Genetic characterization of the nef gene from human immunodeficiency virus type 1 group M strains representing genetic subtypes A, B, C, E, F, G, and H

AIDS Research and Human Retroviruses

Volumn 15, Issue 1, 1999, Pages 23-32

  Jubier Maurin, Veronique ^a   Saragosti, Sentob ^b   Perret, Jean Luc ^c   Mpoudi, Eitel ^d   Esu Williams, Eka ^e   Mulanga, Claire ^a   Liegeois, Florian ^a   Ekwalanga, Michel ^f   Delaporte, Eric ^a   Peeters, Martine ^a  

^a INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^b INSERM   (France)

^c LAVERAN MILITARY TEACHING HOSPITAL   (France)

^d Military Hospital   (Cameroon)

^e UNIVERSITY OF CALABAR   (Nigeria)

^f INRB ^*  (Congo)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ENVELOPE GENE; FRANCE; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; LONG TERMINAL REPEAT; MYRISTYLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STRUCTURAL GENE; VIRUS RECOMBINANT;

AMINO ACID SEQUENCE; CONSENSUS SEQUENCE; DNA, VIRAL; GENES, ENV; GENES, NEF; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

EID: 0032938988     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/088922299311673     Document Type: Article

References (49)

1. Kirchhoff F, Greenough TC, Brettler DB, Sullivan JL, and Desrosiers RC: Absence of intact Nef sequences in a long-term survivor with nonprogressive HIV-1. N Engl J Med 1995;332: 228-232.
2. Deacon NJ, Tsykin A, Solomon A, Smith K, Ludford-Menting M, Hooker DJ, McPhee DA, Greenway AL, Ellett A, Chatfield C, Lawson VA, Crowe S, Maerz A, Sonza S, Learmont J, Sullivan JS, Cunningham A, Dwyer D, Dowton D, and Mills J: Genomic structure of an attenuated quasi species of HIV-1 from a blood transfusion donor and recipients. Science 1995;270:988-991.
3. Kestler HW, Ringler DJ, Mori K, Panicali DL, Sehgal PK, Daniel MD, and Desrosiers RC: Importance of the Nef gene for maintenance of high virus loads and for development of AIDS. Cell 1991;65:651-662.
4. Daniel MD, Kirchhoff F, Czajak SC, Sehgal PK and Desrosiers, RC: Protective effects of a live attenuated SIV vaccine with a deletion in the Nef gene. Science 1992;258:1938-1941.
5. Michael NL, Chang G, d'Arcy LA, Tseng CJ, Birx DL, and Sheppard HW: Functional characterization of human immunodeficiency virus type 1 Nef genes in patients with divergent rates of disease progression. J Virol 1995;69:6758-6769.
6. Huang Y, Zhang L, and Ho DD: Biological characterization of Nef in long-term survivors of human immunodeficiency virus type 1 infection. J Virol 1995;69:8142-8146.
7. Jamieson BD, Aldrovandi GM, Planelles V, Jowett JB, Gao L, Bloch LM, Chen IS, and Zack JA: Requirement of human immunodeficiency virus type 1 Nef for in vivo replication and pathogenicity. J Virol 1994;68:3478-3485.
8. Miller MD, Warmerdam MT, Gaston I, Greene WC, and Feinberg MB: The human immunodeficiency virus-1 Nef gene product: A positive factor for viral infection and replication in primary lymphocytes and macrophages. J Exp Med 1994;179:101-113.
9. Zazopoulos E and Haseltine WA: Effect of Nef alleles on replication of human immunodeficiency virus type 1. Virology 1993; 194:20-27.
10. Goldsmith MA, Warmerdam MT, Atchison RE, Miller MD, and Greene WC: Dissociation of the CD4 downregulation and viral infectivity enhancement functions of human immunodeficiency virus type 1 Nef. J Virol 1995;69:4112-4121.
11. Shugars DC, Smith MS, Glueck DH, Nantermet PV, Seillier-Moiseiwitsch F, and Swanstrom R: Analysis of human immunodeficiency virus type 1 Nef gene sequences present in vivo. J Virol 1993;67:4639-4650.
12. Anderson S, Shugars DC, Swanstrom R, and Garcia JV: Nef from primary isolates of human immunodeficiency virus type 1 suppresses surface CD4 expression in human and mouse T cells. J Virol 1993;67:4923-4931.
13. Brady HJ, Pennington DJ, Miles CG, and Dzierzak EA: CD4 cell surface downregulation in HIV-1 Nef transgenic mice is a consequence of intracellular sequestration. EMBO J 1993;12:4923-4932.
14. Culmann-Penciolelli B, Lamhamedi-Cherradi S, Couillin I, Guegan N, Levy JP, Guillet JG, and Gomard E: Identification of multirestricted immunodominant regions recognized by cytolytic T lymphocytes in the human immunodeficiency virus type 1 Nef protein. J Virol 1994;68:7336-7343.
15. Lamhamedi-Cherradi S, Culmann-Penciolelli B, Guy B, Kieny MP, Dreyfus F, Saimot AG, Sereni D, Sicard D, Levy JP, and Gomard E: Qualitative and quantitative analysis of human cytotoxic T-lymphocyte responses to HIV-1 proteins. AIDS 1992;6:1249-1258.
16. Couillin I, Culmann-Penciolelli B, Gomard E, Choppin J, Levy JP, Guillet JG, and Saragosti S: Impaired cytotoxic T lymphocyte recognition due to genetic variations in the main immunogenic region of the human immunodeficiency virus 1 NEF protein. J Exp Med 1994;180:1129-1134.
17. Price DA, Goulder PJ, Klenerman P, Sewell AK, Easterbrook PJ, Troop M, Bangham CR, and Phillips RE: Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection. Proc Natl Acad Sci USA 1997;94:1890-1895.
18. Louwagie J, McCutchan FE, Peeters M, Brennan TP, Sanders-Buell E, Eddy G, van der Groen G, Fransen K, Gershy-Damet GM, Deleys R and Burke D: Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes. AIDS 1993;7:769-780.
19. Myers G, Hahn B, Mellors JW, Henderson LE, Korber B, Jeang K-T, McCutchan FE, and Pavlakis GN: Human Retroviruses and AIDS Database: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Los Alamos National Laboratory, Los Alamos, New Mexico, 1995.
20. Robertson DL, Gao F, Hahn BH, and Sharp PM: Human Retroviruses and AIDS Database: Intersubtype Recombinant HIV-1 Sequences. Los Alamos National Laboratory, Los Alamos, New Mexico, 1997.
21. McCutchan FE, Salminen MO, Carr JK, and Burke DS: HIV-1 genetic diversity. AIDS 1996;10(Suppl. 3):S13-20.
22. Cornelissen M, Kampinga G, Zorgdrager F, and Goudsmit J: Human immunodeficiency virus type 1 subtypes defined by env show high frequency of recombinant gag genes. The UNAIDS Network for HIV Isolation and Characterization. J Virol 1996;70: 8209-8212.
23. Gao F, Robertson DL, Morrison SG, Hui H, Craig S, Decker J, Fultz P, Girard M, Shaw GM, Hahn BH, and Sharp PM: The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. J Virol 1996;70:7013-7029.
24. European Commission (DG XII, INCO-DC) and the Joint United Nations Programme on HIV/AIDS: HIV-1 subtypes: Implications for epidemiology, pathogenicity, vaccines and diagnostics. AIDS 1997;11:UNAIDS17-UNAIDS36. [Workship report]
25. Lasky M, Perret JL, Peeters M, Bibollet-Ruche F, Liegeois F, Patrel D, Molinier S, Gras C, and Delaporte E: Presence of multiple non-B subtypes and divergent subtype B strains of HIV-1 in individuals infected after overseas deployment. AIDS 1997;11:43-51.
26. Delwart EL, Shpaer EG, Louwagie J, McCutchan FE, Grez M, Rübsamen-Waigmann H, and Mullins JI: Genetic relationships determined by a DNA heteroduplex mobility assay: Analysis of HIV-1 env genes. Science 1993;262:1257-1261.
27. Artenstein AW, Hegerich PA, Beyrer C, Rungruengthanakit K, Michael NL, and Natpratan C: Sequences and phylogenetic analysis of the Nef gene from Thai subjects harboring subtype E HIV-1. AIDS Res Hum Retroviruses 1996;12:557-560.
28. Thompson J, Higgins D, and Gibson T: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res 1994;22:4673-4680.
29. Kimura M: A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotides sequences. J Mol Evol 1980;16:111-120.
30. Siepel AC, Halpern AL, Macken C, and Korber BT: A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res Hum Retroviruses 1995;11: 1413-1416.
31. Robertson D, Hahn B, and Sharp P: Recombination in AIDS viruses. J Mol Evol 1995;40:249-259.
32. Korber B and Myers G: Signature pattern analysis: A method for assessing viral sequence relatedness. AIDS Res Hum Retroviruses 1992;8:1549-1560.
33. Choi DJ, Dube S, Spicer TP, Slade HB, Jensen FC, and Poiesz BJ: HIV type 1 isolate Z321, the strain used to make a therapeutic HIV type 1 immunogen, is intersubtype recombinant. AIDS Res Hum Retroviruses 197;13:357-361.
34. Premkumar DR, Ma XZ, Maitra RK, Chakrabarti BK, Salkowitz J, Yen-Lieberman B, Hirsch MS, and Kestler HW: The Nef gene from a long-term HIV type 1 nonprogressor. AIDS Res Hum Retroviruses 1996;12:337-345.
35. Cornelissen M, van den Burg R, Zorgdrager F, Lukashov V, and Goudsmit J: Pol gene diversity of five human immunodeficiency virus type 1 subtypes: Evidence for naturally occurring mutations that contribute to drug resistance, limiting recombination patterns, and common ancestry for subtypes B and D. J Virol 1997; 71:6348-6358.
36. Zhu T, Korber BT, Nahmias AJ, Hooper E, Sharp PM, and Ho DD: An African HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature (London) 1998;391:594-597.
37. Kaminchik J, Bashan N, Itach A, Sarver N, Gorecki M, and Panet A: Genetic characterization of human immunodeficiency virus type 1 Nef gene products translated in vitro and expressed in mammalian cells. J Virol 1991;65:583-588.
38. Zweig M, Samuel KP, Showalter SD, Bladen SV, Dubois GC, Lautenberger JA, Hodge DR, and Papas TS: Heterogeneity of Nef proteins in cells infected with human immunodeficiency virus type 1. Virology 1990;179:504-507.
39. Kennelly PJ and Krebs EG: Consensus sequences as substrate specificity detreminants for protein kinases and protein phosphatases. J Biol Chem 1991;266:15555-15558.
40. Kawano Y, Tanaka Y, Misawa N, Tanaka R, Kira JI, Kimura T, Fukushi M, Sano K, Goto T, Nakai M, Kobayashi T, Yamamoto N, and Koyanagi Y: Mutational analysis of human immunodeficiency virus type 1 (HIV-1) accessory genes: Requirement of a site in the Nef gene for HIV-1 replication in activated CD4+ T cells in vitro and in vivo. J Virol 1997;71:8456-8466.
41. Saksela K, Cheng G, and Baltimore D: Proline-rich (PxxP) motifs in HIV-1 Nef bind to SH3 domains of a subset of Src kinases and are required for the enhanced growth of Nef+ viruses but not for down-regulation of CD4. EMBO J 1995;14:484-491.
42. Zazopoulos E and Haseltine WA: Disulfide bond formation in the human immunodeficiency virus type 1 Nef protein. J Virol 1993; 67:1676-1680.
43. Blaak H, Brouwer M, Ran LJ, de Wolf F, and Schuitemaker H: In vitro replication kinetics of human immunodeficiency virus type 1 (HIV-1) variants in relation to virus load in long-term survivors of HIV-1 infection. J Infect Dis 1998;177:600-610.
44. Saksena NK, Ge YC, Wang B, Xiang SH, Ziegler J, Palasanthiran P, Bolton W, and Cunningham AL: RNA and DNA sequence analysis of the Nef gene of HIV type 1 strains from the first HIV type 1-infected long-term nonprogressing mother-child pair. AIDS Res Hum Retroviruses 1997;13:729-732.
45. Cao H, Kanki P, Sankale JL, Dieng-Sarr A, Mazzara G, Kalams S, Korber B, Mboup S, and Walker B: Cytotoxic T-lymphocyte cross-reactivity among different human immunodeficiency virus type 1 clades: Implications for vaccine development. J Virol 1997; 71:8615-8623.
46. Bertoletti A, Cham F, McAdam S, Rostron T, Rowland-Jones S, Sabally S, Corrah T, Ariyosha K, and Whittle H: Cytotoxic T cells from human immunodeficiency virus type 2-infected patients frequently cross-react with different human immunodeficiency virus type 1 clades. J Virol 1998;72:2439-2448.
47. Betts MR, Krowka J, Santamaria C, Balsamo K, Gao F, Mulundu G, Luo C, N'Gandu N, Sheppard H, Hahn B, Allen S, and Frelinger JA: Cross-clade human immunodeficiency virus (HIV)-specific cytotoxic T-lymphocyte responses in HIV-infected Zambians. J Virol 1997;71:8908-8911.
48. Schwartz O, Marechal V, Le Gall S, Lemonnier F, and Heard JM: Endocytosis of major histocompatibility complex class I molecules is induced by the HIV-1 Nef protein. Nature Med 1996;2:338-342.
49. Collins KL, Chen BK, Kalams SA, Walker BD, and Baltimore D: HIV-1 Nef protein protects infected primary cells against killing by cytotoxic T lymphocytes. Nature (London) 1998;391:397-401.