting drug users in Bangkok, Thailand, using peptide binding enzyme immunoassay and the heteroduplex mobility assay: evidence of increasing infection with HIV-1 subtype E. AIDS 9:943-949.
111. Wei, X., S. K. Ghosh, M. E. Taylor, V. A. Johnson, E. A. Emini, P. Deutsch, J. D. Lifson, S. Bonhoeffer, M. A. Nowak, B. H. Hahn, M. S. Saag, and G. M. Shaw. 1995. Viral dynamics in HIV-1 infection. Nature (London) 73:117-122.
112. Weniger, B. G., K. Limpakarnjanarat, K. Ungchusak, S. Thanprasertsuk, K. Choopanya, S. Vanichseni, T. Uneklabh, P. Thongcharoen, and C. Wasi. 1991. The epidemiology of HIV infection and AIDS in Thailand. AIDS 5(suppl. 2):S71-S85.
113. Weniger, B. G., Y. Takebe, C.-Y. Ou, and S. Yamazaki. 1994. The molecular epidemiology of HIV in Asia. AIDS 8(suppl. 2):S13-S28.
114. WHO Network for HIV Isolation and Characterization. 1994. HIV type 1 variation in World Health Organization-sponsored vaccine evaluation sites: genetic screening, sequence analysis, and preliminary biological characterization of selected viral strains. AIDS Res. Hum. Retroviruses 10:1327-1343.
115. Yu, X.-F., Z. Wang, C. Beyrer, D. D. Celentano, C. Khamboonruang, E. Allen, and K. Nelson. 1995. Phenotypic and genotypic characteristics of human immunodeficiency virus type 1 from patients with AIDS in northern Thailand. J. Virol. 69:4649-4655.