Characterization of gag and pol sequences from long-term survivors of human immunodeficiency virus type 1 infection

Virology

Volumn 240, Issue 1, 1998, Pages 36-49

  Huang, Yaoxing ^a   Zhang, Linqi ^a   Ho, David D ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; GAG PROTEIN; GUANINE; NEF PROTEIN; POL PROTEIN; VIF PROTEIN; VIRUS ENVELOPE PROTEIN; VIRUS PROTEIN; VPR PROTEIN; VPU PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CLINICAL ARTICLE; DEFECTIVE VIRUS; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; LONG TERM CARE; LONG TERMINAL REPEAT; OPEN READING FRAME; PRIORITY JOURNAL; PROVIRUS; SURVIVAL; VIRUS ATTENUATION; VIRUS MUTATION;

EID: 0032484475     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1006/viro.1997.8913     Document Type: Article

References (58)

1. Borman A., Quillent C., Charneau P., Kean K. M., Clavel F. A highly defective HIV-1 group O provirus: Evidence for the role of local sequence determinants in G to A hypermutation during negative-strand viral DNA synthesis. Virology. 208:1995;601-609.
2. Cannon P. M., Wilson W., Byles E., Kingsman S. M., Kingsman A. J. Human immunodeficiency virus type 1 integrase: Effect on viral replication of mutations at highly conserved residues. J. Virol. 68:1994;4768-4775.
3. Cao Y., Qing L., Zhang L., Safrit J., Ho D. D. Virological and immunological characterization of long-term survivors of human immunodeficiency virus type 1 infection. N. Engl. J. Med. 332:1995;201-208.
4. Cocchi F., DeVico A. L., Garzino-Demo A., Arya S. K., Gallo R. C., Lusso P. Identification of RANTES, MIP-1 alpha, and MIP-1 beta as the major HIV-suppressive factors produced by CD8+ T cells. Science. 270:1995;1811-1815.
5. Connor R. I., Sheridan K. E., Lai C., Zhang L., Ho D. D. Characterization of the functional properties of env genes from long-term survivors of human immunodeficiency virus type 1 infection. J. Virol. 70:1996;5306-5311.
6. Deacon N. J., Tsykin A., Solomon A., Smith K., Ludford-Menting M., Hooker D. J., McPhee D. A., Greenway A. L., Ellett A., Chatfield C., Lawson V. A., Crower S., Maerz A., Snoza S., Learmont J., Sullivan J. S., Cunningham A., Dwyer D., Dowton D., Mills J. Genomic structure of an attenuated quasispecies of HIV-1 from a blood transfusion donor and recipients. Science. 270:1995;988-991.
7. Dean M., Carrington M., Winkler C., Huttley G. A., Smith M. W., Allikmets R., Goedert J. J., Buchbinder S. P., Vittinghoff E., Gomperts E., Confield S., Vlahov D., Kaslow R., Saah A., Rinaldo C., Detels R., O'Brient S. J. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science. 273:1996;1856-1862.
8. Dorfman T., Bukovsky A., Ohagen A., Hoglund S., Gottlinger H. G. Functional domains of the capsid protein of human immunodeficiency virus type 1. J. Virol. 68:1994;8180-8187.
9. Dorfman T., Luban J., Goff S. P., Haseltine W. A., Gottlinger H. G. Mapping of functionally important residues of cysteine-histidine box in the human immunodeficiency virus type 1 nucleocapsid protein. J. Virol. 67:1993;6159-6169.
10. Drelich M., Wilheim R., Mous J. Identification of amino acid residues critical for endonuclease and integration activities of HIV-1 IN protein in vitro. Virology. 188:1992;459-468.
11. Engelman A., Craigie R. Identification of amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J. Virol. 66:1992;6361-6369.
12. Felsenstein J. Phylogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22:1988;521-565.
13. Fitzgibbon J. E., Mazar S., Dubin D. T. A new type of G to A hypermutation affecting human immunodeficiency virus. AIDS Res. Hum. Retroviruses. 9:1993;833-838.
14. Greenough T. C., Somasundaran M., Brettler D. B., Hesselton R. M., Alimenti A., Kirchhoff F., Panicali D., Sullivan J. L. Normal immune function and inability to isolate virus in culture in an individual with long-term human immunodeficiency virus type 1 infection. AIDS Res. Hum. Retroviruses. 10:1994;395-403.
15. Gu Z., Gao Q., Li X., Parniak M. A., Wainberg M. A. Novel mutation in the human immunodeficiency virus type 1 reverse transcriptase gene that encodes cross-resistance to 2′, 3′, -dideoxyinosine and 2′, 3′, -dideoxycytidine. J. Virol. 66:1992;7128-7135.
16. Higgins D. G., Sharp P. M. Fast and sensitive multiple sequence alignments on a microcomputer. CABIO. 5:1989;151-153.
17. Ho D. D., Neumann A. U., Perelson A. S., Chen W., Leonard J. M., Markowitz M. Rapid turnover of plasma virion and CD4 lymphocytes in HIV-1 infection. Nature (London). 373:1995;123-126.
18. Huang Y., Zhang L., Ho D. D. Biological characterization of nef in long-term survivors of human immunodeficiency virus type 1 infection. J. Virol. 69:1995a;8142-8146.
19. Huang Y., Zhang L., Ho D. D. Characterization of nef sequences in long-term survivors of human immunodeficiency virus type 1 infection. J. Virol. 69:1995b;93-100.
20. Huang Y., Paxton W. A., Wolinsky S. M., Neumann A. U., Zhang L., He T., Kang S., Ceradini D., Jin Z., Yazdanbakhsh K., Kunstman K., Erickson D., Dragon E., Landau N. R., Phir J., Ho D. D., Koup R. A. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat. Med. 2:1996;1240-1243.
21. Johnson M. S., McClure M. A., Feng D.-F., Gray J., Doolittle R. F. Computer analysis of retroviral pol genes: Assignment of enzymatic functions to specific sequences and homologies with nonviral enzymes. Proc. Natl. Acad. Sci. USA. 83:1986;7648-7652.
22. Kestler H. W., Ringler D. J., Mori M., Panicali D. L., Sehgal P. K., Daniel M. D., Desrosiers R. D. Importance of the nef gene for maintenance of high virus loads and/or development of AIDS. Cell. 65:1991;651-662.
23. Khan S., Mack J. P. G., Katz R. A., Kulkosky J., Skalka A. M. Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucleic Acids Res. 19:1991;851-860.
24. Kirchhoff F., Greenough T. C., Brettler D. B., Sullivan J. L., Desrosiers R. C. Absence of intact nef sequences in a long-term survivor with nonprogressive HIV-1 infection. N. Engl. J. Med. 332:1995;228-232.
25. Kulkosky J., Jones K. S., Katz R. A., Mack J. P. G., Salka A. M. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transportases. Mol. Cell. Biol. 12:1992;2331-2338.
26. Larder B. A., Kemp S. D., Purifoy J. M. Infectious potential of human immunodeficiency virus type 1 reverse transcriptase mutants with altered inhibitor sensitivity. Proc. Natl. Acad. Sci. USA. 86:1989;4803-4807.
27. Learmont J., Tindall B., Evans L., Cunningham A., Cunningham P., Wells J., Penny R., Kaldor J., Cooper D. A. Long-term symptom-less HIV-1 infection in recipients of blood products from a single donor. Lancet. 340:1992;863-867.
28. Leavitt A. D., Shiue L., Varmus H. E. Site-directed mutagenesis of HIV-1 integrase demonstrates differential effects on integrase function in vitro. J. Biol. Chem. 268:1993;2113-2119.
29. Leigh Brown A. J. Sequence variability in human immunodeficiency viruses: Pattern and process in viral evolution. AIDS. 1991;s35-s42.
30. Lifson A. R., Rutherford G. W., Jaff H. W. The natural history of human immunodeficiency virus infection. J. Infect. Dis. 158:1988;1360-1367.
31. Mammano F., Ohagen A., Hoglund S., Gottlinger H. G. Role of the major homology region of human immunodeficiency virus type 1 in virion morphogenesis. J. Virol. 68:1994;4927-4936.
32. Mariani R., Kirchhoff F., Greenough T. C., Sullivan J. L., Desrosiers R. C., Skowronski J. High frequency of defective Nef alleles in a long-term survivor with nonprogressive human immunodeficiency virus type 1 infection. J. Virol. 70:1996;7752-7764.
33. McNeary T., Hornickova Z., Markham R., Birdwell A., Arens M., Saah A., Ratner L. Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage disease. Proc. Natl. Acad. Sci. USA. 89:1992;10247-10251.
34. Michael N. L., Chang G., d'Arcy L. A., Ehrenberg P. K., Mariani R., Busch M. P., Birx D., Schwartz D. H. Defective accessory genes in a human immunodeficiency virus type 1-infected long-term survivor lacking recoverable virus. J. Virol. 69:1995a;4228-4236.
35. Michael N. L., Chang G., d'Arcy L. A., Tseng C. J., Birx D. L., Sheppard H. W. Functional characterization of human immunodeficiency virus type 1 nef genes in patients with divergent rates of disease progression. J. Virol. 69:1995b;6758-6769.
36. Montefiori D. C., Pantaleo G., Fink L. M., Zhou J.-T., Zhou J.-M., Bilska M., Miralles G. D., Fauci A. S. Neutralizing and infection-enhancing antibody responses to human immunodeficiency virus type 1 in long-term nonprogressors. J. Infect. Dis. 173:1996.
37. Moriuchi H., Moriuchi M., Combadiere C., Murphy P. M., Fauci A. S. CD8+ T-cell-derived soluble factor(s), but not beta-chemokines RANTES, MIP-1alpha, and MIP-1beta, suppress HIV-1 replication in monocyte/macrophages. Proc. Natl. Acad. Sci. USA. 93:1996;15341-15345.
38. Munoz A., Wang M. C., Bass S., Taylor J. M., Kingsley L. A., Chmiel J. S., Polk B. F. Acquired immunodeficiency syndrome (AIDS)-free time after human immunodeficiency virus type 1 (HIV-1) seroconversion in homosexual men. Am. J. Epidemiol. 130:1989;530-539.
39. Ottamnn M., Gabus C., Darlix J.-L. The central globular domain of the nucleocapsid protein of human immunodeficiency virus type 1 is critical for virion structure and infectivity. J. Virol. 69:1995;1778-1784.
40. Pantaleo G., Menzo S., Vaccarezza M., Graziosi C., Cohen O. J., Demarest J. F., Montefiori D., Orenstein J. M., Fox C., Schrager L. K., Margolick J. B., Buchbinder S., Giorgi J. V., Fauci A. S. Studies in subjects with long-term nonprogressive humanimmunodeficiency virus infection. N. Engl. J. Med. 332:1995;209-216.
41. Pathak V. K., Temin H. M. Broad spectrum of in-vitro forward mutations, hypermutations, and mutational hotspots in a retroviral shuttle vector after a single replication cycle: Substitutions, frameshifts, and hypermutations. Proc. Natl. Acad. Sci. USA. 87:1990;6019-6023.
42. Premkumer D. R. D., Ma X.-Z., Maitra R. K., Chakrabarti B. K., Salkowitz J., Yen-Lieberman B., Hirsch M. S., Kestler H. W. The nef gene from a long-term HIV type 1 nonprogressor. AIDS Res. Hum. Retroviruses. 12:1996;337-345.
43. Rinaldo C., Huang X.-L., Fan Z., Ding M., Beltz L., Logar A., Panicall D., Mazzara G., Liebmann J., Cottrill M., Gupta P. High levels of anti-human immunodeficiency virus type 1 (HIV-1) memory cytotoxic T-lymphocyte activity and low viral load are associated with lack of disease in HIV-1-infected long-term nonprogressors. J. Virol. 69:1995;5838-5842.
44. Rutherford G. W., Lifson A. R., Hessol N. A., Darrow W. W., O'Malley P. M., Buchbinder S. P., Barrhart J. Course of HIV-1 infection in a cohort of homosexual and bisexual men: An 11 year follow up study. Br. Med. J. 301:1990;1183-1188.
45. Sabino E., Cheng-Mayer C., Mayer A. An individual with a high prevalence of a Tat-defective provirus in peripheral blood. AIDS Res. Hum. Retroviruses. 9:1993;1265-1268.
46. Sheppard H. W., Lang W., Ascher M. S., Vittinghoff E., Winkelstein W. The characterization of a non-progressor: Long-term HIV-1 infection with stable CD4+ T-cell levels. AIDS. 7:1993;1159-1166.
47. Simmonds P., Balfe P., Peutherer L. F., Ludlam C. A., Bishop J. O., Leigh Brown A. J. Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cells and at low copy numbers. J. Virol. 64:1990;864-872.
48. Smith M. W., Dean M., Carrington M. C. W., Huttley G. A., Lomb D. A., Goedert J. J., O'Brien T. R., Jacobson L. P., Kaslow R., Buchbinder S., Vittinghoff E., Vlahov D., Hoots K., Hilgartner M. W., O'Brien S. J. Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Science. 277:1997;956-965.
49. Tisdale M., Kemp S. D., Parry N. R., Larder B. A. Rapid in vitro selection of human immunodeficiency virus type 1 resistant to 3′-thiacytidine inhibitors due to a mutation in the YMDD region of reverse transcriptase. Proc. Natl. Acad. Sci. USA. 90:1993;5653-5656.
50. Vartanian J.-P., Meyerhans A., Asjo B., Wain-Hobson S. Selection, recombination, and G to A hypermutation of human immunodeficiency virus type 1 genomes. J. Virol. 65:1991;1779-1788.
51. von Gent D. C., Oude Groeneger A. A. M., Plasterk R. H. A. Mutational analysis of the integrase protein of human immunodeficiency virus type 2. Proc. Natl. Acad. Sci. USA. 89:1992;9598-9602.
52. von Schwedler U., Kornbluth R. S., Trono D. The nuclear localization signal of the matrix protein of human immunodeficiency virus type 1 allows the establishment of infection in marcrophages and quiescent T lymphocytes. Proc. Natl. Acad. Sci. USA. 91:1994;6992-6996.
53. Wakefield J. K., Jablonsik S. A., Morrow C. D. In vitro enzymatic activity of human immunodeficiency virus type 1 reverse transcriptase mutants in the highly conserved YMDD amino acid motif correlated with the infectious potential of the proviral genome. J. Virol. 66:1992;6806-6812.
54. Wang B., Ge Y.-C., Palasanthiran P., Xiang S.-H., Ziegler J., Dwyer D. E., Randle C., Dowton D., Cunningham A., Saksena N. K. Gene defects clustered at the C-terminus of the vpr gene of HIV-1 in long-term nonprogressing mother and child pair:In vivo. Virology. 223:1996;224-232.
55. Wei X., Ghosh S. K., Taylor M. E., Johnson V. A., Emini E. A., Deutsch P., Lifson J. D., Bonhoeffer S., Nowak M. A., Hahn B. H., Saag M. S., Shaw G. M. Viral dynamics in human immunodeficiency virus type 1 infection. Nature (London). 373:1995;117-122.
56. Wilson J. E., Aulabaugh A., Caligan B., McPherson S., Wakefield J. K., Jablonski S., Morrow C. D., Reardon J. E., Furman P. A. Human immunodeficiency virus type-1 reverse transcriptase: Contribution of Met-184 to binding of nucleoside 5′-triphosphate. J. Biol. Chem. 271:1996;13656-13662.
57. Zhang L., Huang Y., Yuan H., Chen B. K., Ip J., Ho D. D. Genotypic and phenotypic characterization of long terminal repeat sequences from long-term survivors of human immunodeficiency virus type 1 infection. J. Virol. 71:1997a;5608-5613.
58. Zhang L., Huang Y., Yuan H., Tuttleton S., Ho D. D. Genetic characterization of vif, vpr, and vpu sequences from long-term survivors of human immunodeficiency virus type 1 infection. Virology. 228:1997b;340-349.