Mosaic structure of the human immunodeficiency virus type 1 genome infecting lymphoid cells and the brain: Evidence for frequent in vivo recombination events in the evolution of regional populations

Journal of Virology

Volumn 73, Issue 10, 1999, Pages 8720-8731

  Morris, A ^a   Marsden, M ^a   Halcrow, K ^a   Hughes, E S ^a   Brettle, R P ^b   Bell, J E ^a   Simmonds, P ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b WESTERN GENERAL HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BRAIN; COGNITIVE DEFECT; CONTROLLED STUDY; CYTOTOXIC T LYMPHOCYTE; DEMENTIA; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN TISSUE; LYMPHOID CELL; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VIRUS ENCEPHALITIS; VIRUS RECOMBINATION;

EID: 0032844935     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.73.10.8720-8731.1999     Document Type: Article

References (50)

1. Alkhatib, G., C. Combadiere, C. C Broder, Y. Feng, P. E. Kennedy, P. M. Murphy, and E. A. Berger. 1996. CC CKR5: a RANTES, MIP-1 alpha, MIP-1 beta receptor as a fusion cofactor for macrophage-tropic HIV-1 Science 272:1955-1958.
2. Asjo, B., J. Albert, A. Karlsson, L. Morfeldt Manson, G. Biberfeld, K. Lidman, and E. M. Fenyo. 1986. Replicative capacity of human immunodeficiency virus from patients with varying severity of HIV infection. Lancet 11:660-662.
3. Ball, J. K., E. C. Holmes, H. Whitwell, and U. Desselberger. 1994. Genomic variation of human immunodeficiency virus type 1 (HIV-1) - molecular analyses of HIV-1 in sequential blood samples and various organs obtained at autopsy. J. Gen. Virol. 75:867-879.
4. Bell, J. E., A. Busuttil, J. W. Ironside, S. Rebus, Y. K. Donaldson, P. Simmonds, and J. F. Peutherer. 1993. Human immunodeficiency virus and the brain - investigation of virus load and neuropathologic changes in pre-AIDS subjects. J. Infect. Dis. 168:818-824.
5. Berson, J. F., D. Long, B. J. Doranz, J. Rucker, F. R Jirik, and R. W. Doms. 1996. A seven-transmembrane domain receptor involved in fusion and entry of T-cell-tropic human immunodeficiency virus type 1 strains. J. Virol. 70: 6288-6295.
6. Brown, A. J. L., and A. Cleland. 1996. Independent evolution of the env and pol genes of HIV-1 during zidovudine therapy. AIDS 10:1067-1073.
7. 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.
8. Chang, J., R. Jozwiak, B. Wang, T. Ng, Y. C. Ge, W. Bolton, D. E. Dwyer, C. Randle, R. Osborn, A. L. Cunningham, and N. K. Saksena. 1998. Unique HIV type 1 V3 region sequences derived from six different regions of brain: region-specific evolution within host-determined quasispecies - short communication. AIDS Res. Hum. Retroviruses 14:25-30.
9. Cheng-Mayer, C., D. Seto, M. Tateno, and J. A. Levy. 1988. Biological features of HIV-1 that correlate with virulence in the host. Science 240:80-82.
10. Cornelissen, M., G. Kampinga, F. Zorgdrager, and J. Goudsmit. 1996. Human immunodeficiency virus type 1 subtypes defined by env show high frequency of recombinant gag genes. J. Virol. 70:8209-8212.
11. Deng, H. K., R. Liu, W. Ellmeier, S. Choe, D. Unutmaz, M. Burkhart, P. Dimarzio, S. Marmon, R. E. Sutton, C. M. Hill, C. B. Davis, S. C. Peiper, T. J. Schall, D. R Littman, and N. R. Landau. 1996. Identification of a major co-receptor for primary isolates of HIV-1. Nature 381:661-666.
12. Diaz, R. S., E. C. Sabino, A. Mayer, J. W. Mosley, and M. P. Busch. 1995. Dual human immunodeficiency virus type 1 infection and recombination in a dually exposed transfusion recipient. J. Virol. 69:3273-3281.
13. Di Stefano, M., S. Wilt, F. Gray, M. DuboisDaleq, and F. Chiodi. 1996. HIV type 1 V3 sequences and the development of dementia during AIDS. AIDS Res. Hum. Retroviruses 12:471-476.
14. Donaldson, Y. K., J. E. Bell, E. C. Holmes, E. S. Hughes, H. K. Brown, and P. Simmonds. 1994. In vivo distribution and cytopathology of variants of human immunodeficiency virus type 1 showing restricted sequence variability in the V3 loop. J. Virol. 68:5991-6005.
15. Donaldson, Y. K., J. E. Bell, J. W. Ironside, R. P. Brettle, J. R. Robertson, A. Busuttil, and P. Simmonds. 1994. Redistribution of HIV outside the lymphoid system with onset of AIDS. Lancet 343:382-385.
16. Dragic, T., V. Litwin, G. P. Allaway, S. R. Martin, Y. X. Huang, K. A. Nagashima, C. Cayanan, P. J. Maddon, R. A, Koup, J. P. Moore, and W. A. Paxton. 1996. HIV-1 entry into CD4(+) cells is mediated by the chemokine receptor CC-CKR-5. Nature 381:667-673.
17. Epstein, L. G., C. Kuiken, B. M. Blumberg, S. Hartman, L. R. Sharer, M. Clement, and J. Goudsmit. 1991. HIV-1 V3 domain variation in brain and spleen of children with AIDS: tissue-specific evolution within host-determined quasispecies. Virology 180:583-590.
18. Felsenstein, J. 1989. PHYLIP - phytogeny inference package (version 3.2). Cladistics 5:164-166.
19. Feng, Y., C. C. Broder, P. E. Kennedy, and E. A. Berger. 1996. HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor. Science 272:872-877.
20. Fenyo, E. M., L, Morfeldt Manson, F. Chiodi, B. Lind, A. von Gegerfelt, J. Albert, E. Olausson, and B. Asjo. 1988. Distinct replicative and cytopathic characteristics of human immunodeficiency virus isolates. J. Virol. 62:4414-4419.
21. Gao, F., D. L. Robertson, C. D. Carruthers, Y. Y. Li, E. Bailes, L. G. Kostrikis, M. O. Salminen, F. Bibolletruche, M. Peeters, D. D. Ho, G. M. Shaw, P. M. Sharp, and B. H. Hahn. 1998. An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I). J. Virol. 72:10234-10241.
22. Haggerty, S., and M. Stevenson. 1991. Predominance of distinct viral genotypes in brain and lymph node compartments of HIV-infected individuals. Viral Immunol. 4:123-131.
23. Hughes, E. S., J. E. Bell, and P. Simmonds. 1997. Investigation of population diversity of human immunodeficiency virus type 1 in vivo by nucleotide sequencing and length polymorphism analysis of the V1/V2 hypervariable region of env. J. Gen. Virol. 78:2871-2882.
24. gag and env genes. J. Virol. 71:1272-1280.
25. Kasper, P., P. Simmonds, K. E. Schneweis, R. Kaiser, B. Matz, J. Oldenburg, H. H. Brackmann, and E. C. Holmes. 1995. The genetic diversification of the HIV type 1 gag p17 gene in patients infected from a common source. AIDS Res. Hum. Retroviruses 11:1197-1201.
26. Keys, B., J. Karis, B. Fadeel, A. Valentin, G. Norkrans, L. Hagberg, and F. Chiodi. 1993. V3 sequences of paired HIV-1 isolates from blood and cerebrospinal fluid cluster according to host and show variation related to the clinical stage of disease. Virology 196:475-483.
27. Korber, B. T. M., K. J. Kunstman, B. K. Patterson, M. Furtado, M. M. Mcevilly, R. Levy, and S. M. Wolinsky. 1994. Genetic differences between blood- and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients: evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences. J. Virol. 68:7467-7481.
28. Kozak, S. L., E. J. Platt, N. Madani, F. E. Ferro, K. Peden, and D. Kabat. 1997. CD4, CXCR-4, and CCR-5 dependencies for infections by primary and laboratory-adapted isolates of human immunodeficiency virus type 1. J. Virol. 71:873-882.
29. Kumar, S., K. Tamura, and M. Nei. 1993. MEGA: Molecular Evolutionary Genetics Analysis, version 1.0. The Pennsylvania State University, University Park, Pa.
30. Li, Y. X., 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.
31. Liu, Z. Q., C. Wood, J. A. Levy, and C. Cheng Mayer. 1990. The viral envelope gene is involved in macrophage tropism of a human immunodeficiency virus type 1 strain isolated from brain tissue. J. Virol. 64:6148-6153.
32. Moutouh, L., J. Corbeil, and D. D. Richman. 1996. Recombination leads to the rapid emergence of HIV-1 dually resistant mutants under selective drug pressure. Proc. Natl. Acad. Sci. USA 93:6106-6111.
33. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and non-synonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
34. Pang, S., H. V. Vinters, T. Akashi, W. A. O'Brien, and I. S. Chen. 1991. HIV-1 env sequence variation in brain tissue of patients with AIDS-related neurologic disease. J. Acquir. Immune. Defic. Syndr. 4:1082-1092.
35. Power, C., J. C. Mcarthur, R. T. Johnson, D. E. Griffin, J. D. Glass, S. Perryman, and B. Chesebro. 1994. Demented and nondemented patients with AIDS differ in brain-derived human immunodeficiency virus type 1 envelope sequences. J. Virol. 68:4643-4649.
36. Reddy, R. T., C. L. Achim, D. A. Sirko, S. Tehranchi, F. G. Kraus, F. Wong-Staal, C. A. Wiley, I. Grant, J. H. Atkinson, M. Kelly, J. L. Chandler, M. R. Wallace, J. A. McCutchan, S. A. Spector, L. Thai, R. K. Heaton, J. Hesselink, T. Jernigan, E. Masliah, I. Abramson, N. Butters, T. Patterson, S. Zisook, and D. Jeste. 1996. Sequence analysis of the V3 loop in brain and spleen of patients with HIV encephalitis. AIDS Res. Hum. Retroviruses 12:477-482.
37. Robertson, D. L., P. M. Sharp, F. E. McCutchan, and B. H. Hahn. 1995. Recombination of HIV-1. Nature 374:124-126.
38. Simmonds, P., P. Balfe, C. A. Ludlam, J. O. Bishop, and A. J. Leigh Brown. 1990. Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1. J. Virol. 64:5840-5850.
39. Simmonds, P., P. Balfe, J. F. Peutherer, C. A. Ludlam, J. O. Bishop, and A. J. Leigh Brown. 1990. Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cells and at low copy numbers. J. Virol. 64:864-872.
40. Simmons, G., D. Wilkinson, J. D. Reeves, M. Dittmar, S. Beddows, J. Weber, G. Carnegie, U. Desselberger, P. W. Gray, R. A. Weiss, and P. R. Clapham. 1996. Primary, syncytium-inducing human immunodeficiency virus type 1 isolates are dual-tropic and most can use either Lestr or CCR5 as coreceptors for virus entry. J. Virol. 70:8355-8360.
41. Sinclair, E., F. Gray, and F. Scaravilli. 1992. PCR detection of HIV proviral DNA in the brain of an asymptomatic HIV-positive patient. J. Neurol. 239:469-471.
42. Steuler, H., B. Storch Hagenlocher, and B. Wildemann. 1992. Distinct populations of human immunodeficiency virus type 1 in blood and cerebrospinal fluid. AIDS Res. Hum. Retroviruses 8:53-59.
43. Strappe, P. Personal communication.
44. Stuyver, L., A. Wyseur, A. Rombout, T. Scarcez, C. Verhofstede, D. Rimland, R. F. Schinazi, and R. Rossau. 1997. Line probe assay for rapid detection of drug-selected mutations in the human immunodeficiency virus type 1 reverse transcriptase gene. Antimicrob. Agents Chemother. 41:284-291.
45. Tersmette, M., J. M. Lange, R. E. de Goede, F. de Wolf, J. K. Eeftink Schattenkerk, P. T. Schellekens, R. A. Coutinho, J. G. Huisman, J. Goudsmit, and F. Miedema. 1989. Association between biological properties of human immunodeficiency virus variants and risk for AIDS and AIDS mortality. Lancet 1:983-985.
46. Vanderhoek, L., C. J. A. Sol, J. Maas, V. V. Lukashov, C. L. Kuiken, and J. Goudsmit. 1998. Genetic differences between human immunodeficiency virus type 1 subpopulations in faeces and serum. J. Gen. Virol. 79:259-267.
47. Vanderhoek, L., C. J. A. Sol, F. Snijders, J. F. W. Bartelsman, R. Boom, and J. Goudsmit. 1996. Human immunodeficiency virus type 1 RNA populations in faeces with higher homology to intestinal populations than to blood populations. J. Gen. Virol. 77:2415-2425.
48. Wei, Q., and P. N. Fultz. 1998. Extensive diversification of human immunodeficiency virus type 1 subtype B strains during dual infection of a chimpanzee that progressed to AIDS. J. Virol. 72:3005-3017.
49. Wong, J. K., C. C. Ignacio, F. Torriani, D. Havlir, N. J. S. Fitch, and D. D. Richman. 1997. In vivo compartmentalization of human immunodeficiency virus: evidence from the examination of pol sequences from autopsy tissues. J. Virol. 71:2059-2071.
50. Zhu, T. F., N. Wang, A. Carr, S. Wolinsky, and D. D. Ho. 1995. Evidence for coinfection by multiple strains of human immunodeficiency virus type 1 subtype b in an acute seroconvertor. J. Virol. 69:1324-1327.