Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1

Journal of Virology

Volumn 72, Issue 10, 1998, Pages 8240-8251

  Poss, Mary ^a   Rodrigo, Allen G ^a   Gosink, John J ^a   Learn, Gerald H ^a   De Vange Panteleeff, Dana ^a   Martin Jr , Harold L ^a   Bwayo, Job ^b   Kreiss, Joan K ^a   Overbaugh, Julie ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF NAIROBI   (Kenya)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; CASE REPORT; FEMALE; GENE DELETION; GENE INSERTION; GENETIC DRIFT; GENETIC VARIABILITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEROCONVERSION; VIRUS ENVELOPE; VIRUS PATHOGENESIS; VIRUS TRANSMISSION;

EID: 0031694637     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.72.10.8240-8251.1998     Document Type: Article

References (77)

1. Albert, J., B. Abrahamsson, K. Nagy, E. Aurelius, H. Gaines, G. Nystrom, and E. M. Fenyo. 1990. Rapid development of isolate-specific neutralizing antibodies after primary HIV-1 infection and consequent emergence of virus variants which resist neutralization by autologous sera. AIDS 4:107-112.
2. Arendrup, M., C. Nielsen, J.-E. S. Hansen, C. Pedersen, L. Mathiesen, and J. O. Nielsen. 1992. Autologous HIV-1 neutralizing antibodies: emergence of neutralization-resistant escape virus and subsequent development of escape virus neutralizing antibodies. J. Acquired Immune Defic. Syndr. 5:303-307.
3. Balfe, P., P. Simmonds, C. A. Ludlam, J. O. Bishop, and A. J. Leigh Brown. 1990. Concurrent evolution of human immunodeficiency virus type 1 in patients infected from the same source: rate of sequence change and low frequency of inactivating mutations. J. Virol. 64:6221-6233.
4. Barnett, S. W., A. Barboza, C. M. Wilcox, C. E. Forsmark, and J. A. Levy. 1991. Characterization of human immunodeficiency virus type 1 strains recovered from the bowel of infected individuals. Virology 182:802-809.
5. Bonhoeffer, S., E. C. Holmes, and M. A. Nowak. 1995. Causes of HIV diversity. Nature 376:125. (Letter.)
6. Boom, R., C. M. Sol, M. M. Salimans, C. L. Jansen, P. M. Wertheim-van Dillen, and J. van der Noordaa. 1990. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28:493-503.
7. Borrow, P., H. Lewicki, X. Wei, M. S. Horwitz, N. Peffer, H. Meyers, J. A. Nelson, J. E. Gairin, B. H. Hahn, M. B. A. Oldstone, and G. M. Shaw. 1997. Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat. Med. 3:205-217.
8. Bosch, M. L., A. C. Andeweg, R. Schipper, and M. Kenter. 1994. Insertion of N-linked glycosylation sites in the variable regions of the human immunodeficiency virus type 1 surface glycoprotein through AAT triplet reiteration. J. Virol. 68:7566-7569.
9. Boyd, M. T., G. R. Simpson, A. J. Cann, M. A. Johnson, and R. A. Weiss. 1993. A single amino acid substitution in the V1 loop of human immunodeficiency virus type 1 gp120 alters cellular tropism. J. Virol. 67:3649-3652.
10. Cann, A. J., M. J. Churcher, M. Boyd, W. O'Brien, J. Q. Zhao, J. Zack, and I. S. Chen. 1992. The region of the envelope gene of human immunodeficiency virus type 1 responsible for determination of cell tropism. J. Virol. 66:305-309.
11. Cheng-Mayer, C. 1990. Biological and molecular features of HIV-1 related to tissue tropism. AIDS 4(Suppl. 1):s49-s56.
12. Cheng-Mayer, C., C. Weiss, D. Seto, and J. A. Levy. 1989. Isolates of human immunodeficiency virus type 1 from the brain may constitute a special group of the AIDS virus. Proc. Natl. Acad. Sci. USA 86:8575-8579.
13. Coffin, J. M. 1986. Genetic variation in AIDS viruses. Cell 46:1-4.
14. Coffin, J. M. 1995. HIV pathogenesis. Lines drawn in epitope wars. Nature 375:534-535.
15. Coffin, J. M. 1995. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267:483-489.
16. Cordonnier, A., L. Montagnier, and M. Emerman. 1989. Single amino-acid changes in HIV envelope affect viral tropism and receptor binding. Nature 340:571-574.
17. Delwart, E. L., J. I. Mullins, P. Gupta, G. H. Learn, Jr., M. Holodniy, D. Katzenstein, B. D. Walker, and M. K. Singh. 1998. Human immunodeficiency virus type 1 populations in blood and semen. J. Virol. 72:617-623.
18. Delwart, E. L., H. Pan, H. W. Sheppard, D. Wolpert, A. U. Neumann, and J. I. Mullins. 1997. Slower evolution of human immunodeficiency virus type 1 quasispecies during progression to AIDS. J. Virol. 71:7498-7508.
19. Delwart, E. L., H. W. Sheppard, B. D. Walker, J. Goudsmit, and J. I. Mullins. 1994. Human immunodeficiency virus type 1 evolution in vivo tracked by DNA heteroduplex mobility assays. J. Virol. 68:6672-6683.
20. Embretson, J., M. Zupancic, J. L. Ribas, A. Burke, P. Racz, K. Tenner-Racz, and A. T. Haase. 1993. Massive covert infection of helper T lymphocytes and macrophages by HIV during the incubation period of AIDS. Nature 362:359-362.
21. 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.
22. Felsenstein, J. 1989. PHYLlP - Phylogeny Inference Package (version 3.2). Cladistics 5:164-166.
23. Fisher, A. G., B. Ensoli, D. Looney, A. Rose, R. C. Gallo, M. S. Saag, G. M. Shaw, B. H. Hahn, and F. Wong-Staal. 1988. Biologically diverse molecular variants within a single HIV-1 isolate. Nature 334:444-447.
24. Holmes, E. C., L. Q. Zhang, P. Simmonds, C. A. Ludlam, and A. J. Leigh Brown. 1992. Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc. Natl. Acad. Sci. USA 89:4835-4839.
25. Hwang, S. S., T. J. Boyle, H. K. Lyerly, and B. R. Cullen. 1991, Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 253:71-74.
26. Itescu, S., P. F. Simonelli, R. J. Winchester, and H. S. Ginsberg. 1994. Human immunodeficiency virus type 1 strains in the lungs of infected individuals evolve independently from those in peripheral blood and are highly conserved in the C-terminal region of the envelope V3 loop. Proc. Natl. Acad. Sci. USA 91:11378-11382.
27. Ji, J., J. S. Hoffmann, and L. Loeb. 1994. Mutagenicity and pausing of HIV reverse transcriptase during HIV plus-strand DNA synthesis. Nucleic Acids Res. 22:47-52.
28. Kampinga, G. A., A. Simonon, P. Van de Perre, E. Karita, P. Msellati, and J. Goudsmit. 1997. Primary infections with HIV-1 of women and their offspring in Rwanda: findings of heterogeneity at seroconversion, coinfection, and recombinants of HIV-1 subtypes A and C. Virology 227:63-76.
29. Koito, K., G. Harrowe, J. A. Levy, and C. Cheng-Meyer. 1994. Functional role of the V1/V2 region of human immunodeficiency virus type 1 envelope glycoprotein gp120 in infection of primary macrophages and soluble CD4 neutralization. J. Virol. 68:2253-2259.
30. Korber, B. T., K. J. Kunstman, B. K. Pattersin, 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.
31. Koup, R. A. 1994. Virus escape from CTL recognition. J. Exp. Med. 180:779-782. (Comment.)
32. Koup, R. A., J. T. Safrit, Y. Cao, C. A. Andrews, G. McLeod, W. Borkowsky, C. Farthing, and D. D. Ho. 1994. Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J. Virol. 68:4650-1655.
33. Kuiken, C. L., G. Zwart, E. Baan, R. A, Coutinho, J. A. van den Hoek, and J. Goudsmit. 1993. Increasing antigenic and genetic diversity of the V3 variable domain of the human immunodeficiency virus envelope protein in the course of the AIDS epidemic. Proc. Natl. Acad. Sci. USA 90:9061-9065.
34. Kumar, S., K. Tamura, and M. Nei. 1994. Molecular evolutionary genetics analysis software tor microcomputers. Comput. Appl. Biosei. 10:189-191.
35. Lewis, P., J. K. Kreiss, G. C. John, B. A. Richardson, D. Mbori Ngacha, J. Ndinya Achola, and J. Overbaugh. 1998. Cell-free human immunodeficiency virus type 1 in breast milk. J. Infect. Dis. 177:34-39.
36. Liu, S.-L., T. Schacker, L. Musey, D. Shriner, M. J. McElrath, L. Corey. and J. I. Mullins. 1997. Divergent pattern of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses. J. Virol. 71:4284-4295.
37. Lukashov, V. V., C. L. Kuiken, and J. Goudsmit. 1995. Intrahost human immunodeficiency virus type 1 evolution is related to length of the immunocompetent period. J. Virol. 69:6911-6916.
38. Mackay, C. R., W. Marston, and L. Dudler. 1992. Altered patterns of T cell migration through lymph nodes and skin following antigen challenge. Eur. J. Immunol. 22:2205-2210.
39. Mackay, C. R., W. L. Marston, L. Dudler, O. Spertini, T. F. Tedder, and W. R. Hein. 1992. Tissue-specific migration pathways by phenotypically distinct subpopulations of memory T cells. Eur. J. Immunol. 22:887-895.
40. Maddison, W. P., and D. R. Maddison. 1992. MacClade: analysis of phylogeny and character evolution, 3rd ed. Sinauer Associates. Sunderland, Mass.
41. Martin, H. L., D. J. Jackson, K. Mandaliya, J. Bwayo, J. P. Rakwar, P. Nyange, S. Moses, J. O. Ndinya-Achola, K. Holmes, F. Plummer, E. Ngugi, and J. Kreiss. 1994. Preparation for AIDS vaccine evaluation in Mombasa, Kenya: establishment of seronegative cohorts of commercial sex workers and trucking company employees. AIDS Res. Hum. Retroviruses 10:S235-S237.
42. McDonald, R. A., D. L. Mayers, R. C.-Y. Chung, K. F. Wagner, S. Ratto-Kim, D. L. Birx, and N. L. Michael. 1997. Evolution of human immunodeficiency virus type 1 env sequence variation in patients with diverse rates of disease progression and T-cell function. J. Virol. 71:1871-1879.
43. McKeating, J. A., J. Gow, J. Goudsmit, L. H. Pearl, C. Mulder, and R. A. Weiss. 1989. Characterization of HIV-1 neutralization escape mutants. AIDS 3:777-784.
44. McNearney, T., Z. Hornickova, R. Markham, A. Birdwell, M. Arens, A. Saah, and L. Ratner. 1992. Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease. Proc. Natl. Acad. Sci. USA 89:10247-10251.
45. Mulder, J., N. McKinney, C. Christopherson, J. Sninsky, L. Greenfleld, and S. Kwok. 1994. Rapid and simple PCR assay for quantitation of human immunodeficiency virus type 1 RNA in plasma: application to acute retroviral infection. J. Clin. Microbiol. 32:292-300.
46. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
47. Nowak, M. A., R. M. Anderson, A. R. McLean, T. F. Wolfs, J. Goudsmit, and R. M. May. 1991. Antigenic diversity thresholds and the development of AIDS. Science 254:963-969.
48. Nowak, M. A., R. M. May, R. E. Phillips, S. Rowland-Jones, D. G. Lalloo, S. McAdam, P. Klenerman, B. Koppe, K. Sigmund, C. R. Bangham, and A. J. McMichael. 1995. Antigenic oscillations and shifting immunodominance in HIV-1 infections. Nature 375:606-611.
49. O'Brien, W. A., Y. Koyanagi, A. Namazie, J.-Q. Zhao, A. Diagne, K. Idler, J. A. Zack, and I. S. Y. Chen. 1990. HIV-1 tropism for mononuclcar phagocytes can be determined by regions of gp120 outside the CD4-binding domain. Nature 348:69-73.
50. Overbaugh, J., R. J. Anderson, J. O. Ndinya-Achola, and J. K. Kreiss. 1996. Distinct but related human immunodeficiency virus type 1 variant populations in genital secretions and blood. AIDS Res. Hum. Retroviruses 12:107-115.
51. Overbaugh, J., and L. M. Rudensey. 1992. Alterations in potential sites for glycosylation predominate during evolution of the simian immunodeficiency virus envelope gene in macaques. J. Virol. 66:5937-5948.
52. Palmer, C., P. Balfe, D. Fox, J. C. May, R. Frederiksson, E.-M. Rnyo, and J. A. McKeating. 1996. Functional characterization of the V1/V2 region of human immunodeficiency virus type 1. Virology 220:436-449.
53. Pang, S., E. S. Shlesinger, E. S. Daar, T. Moudgil, D. D. Ho, and I. S. Chen. 1992. Rapid generation of sequence variation during primary HIV-1 infection. AIDS 6:453-460.
54. Pantaleo, G., C. Graziosi, J. F. Demarest, L. Butini, M. Montroni, C. H. Fox, J. M. Orenstein, D. P. Kotler, and A. S. Fauci. 1993. HIV infection is active and progressive in lymphoid tissue during the clinically latent stage of disease. Nature 362:355-358.
55. 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 life-span, and viral generation time. Science 271:1582-1586.
56. Poss, M., J. J. Gosink, E. Thomas, J. K. Kreiss, J. Ndinya-Achola, K. Mandaliya, J. Bwayo, and J. Overbaugh. 1997. Phylogenetic evaluation of Kenyan HIV-1 isolates. AIDS Res. Hum. Retroviruses 13:493-499.
57. Poss, M., H. Martin, J. Kreiss, P. Nyange, K. Mandaliya, B. Chohan, and J. Overbaugh. 1995. Diversity in virus populations from genital mucosa and peripheral blood in women recently infected with human immunodeficiency virus. J. Virol. 69:8118-8122.
58. Power, C., J. C. McArthur, R. T. Johnson, D. E. Griffen, 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.
59. Rodrigo, A., and J. I. Mullins. 1996. Human immunodeficiency virus type 1 molecular evolution and the measure of selection. AIDS Res. Hum. Retroviruses 12:1681-1685.
60. Saag, M. S., B. H. Hahn, J. Gibbons, Y. X. Li, E. S. Parks, W. P. Parks, and G. M. Shaw. 1988. Extensive variation of human immunodeficiency virus type 1 in vivo. Nature 334:440-444.
61. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
62. Shioda, T., J. A. Levy, and C. Cheng-Mayer. 1991. Macrophage and T cell-line tropisms of HIV-1 are determined by specific regions of the envelope gpl20 gene. Nature 349:167-169.
63. Slatkin, M., and R. R. Hudson. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555-562.
64. Slatkin, M., and W. P. Maddison. 1989. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123:603-613.
65. Slatkin, M., and W. P. Maddison. 1990. Detecting isolation by distance using phylogenies of genes. Genetics 126:249-260.
66. Smouse, P. E., J. C. Long, and R. R. Sokal. 1986. Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Syst. Zool. 35:627-632.
67. Waddle, D. M. 1994. Matrix correlation tests support a single origin for modern humans. Nature 368:452-454.
68. Wang, N., T. Zhu, and D. D. Ho. 1995. Sequence diversity of V1 and V2 domains of gp120 from human immunodeficiency virus type 1: lack of correlation with viral phenotype. J. Virol. 69:2708-2715.
69. 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. Hahn, M. S. Saag, and G. M. Shaw. 1995. Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373:117-126.
70. Wolfs, T. F., G. Zwart, M. Bakker, and J. Goudsmit. 1992. HIV-1 genomic RNA diversification following sexual and parenteral virus transmission. Virology 189:103-110.
71. Wolinsky, S. M., B. T. M. Korber, A. U. Neumann, M. Daniels, K. J. Kunstman, A. J. Whetsell, M. R. Furtado, Y. Cao, D. D. Ho, J. T. Safrit, and R. A. Koup. 1996. Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 272:537-542.
72. Yamaguchi, Y., and T. Gojobori. 1997. Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc. Natl. Acad. Sci. USA 94:1264-1269.
73. Zhang, L., R. S. Diaz, D. D. Ho, J. W. Mosley, M. P. Busch, and A. Mayer. 1997. Host-specific force in human immunodeficiency virus type 1 evolution in vivo. J. Virol. 71:2555-2561.
74. Zhang, L. Q., P. MacKenzie, A. Cleland, E. C. Holmes, A. J. Leigh Brown, and P. Simmonds. 1993. Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J. Virol. 67:3345-3356.
75. Zhu, T., H. Ho, N. Wang, D. S. Nam, Y. Cao, R. A. Koup, and D. D. Ho. 1993. Genotypic and phenotypic charcterization of HIV-1 in patients with primary infection. Science 261:1179-1181.
76. Zhu, T., N. Wang, A. Carr, D. S. Nam, R. Moor-Jankowski, D. A. Cooper, and D. D. Ho. 1996. Genetic characterization of human immunodeficiency virus type 1 in blood and genital secretions: evidence for viral compartmentalization and selection during sexual transmission. J. Virol. 70:3098-3107.
77. Zwart, G., H. Langedijk, L. van der Hoek, J. J. de Jong, T. F. Wolfs, C. Ramautarsing, M. Bakker, A. de Ronde, and J. Goudsmit. 1991. Immunodominance and antigenic variation of the principal neutralization domain of HIV-1. Virology 181:481-489.