Skip to main content
PMC home page
Journal of Virology logoLink to Journal of Virology
. 1995 Jan;69(1):93–100. doi: 10.1128/jvi.69.1.93-100.1995

Characterization of nef sequences in long-term survivors of human immunodeficiency virus type 1 infection.

Y Huang 1, L Zhang 1, D D Ho 1
PMCID: PMC188552  PMID: 7983771

Abstract

Studies with the simian immunodeficiency virus have shown that nef deletion results in a low level of viremia and a lack of disease progression in monkeys. Given the similarity of this clinical profile to that observed in long-term survivors of human immunodeficiency virus type 1 (HIV-1) infection, we sought to examine the nef gene in 10 patients who are clinically healthy and immunologically normal despite 12 to 15 years of infection. PCR and DNA sequencing were used to determine nef sequences in peripheral blood mononuclear cells obtained from long-term survivors. We found that there is no gross deletion within nef in the cases studied; most nef sequences (91.1%) obtained from 10 subjects contained a full-length and intact open reading frame. In addition, at the protein level, there were no discernible differences between the Nef consensus sequences derived from long-term survivors and those from patients with AIDS. We therefore conclude that deletion of or gross sequence abnormality within nef is not likely to be a common explanation for the well-being of long-term survivors of HIV-1 infection. Moreover, phylogenetic analysis of nef sequences suggests that HIV-1 strains found in our study subjects do not have a common origin.

Full Text

The Full Text of this article is available as a PDF (319.2 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ahmad N., Venkatesan S. Nef protein of HIV-1 is a transcriptional repressor of HIV-1 LTR. Science. 1988 Sep 16;241(4872):1481–1485. doi: 10.1126/science.3262235. [DOI] [PubMed] [Google Scholar]
  2. Bacchetti P., Moss A. R. Incubation period of AIDS in San Francisco. Nature. 1989 Mar 16;338(6212):251–253. doi: 10.1038/338251a0. [DOI] [PubMed] [Google Scholar]
  3. Blumberg B. M., Epstein L. G., Saito Y., Chen D., Sharer L. R., Anand R. Human immunodeficiency virus type 1 nef quasispecies in pathological tissue. J Virol. 1992 Sep;66(9):5256–5264. doi: 10.1128/jvi.66.9.5256-5264.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cheng-Mayer C., Iannello P., Shaw K., Luciw P. A., Levy J. A. Differential effects of nef on HIV replication: implications for viral pathogenesis in the host. Science. 1989 Dec 22;246(4937):1629–1632. doi: 10.1126/science.2531920. [DOI] [PubMed] [Google Scholar]
  5. Chowers M. Y., Spina C. A., Kwoh T. J., Fitch N. J., Richman D. D., Guatelli J. C. Optimal infectivity in vitro of human immunodeficiency virus type 1 requires an intact nef gene. J Virol. 1994 May;68(5):2906–2914. doi: 10.1128/jvi.68.5.2906-2914.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Colombini S., Arya S. K., Reitz M. S., Jagodzinski L., Beaver B., Wong-Staal F. Structure of simian immunodeficiency virus regulatory genes. Proc Natl Acad Sci U S A. 1989 Jul;86(13):4813–4817. doi: 10.1073/pnas.86.13.4813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Connor R. I., Mohri H., Cao Y., Ho D. D. Increased viral burden and cytopathicity correlate temporally with CD4+ T-lymphocyte decline and clinical progression in human immunodeficiency virus type 1-infected individuals. J Virol. 1993 Apr;67(4):1772–1777. doi: 10.1128/jvi.67.4.1772-1777.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Delassus S., Cheynier R., Wain-Hobson S. Evolution of human immunodeficiency virus type 1 nef and long terminal repeat sequences over 4 years in vivo and in vitro. J Virol. 1991 Jan;65(1):225–231. doi: 10.1128/jvi.65.1.225-231.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet. 1988;22:521–565. doi: 10.1146/annurev.ge.22.120188.002513. [DOI] [PubMed] [Google Scholar]
  10. Garcia J. V., Miller A. D. Serine phosphorylation-independent downregulation of cell-surface CD4 by nef. Nature. 1991 Apr 11;350(6318):508–511. doi: 10.1038/350508a0. [DOI] [PubMed] [Google Scholar]
  11. 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. 1994 Apr;10(4):395–403. doi: 10.1089/aid.1994.10.395. [DOI] [PubMed] [Google Scholar]
  12. Hammes S. R., Dixon E. P., Malim M. H., Cullen B. R., Greene W. C. Nef protein of human immunodeficiency virus type 1: evidence against its role as a transcriptional inhibitor. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9549–9553. doi: 10.1073/pnas.86.23.9549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Harris M., Hislop S., Patsilinacos P., Neil J. C. In vivo derived HIV-1 nef gene products are heterogeneous and lack detectable nucleotide binding activity. AIDS Res Hum Retroviruses. 1992 May;8(5):537–543. doi: 10.1089/aid.1992.8.537. [DOI] [PubMed] [Google Scholar]
  14. Higgins D. G., Sharp P. M. Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci. 1989 Apr;5(2):151–153. doi: 10.1093/bioinformatics/5.2.151. [DOI] [PubMed] [Google Scholar]
  15. Ho D. D., Moudgil T., Alam M. Quantitation of human immunodeficiency virus type 1 in the blood of infected persons. N Engl J Med. 1989 Dec 14;321(24):1621–1625. doi: 10.1056/NEJM198912143212401. [DOI] [PubMed] [Google Scholar]
  16. Kaslow R. A., Duquesnoy R., VanRaden M., Kingsley L., Marrari M., Friedman H., Su S., Saah A. J., Detels R., Phair J. A1, Cw7, B8, DR3 HLA antigen combination associated with rapid decline of T-helper lymphocytes in HIV-1 infection. A report from the Multicenter AIDS Cohort Study. Lancet. 1990 Apr 21;335(8695):927–930. doi: 10.1016/0140-6736(90)90995-h. [DOI] [PubMed] [Google Scholar]
  17. Kestler H. W., 3rd, Ringler D. J., Mori K., Panicali D. L., Sehgal P. K., Daniel M. D., Desrosiers R. C. Importance of the nef gene for maintenance of high virus loads and for development of AIDS. Cell. 1991 May 17;65(4):651–662. doi: 10.1016/0092-8674(91)90097-i. [DOI] [PubMed] [Google Scholar]
  18. Kim S. Y., Byrn R., Groopman J., Baltimore D. Temporal aspects of DNA and RNA synthesis during human immunodeficiency virus infection: evidence for differential gene expression. J Virol. 1989 Sep;63(9):3708–3713. doi: 10.1128/jvi.63.9.3708-3713.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kim S., Ikeuchi K., Byrn R., Groopman J., Baltimore D. Lack of a negative influence on viral growth by the nef gene of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9544–9548. doi: 10.1073/pnas.86.23.9544. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kitamura T. Summary of the epidemiology of HIV/AIDS in Japan. AIDS. 1994;8 (Suppl 2):S95–S97. [PubMed] [Google Scholar]
  21. Learmont J., Tindall B., Evans L., Cunningham A., Cunningham P., Wells J., Penny R., Kaldor J., Cooper D. A. Long-term symptomless HIV-1 infection in recipients of blood products from a single donor. Lancet. 1992 Oct 10;340(8824):863–867. doi: 10.1016/0140-6736(92)93281-q. [DOI] [PubMed] [Google Scholar]
  22. Lifson A. R., Buchbinder S. P., Sheppard H. W., Mawle A. C., Wilber J. C., Stanley M., Hart C. E., Hessol N. A., Holmberg S. D. Long-term human immunodeficiency virus infection in asymptomatic homosexual and bisexual men with normal CD4+ lymphocyte counts: immunologic and virologic characteristics. J Infect Dis. 1991 May;163(5):959–965. doi: 10.1093/infdis/163.5.959. [DOI] [PubMed] [Google Scholar]
  23. Luciw P. A., Cheng-Mayer C., Levy J. A. Mutational analysis of the human immunodeficiency virus: the orf-B region down-regulates virus replication. Proc Natl Acad Sci U S A. 1987 Mar;84(5):1434–1438. doi: 10.1073/pnas.84.5.1434. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Luria S., Chambers I., Berg P. Expression of the type 1 human immunodeficiency virus Nef protein in T cells prevents antigen receptor-mediated induction of interleukin 2 mRNA. Proc Natl Acad Sci U S A. 1991 Jun 15;88(12):5326–5330. doi: 10.1073/pnas.88.12.5326. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mariani R., Skowronski J. CD4 down-regulation by nef alleles isolated from human immunodeficiency virus type 1-infected individuals. Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5549–5553. doi: 10.1073/pnas.90.12.5549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. McLean K. A., Holmes D. A., Evans B. A., McAlpine L., Thorp R., Parry J. V., Glaser M. G. Rapid clinical and laboratory progression of HIV infection. AIDS. 1990 Apr;4(4):369–371. doi: 10.1097/00002030-199004000-00018. [DOI] [PubMed] [Google Scholar]
  27. Miller M. D., Warmerdam M. T., Gaston I., Greene W. C., Feinberg M. B. 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 Jan 1;179(1):101–113. doi: 10.1084/jem.179.1.101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Murti K. G., Brown P. S., Ratner L., Garcia J. V. Highly localized tracks of human immunodeficiency virus type 1 Nef in the nucleus of cells of a human CD4+ T-cell line. Proc Natl Acad Sci U S A. 1993 Dec 15;90(24):11895–11899. doi: 10.1073/pnas.90.24.11895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Niederman T. M., Thielan B. J., Ratner L. Human immunodeficiency virus type 1 negative factor is a transcriptional silencer. Proc Natl Acad Sci U S A. 1989 Feb;86(4):1128–1132. doi: 10.1073/pnas.86.4.1128. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ratner L., Starcich B., Josephs S. F., Hahn B. H., Reddy E. P., Livak K. J., Petteway S. R., Jr, Pearson M. L., Haseltine W. A., Arya S. K. Polymorphism of the 3' open reading frame of the virus associated with the acquired immune deficiency syndrome, human T-lymphotropic virus type III. Nucleic Acids Res. 1985 Nov 25;13(22):8219–8229. doi: 10.1093/nar/13.22.8219. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Saksela K., Stevens C., Rubinstein P., Baltimore D. Human immunodeficiency virus type 1 mRNA expression in peripheral blood cells predicts disease progression independently of the numbers of CD4+ lymphocytes. Proc Natl Acad Sci U S A. 1994 Feb 1;91(3):1104–1108. doi: 10.1073/pnas.91.3.1104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Schnittman S. M., Greenhouse J. J., Psallidopoulos M. C., Baseler M., Salzman N. P., Fauci A. S., Lane H. C. Increasing viral burden in CD4+ T cells from patients with human immunodeficiency virus (HIV) infection reflects rapidly progressive immunosuppression and clinical disease. Ann Intern Med. 1990 Sep 15;113(6):438–443. doi: 10.7326/0003-4819-113-6-438. [DOI] [PubMed] [Google Scholar]
  33. Schwartz S., Felber B. K., Benko D. M., Fenyö E. M., Pavlakis G. N. Cloning and functional analysis of multiply spliced mRNA species of human immunodeficiency virus type 1. J Virol. 1990 Jun;64(6):2519–2529. doi: 10.1128/jvi.64.6.2519-2529.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Sheppard H. W., Lang W., Ascher M. S., Vittinghoff E., Winkelstein W. The characterization of non-progressors: long-term HIV-1 infection with stable CD4+ T-cell levels. AIDS. 1993 Sep;7(9):1159–1166. [PubMed] [Google Scholar]
  35. Shibata R., Miura T., Hayami M., Ogawa K., Sakai H., Kiyomasu T., Ishimoto A., Adachi A. Mutational analysis of the human immunodeficiency virus type 2 (HIV-2) genome in relation to HIV-1 and simian immunodeficiency virus SIV (AGM). J Virol. 1990 Feb;64(2):742–747. doi: 10.1128/jvi.64.2.742-747.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Shugars D. C., Smith M. S., Glueck D. H., Nantermet P. V., Seillier-Moiseiwitsch F., Swanstrom R. Analysis of human immunodeficiency virus type 1 nef gene sequences present in vivo. J Virol. 1993 Aug;67(8):4639–4650. doi: 10.1128/jvi.67.8.4639-4650.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Simmonds P., Balfe P., Peutherer J. F., Ludlam C. A., Bishop J. O., Brown A. J. Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cells and at low copy numbers. J Virol. 1990 Feb;64(2):864–872. doi: 10.1128/jvi.64.2.864-872.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Spina C. A., Kwoh T. J., Chowers M. Y., Guatelli J. C., Richman D. D. The importance of nef in the induction of human immunodeficiency virus type 1 replication from primary quiescent CD4 lymphocytes. J Exp Med. 1994 Jan 1;179(1):115–123. doi: 10.1084/jem.179.1.115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Tersmette M., Gruters R. A., de Wolf F., de Goede R. E., Lange J. M., Schellekens P. T., Goudsmit J., Huisman H. G., Miedema F. Evidence for a role of virulent human immunodeficiency virus (HIV) variants in the pathogenesis of acquired immunodeficiency syndrome: studies on sequential HIV isolates. J Virol. 1989 May;63(5):2118–2125. doi: 10.1128/jvi.63.5.2118-2125.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Weiss R. A. How does HIV cause AIDS? Science. 1993 May 28;260(5112):1273–1279. doi: 10.1126/science.8493571. [DOI] [PubMed] [Google Scholar]
  41. Williams L. M., Cloyd M. W. Polymorphic human gene(s) determines differential susceptibility of CD4 lymphocytes to infection by certain HIV-1 isolates. Virology. 1991 Oct;184(2):723–728. doi: 10.1016/0042-6822(91)90442-e. [DOI] [PubMed] [Google Scholar]
  42. Wilmot C. M., Thornton J. M. Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol. 1988 Sep 5;203(1):221–232. doi: 10.1016/0022-2836(88)90103-9. [DOI] [PubMed] [Google Scholar]
  43. Yu G., Felsted R. L. Effect of myristoylation on p27 nef subcellular distribution and suppression of HIV-LTR transcription. Virology. 1992 Mar;187(1):46–55. doi: 10.1016/0042-6822(92)90293-x. [DOI] [PubMed] [Google Scholar]
  44. Zazopoulos E., Haseltine W. A. Effect of nef alleles on replication of human immunodeficiency virus type 1. Virology. 1993 May;194(1):20–27. doi: 10.1006/viro.1993.1230. [DOI] [PubMed] [Google Scholar]
  45. de Ronde A., Klaver B., Keulen W., Smit L., Goudsmit J. Natural HIV-1 NEF accelerates virus replication in primary human lymphocytes. Virology. 1992 May;188(1):391–395. doi: 10.1016/0042-6822(92)90772-h. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES