Meta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression

Journal of Virology

Volumn 84, Issue 7, 2010, Pages 3644-3653

  Pushker, Ravindra ^a   Jacqué, Jean Marc ^a   Shields, Denis C ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AMINO ACID SUBSTITUTION; ARTICLE; CONSENSUS SEQUENCE; DISEASE ASSOCIATION; DISEASE COURSE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; NEF GENE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; STOP CODON; VIRUS GENE;

ACQUIRED IMMUNODEFICIENCY SYNDROME; AMINO ACID SUBSTITUTION; CLUSTER ANALYSIS; DISEASE PROGRESSION; GENE DELETION; GENES, NEF; HUMANS; META-ANALYSIS AS TOPIC; NEF GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; PHYLOGENY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 77949404391     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.01959-09     Document Type: Article

References (58)

1. Bailey, J. R., K. O'Connell, H. C. Yang, Y. Han, J. Xu, B. Jilek, T. M. Williams, S. C. Ray, R. F. Siliciano, and J. N. Blankson. 2008. Transmission of human immunodeficiency virus type 1 from a patient who developed AIDS to an elite suppressor. J. Virol. 82:7395-7410.
2. Bailey, J. R., H. Zhang, B. W. Wegweiser, H. C. Yang, L. Herrera, A. Ahonkhai, T. M. Williams, R. F. Siliciano, and J. N. Blankson. 2007. Evolution of HIV-1 in an HLA-B*57-positive patient during virologic escape. J. Infect. Dis. 196:50-55.
3. Benichou, S., M. Bomsel, M. Bodeus, H. Durand, M. Doute, F. Letourneur, J. Camonis, and R. Benarous. 1994. Physical interaction of the HIV-1 Nef protein with -COP, a component of non-clathrin-coated vesicles essential for membrane traffic. J. Biol. Chem. 269:30073-30076.
4. Brambilla, A., L. Turchetto, A. Gatti, C. Bovolenta, F. Veglia, E. Santagostino, A. Gringeri, M. Clementi, G. Poli, P. Bagnarelli, and E. Vicenzi. 1999. Defective nef alleles in a cohort of hemophiliacs with progressing and nonprogressing HIV-1 infection. Virology 259:349-368.
5. Buchbinder, S. P., M. H. Katz, N. A. Hessol, P. M. O'Malley, and S. D. Holmberg. 1994. Long-term HIV-1 infection without immunologic progression. AIDS 8:1123-1128.
6. Calugi, G., F. Montella, C. Favalli, and A. Benedetto. 2006. Entire genome of a strain of human immunodeficiency virus type 1 with a deletion of nef that was recovered 20 years after primary infection: large pool of proviruses with deletions of env. J. Virol. 80:11892-11896.
7. Cao, Y., L. Qin, L. Zhang, J. Safrit, and D. D. Ho. 1995. Virologic and immunologic characterization of long-term survivors of human immunodeficiency virus type 1 infection. N. Engl. J. Med. 332:201-208.
8. Carl, S., R. Daniels, A. J. Iafrate, P. Easterbrook, T. C. Greenough, J. Skowronski, and F. Kirchhoff. 2000. Partial "repair" of defective nef genes in a long-term nonprogressor with human immunodeficiency virus type 1 infection. J. Infect. Dis. 181:132-140.
9. Carl, S., A. J. Iafrate, J. Skowronski, C. Stahl-Hennig, and F. Kirchhoff. 1999. Effect of the attenuating deletion and of sequence alterations evolving in vivo on simian immunodeficiency virus C8-Nef function. J. Virol. 73:2790-2797.
10. Casartelli, N., G. Di Matteo, C. Argentini, C. Cancrini, S. Bernardi, G. Castelli, G. Scarlatti, A. Plebani, P. Rossi, and M. Doria. 2003. Structural defects and variations in the HIV-1 nef gene from rapid, slow and nonprogressor children. AIDS 17:1291-1301.
11. Catucci, M., G. Venturi, L. Romano, P. E. Valensin, and M. Zazzi. 2000. Analysis of the HIV-1 nef gene in five intravenous drug users with long-term nonprogressive HIV-1 infection in Italy. J. Med. Virol. 60:294-299.
12. Chakraborty, R., G. M. Gillespie, M. Reinis, T. Rostron, T. Dong, S. Philpott, H. Burger, B. Weiser, T. Peto, and S. L. Rowland-Jones. 2002. HIV-1-specific CD8 T-cell responses in a pediatric slow progressor infected as a premature neonate. AIDS 16:2085-2087.
13. Chakraborty, R., M. Reinis, T. Rostron, S. Philpott, T. Dong, A. D'Agostino, R. Musoke, E. Silva, M. Stumpf, B. Weiser, H. Burger, and S. L. Rowland-Jones. 2006. nef gene sequence variation among HIV-1-infected African children. HIV Med. 7:75-84.
14. Cho, Y. K., J. Y. Lim, Y. S. Jung, S. K. Oh, H. J. Lee, and H. Sung. 2006. High frequency of grossly deleted nef genes in HIV-1-infected long-term slow progressors treated with Korean red ginseng. Curr. HIV Res. 4:447-457.
15. Churchill, M. J., D. I. Rhodes, J. C. Learmont, J. S. Sullivan, S. L. Wesselingh, I. R. Cooke, N. J. Deacon, and P. R. Gorry. 2006. Longitudinal analysis of human immunodeficiency virus type 1 nef/long terminal repeat sequences in a cohort of long-term survivors infected from a single source. J. Virol. 80:1047-1052.
16. Deacon, N. J., A. Tsykin, A. Solomon, K. Smith, M. Ludford-Menting, D. J. Hooker, D. A. McPhee, A. L. Greenway, A. Ellett, C. Chatfield, V. A. Lawson, S. Crowe, A. Maerz, S. Sonza, J. Learmont, J. S. Sullivan, A. Cunningham, D. Dwyer, D. Dowton, and J. Mills. 1995. Genomic structure of an attenuated quasispecies of HIV-1 from a blood transfusion donor and recipients. Science 270:988-991.
17. Du, Z., S. M. Lang, V. G. Sasseville, A. A. Lackner, P. O. Ilyinskii, M. D. Daniel, J. U. Jung, and R. C. Desrosiers. 1995. Identification of a nef allele that causes lymphocyte activation and acute disease in macaque monkeys. Cell 82:665-674.
18. Edgar, R. C. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5:113.
19. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
20. Fang, G., C. Kuiken, B. Weiser, S. Rowland-Jones, F. Plummer, C. H. Chen, R. Kaul, A. O. Anzala, J. Bwayo, J. Kimani, S. M. Philpott, C. Kitchen, J. S. Sinsheimer, B. Gaschen, D. Lang, B. Shi, K. S. Kemal, T. Rostron, C. Brunner, S. Beddows, Q. Sattenau, E. Paxinos, J. Oyugi, and H. Burger. 2004. Long-term survivors in Nairobi: complete HIV-1 RNA sequences and immunogenetic associations. J. Infect. Dis. 190:697-701.
21. Faure, J., R. Stalder, C. Borel, K. Sobo, V. Piguet, N. Demaurex, J. Gruenberg, and D. Trono. 2004. ARF1 regulates Nef-induced CD4 degradation. Curr. Biol. 14:1056-1064.
22. Foster, J. L., R. P. Molina, T. Luo, V. K. Arora, Y. Huang, D. D. Ho, and J. V. Garcia. 2001. Genetic and functional diversity of human immunodeficiency virus type 1 subtype B Nef primary isolates. J. Virol. 75:1672-1680.
23. Fuxreiter, M., P. Tompa, and I. Simon. 2007. Local structural disorder imparts plasticity on linear motifs. Bioinformatics 23:950-956.
24. Geffin, R., D. Wolf, R. Muller, M. D. Hill, E. Stellwag, M. Freitag, G. Sass, G. B. Scott, and A. S. Baur. 2000. Functional and structural defects in HIV type 1 nef genes derived from pediatric long-term survivors. AIDS Res. Hum. Retrovir. 16:1855-1868.
25. Geyer, M., and B. M. Peterlin. 2001. Domain assembly, surface accessibility and sequence conservation in full-length HIV-1 Nef. FEBS Lett. 496:91-95.
26. Greenough, T. C., J. L. Sullivan, and R. C. Desrosiers. 1999. Declining CD4 T-cell counts in a person infected with nef-deleted HIV-1. N Engl. J. Med. 340:236-237.
27. Hanna, Z., D. G. Kay, N. Rebai, A. Guimond, S. Jothy, and P. Jolicoeur. 1998. Nef harbors a major determinant of pathogenicity for an AIDS-like disease induced by HIV-1 in transgenic mice. Cell 95:163-175.
28. Huang, Y., L. Zhang, and D. D. Ho. 1995. Biological characterization of nef in long-term survivors of human immunodeficiency virus type 1 infection. J. Virol. 69:8142-8146.
29. Huang, Y., L. Zhang, and D. D. Ho. 1995. Characterization of nef sequences in long-term survivors of human immunodeficiency virus type 1 infection. J. Virol. 69:93-100.
30. Kestler, H. W., III, D. J. Ringler, K. Mori, D. L. Panicali, P. K. Sehgal, M. D. Daniel, and R. C. Desrosiers. 1991. Importance of the nef gene for maintenance of high virus loads and for development of AIDS. Cell 65:651-662.
31. Khan, I. H., E. T. Sawai, E. Antonio, C. J. Weber, C. P. Mandell, P. Montbriand, and P. A. Luciw. 1998. Role of the SH3-ligand domain of simian immunodeficiency virus Nef in interaction with Nef-associated kinase and simian AIDS in rhesus macaques. J. Virol. 72:5820-5830.
32. Kirchhoff, F., P. J. Easterbrook, N. Douglas, M. Troop, T. C. Greenough, J. Weber, S. Carl, J. L. Sullivan, and R. S. Daniels. 1999. Sequence variations in human immunodeficiency virus type 1 Nef are associated with different stages of disease. J. Virol. 73:5497-5508.
33. Kirchhoff, F., T. C. Greenough, D. B. Brettler, J. L. Sullivan, and R. C. Desrosiers. 1995. Brief report: absence of intact nef sequences in a long-term survivor with nonprogressive HIV-1 infection. N Engl. J. Med. 332:228-232.
34. Kirchhoff, F., M. Schindler, N. Bailer, G. H. Renkema, K. Saksela, V. Knoop, M. C. Muller-Trutwin, M. L. Santiago, F. Bibollet-Ruche, M. T. Dittmar, J. L. Heeney, B. H. Hahn, and J. Munch. 2004. Nef proteins from simian immunodeficiency virus-infected chimpanzees interact with p21-activated kinase 2 and modulate cell surface expression of various human receptors. J. Virol. 78:6864-6874.
35. Kondo, M., T. Shima, M. Nishizawa, K. Sudo, S. Iwamuro, T. Okabe, Y. Takebe, and M. Imai. 2005. Identification of attenuated variants of HIV-1 circulating recombinant form 01-AE that are associated with slow disease progression due to gross genetic alterations in the nef/long terminal repeat sequences. J. Infect. Dis. 192:56-61.
36. Kuiken, C., B. Foley, P. Marx, S. Wolinsky, T. Leitner, B. Hahn, F. McCutchan, and B. Korber (ed.). 2009. HIV sequence compendium 2009. Document LA-UR 06-0680. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM.
37. Lang, S. M., A. J. Iafrate, C. Stahl-Hennig, E. M. Kuhn, T. Nisslein, F. J. Kaup, M. Haupt, G. Hunsmann, J. Skowronski, and F. Kirchhoff. 1997. Association of simian immunodeficiency virus Nef with cellular serine/threonine kinases is dispensable for the development of AIDS in rhesus macaques. Nat. Med. 3:860-865.
38. Lum, J. J., O. J. Cohen, Z. Nie, J. G. Weaver, T. S. Gomez, X. J. Yao, D. Lynch, A. A. Pilon, N. Hawley, J. E. Kim, Z. Chen, M. Montpetit, J. Sanchez-Dardon, E. A. Cohen, and A. D. Badley. 2003. Vpr R77Q is associated with long-term nonprogressive HIV infection and impaired induction of apoptosis. J. Clin. Invest. 111:1547-1554.
39. Mariani, R., F. Kirchhoff, T. C. Greenough, J. L. Sullivan, R. C. Desrosiers, and J. Skowronski. 1996. High frequency of defective nef alleles in a long-term survivor with nonprogressive human immunodeficiency virus type 1 infection. J. Virol. 70:7752-7764.
40. Michael, N. L., G. Chang, L. A. d'Arcy, C. J. Tseng, D. L. Birx, and H. W. Sheppard. 1995. Functional characterization of human immunodeficiency virus type 1 nef genes in patients with divergent rates of disease progression. J. Virol. 69:6758-6769.
41. Mourich, D. V., S. Lee, G. Reyes-Teran, C. E. Mackewicz, and J. A. Levy. 1999. Lack of differences in nef alleles among HIV-infected asymptomatic long-term survivors and those who progressed to disease. AIDS Res. Hum. Retrovir. 15:1573-1575.
42. Parreira, R., E. Padua, J. Piedade, T. Venenno, M. T. Paixao, and A. Esteves. 2005. Genetic analysis of human immunodeficiency virus type 1 nef in Portugal: subtyping, identification of mosaic genes, and amino acid sequence variability. J. Med. Virol. 77:8-16.
43. Ratner, L., T. Joseph, J. Bandres, S. Ghosh, N. Vander Heyden, A. Templeton, B. Hahn, W. Powderly, and M. Arens. 1996. Sequence heterogeneity of Nef transcripts in HIV-1-infected subjects at different stages of disease. Virology 223:245-250.
44. Reinis, M., B. Weiser, C. Kuiken, T. Dong, D. Lang, S. Nachman, Y. Zhang, S. Rowland-Jones, and H. Burger. 2007. Genomic analysis of HIV type 1 strains derived from a mother and child pair of long-term nonprogressors. AIDS Res. Hum. Retrovir. 23:309-315.
45. Rhodes, D. I., L. Ashton, A. Solomon, A. Carr, D. Cooper, J. Kaldor, and N. Deacon. 2000. Characterization of three nef-defective human immunodeficiency virus type 1 strains associated with long-term nonprogression. J. Virol. 74:10581-10588.
46. Rice, P., I. Longden, and A. Bleasby. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16:276-277.
47. Rodes, B., C. Toro, E. Paxinos, E. Poveda, M. Martinez-Padial, J. M. Benito, V. Jimenez, T. Wrin, S. Bassani, and V. Soriano. 2004. Differences in disease progression in a cohort of long-term non-progressors after more than 16 years of HIV-1 infection. AIDS 18:1109-1116.
48. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
49. Salvi, R., A. R. Garbuglia, A. Di Caro, S. Pulciani, F. Montella, and A. Benedetto. 1998. Grossly defective nef gene sequences in a human immunodeficiency virus type 1-seropositive long-term nonprogressor. J. Virol. 72: 3646-3657.
50. + T-cell counts. AIDS Res. Hum. Retrovir. 19:73-76.
51. Sawai, E. T., I. H. Khan, P. M. Montbriand, B. M. Peterlin, C. Cheng-Mayer, and P. A. Luciw. 1996. Activation of PAK by HIV and SIV Nef: importance for AIDS in rhesus macaques. Curr. Biol. 6:1519-1527.
52. Schmokel, J., H. Li, E. Bailes, M. Schindler, G. Silvestri, B. H. Hahn, C. Apetrei, and F. Kirchhoff. 2009. Conservation of Nef function across highly diverse lineages of SIVsmm. Retrovirology 6:36.
53. Shugars, D. C., M. S. Smith, D. H. Glueck, P. V. Nantermet, F. Seillier-Moiseiwitsch, and R. Swanstrom. 1993. Analysis of human immunodefi-ciency virus type 1 nef gene sequences present in vivo. J. Virol. 67:4639-4650.
54. Thompson, J. D., T. J. Gibson, and D. G. Higgins. 2002. Multiple sequence alignment using CLUSTAL W and CLUSTAL X. Curr. Protoc. Bioinform. 2:23.
55. Turk, G., M. M. Gherardi, N. Laufer, M. Saracco, R. Luzzi, J. H. Cox, P. Cahn, and H. Salomon. 2008. Magnitude, breadth, and functional profile of T-cell responses during human immunodeficiency virus primary infection with B and BF viral variants. J. Virol. 82:2853-2866.
56. Wang, B., M. Mikhail, W. B. Dyer, J. J. Zaunders, A. D. Kelleher, and N. K. Saksena. 2003. First demonstration of a lack of viral sequence evolution in a nonprogressor, defining replication-incompetent HIV-1 infection. Virology 312:135-150.
57. Wang, B., T. J. Spira, S. Owen, R. B. Lal, and N. K. Saksena. 2000. HIV-1 strains from a cohort of American subjects reveal the presence of a V2 region extension unique to slow progressors and non-progressors. AIDS 14:213-223.
58. Yamada, T., and A. Iwamoto. 2000. Comparison of proviral accessory genes between long-term nonprogressors and progressors of human immunodeficiency virus type 1 infection. Arch. Virol. 145:1021-1027.