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. 1996 Nov;70(11):7752–7764. doi: 10.1128/jvi.70.11.7752-7764.1996

High frequency of defective nef alleles in a long-term survivor with nonprogressive human immunodeficiency virus type 1 infection.

R Mariani 1, F Kirchhoff 1, T C Greenough 1, J L Sullivan 1, R C Desrosiers 1, J Skowronski 1
PMCID: PMC190845  PMID: 8892896

Abstract

A large number of nef alleles were obtained from peripheral blood mononuclear cells (PBMC) of four long-term nonprogressing survivors of human immunodeficiency virus type 1 (HIV-1) infection and from five individuals with progressive HIV-1 infection. These primary nef alleles were characterized by DNA sequence analysis and for their ability to downregulate CD4 surface expression. Intact nef open reading frames that directed the expression of Nef protein were recovered from all of the individuals. Most of the Nef proteins derived from three of four individuals with nonprogressive infection and from all five individuals with progressive infection were functional as judged by their ability to induce a decrease in surface CD4 expression. In contrast, one individual with nonprogressive HIV-1 infection yielded an unusually high frequency of disrupted nef open reading frames and Nef proteins defective for CD4 downregulation. Approximately 70% of the nef clones obtained from the PBMC of this individual at eight time points over a 12-year period were disrupted or defective for CD4 downregulation. While functional Nef proteins were demonstrated early in the course of infection (1983), functional nef alleles have surprisingly not come to predominate over time in PBMC DNA in this individual.

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Selected References

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  1. Aiken C., Konner J., Landau N. R., Lenburg M. E., Trono D. Nef induces CD4 endocytosis: requirement for a critical dileucine motif in the membrane-proximal CD4 cytoplasmic domain. Cell. 1994 Mar 11;76(5):853–864. doi: 10.1016/0092-8674(94)90360-3. [DOI] [PubMed] [Google Scholar]
  2. Aiken C., Trono D. Nef stimulates human immunodeficiency virus type 1 proviral DNA synthesis. J Virol. 1995 Aug;69(8):5048–5056. doi: 10.1128/jvi.69.8.5048-5056.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Anderson S. J., Lenburg M., Landau N. R., Garcia J. V. The cytoplasmic domain of CD4 is sufficient for its down-regulation from the cell surface by human immunodeficiency virus type 1 Nef. J Virol. 1994 May;68(5):3092–3101. doi: 10.1128/jvi.68.5.3092-3101.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Anderson S., Shugars D. C., Swanstrom R., Garcia J. V. Nef from primary isolates of human immunodeficiency virus type 1 suppresses surface CD4 expression in human and mouse T cells. J Virol. 1993 Aug;67(8):4923–4931. doi: 10.1128/jvi.67.8.4923-4931.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Benson R. E., Sanfridson A., Ottinger J. S., Doyle C., Cullen B. R. Downregulation of cell-surface CD4 expression by simian immunodeficiency virus Nef prevents viral super infection. J Exp Med. 1993 Jun 1;177(6):1561–1566. doi: 10.1084/jem.177.6.1561. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Buchbinder S. P., Katz M. H., Hessol N. A., O'Malley P. M., Holmberg S. D. Long-term HIV-1 infection without immunologic progression. AIDS. 1994 Aug;8(8):1123–1128. doi: 10.1097/00002030-199408000-00014. [DOI] [PubMed] [Google Scholar]
  7. Buchbinder S. P., Katz M. H., Hessol N. A., O'Malley P. M., Holmberg S. D. Long-term HIV-1 infection without immunologic progression. AIDS. 1994 Aug;8(8):1123–1128. doi: 10.1097/00002030-199408000-00014. [DOI] [PubMed] [Google Scholar]
  8. Cao Y., Qin L., Zhang L., Safrit J., Ho D. D. Virologic and immunologic characterization of long-term survivors of human immunodeficiency virus type 1 infection. N Engl J Med. 1995 Jan 26;332(4):201–208. doi: 10.1056/NEJM199501263320401. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. 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. Genomic structure of an attenuated quasi species of HIV-1 from a blood transfusion donor and recipients. Science. 1995 Nov 10;270(5238):988–991. doi: 10.1126/science.270.5238.988. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. 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]
  13. Gibbs J. S., Lackner A. A., Lang S. M., Simon M. A., Sehgal P. K., Daniel M. D., Desrosiers R. C. Progression to AIDS in the absence of a gene for vpr or vpx. J Virol. 1995 Apr;69(4):2378–2383. doi: 10.1128/jvi.69.4.2378-2383.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Gojobori T., Moriyama E. N., Kimura M. Statistical methods for estimating sequence divergence. Methods Enzymol. 1990;183:531–550. doi: 10.1016/0076-6879(90)83035-8. [DOI] [PubMed] [Google Scholar]
  15. Goldsmith M. A., Warmerdam M. T., Atchison R. E., Miller M. D., Greene W. C. Dissociation of the CD4 downregulation and viral infectivity enhancement functions of human immunodeficiency virus type 1 Nef. J Virol. 1995 Jul;69(7):4112–4121. doi: 10.1128/jvi.69.7.4112-4121.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. Huang Y., Zhang L., Ho D. D. Biological characterization of nef in long-term survivors of human immunodeficiency virus type 1 infection. J Virol. 1995 Dec;69(12):8142–8146. doi: 10.1128/jvi.69.12.8142-8146.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Huang Y., Zhang L., Ho D. D. Characterization of nef sequences in long-term survivors of human immunodeficiency virus type 1 infection. J Virol. 1995 Jan;69(1):93–100. doi: 10.1128/jvi.69.1.93-100.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jamieson B. D., Aldrovandi G. M., Planelles V., Jowett J. B., Gao L., Bloch L. M., Chen I. S., Zack J. A. Requirement of human immunodeficiency virus type 1 nef for in vivo replication and pathogenicity. J Virol. 1994 Jun;68(6):3478–3485. doi: 10.1128/jvi.68.6.3478-3485.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. 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]
  21. Kimpton J., Emerman M. Detection of replication-competent and pseudotyped human immunodeficiency virus with a sensitive cell line on the basis of activation of an integrated beta-galactosidase gene. J Virol. 1992 Apr;66(4):2232–2239. doi: 10.1128/jvi.66.4.2232-2239.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kirchhoff F., Greenough T. C., Brettler D. B., Sullivan J. L., Desrosiers R. C. Brief report: absence of intact nef sequences in a long-term survivor with nonprogressive HIV-1 infection. N Engl J Med. 1995 Jan 26;332(4):228–232. doi: 10.1056/NEJM199501263320405. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. Michael N. L., Chang G., d'Arcy L. A., Ehrenberg P. K., Mariani R., Busch M. P., Birx D. L., Schwartz D. H. Defective accessory genes in a human immunodeficiency virus type 1-infected long-term survivor lacking recoverable virus. J Virol. 1995 Jul;69(7):4228–4236. doi: 10.1128/jvi.69.7.4228-4236.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. 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. 1995 Nov;69(11):6758–6769. doi: 10.1128/jvi.69.11.6758-6769.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. 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]
  30. Muñoz 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. Multicenter AIDS Cohort Study Group. Am J Epidemiol. 1989 Sep;130(3):530–539. doi: 10.1093/oxfordjournals.aje.a115367. [DOI] [PubMed] [Google Scholar]
  31. Pantaleo G., Menzo S., Vaccarezza M., Graziosi C., Cohen O. J., Demarest J. F., Montefiori D., Orenstein J. M., Fox C., Schrager L. K. Studies in subjects with long-term nonprogressive human immunodeficiency virus infection. N Engl J Med. 1995 Jan 26;332(4):209–216. doi: 10.1056/NEJM199501263320402. [DOI] [PubMed] [Google Scholar]
  32. 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]
  33. Rhee S. S., Marsh J. W. Human immunodeficiency virus type 1 Nef-induced down-modulation of CD4 is due to rapid internalization and degradation of surface CD4. J Virol. 1994 Aug;68(8):5156–5163. doi: 10.1128/jvi.68.8.5156-5163.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Rutherford G. W., Lifson A. R., Hessol N. A., Darrow W. W., O'Malley P. M., Buchbinder S. P., Barnhart J. L., Bodecker T. W., Cannon L., Doll L. S. Course of HIV-I infection in a cohort of homosexual and bisexual men: an 11 year follow up study. BMJ. 1990 Nov 24;301(6762):1183–1188. doi: 10.1136/bmj.301.6762.1183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Salghetti S., Mariani R., Skowronski J. Human immunodeficiency virus type 1 Nef and p56lck protein-tyrosine kinase interact with a common element in CD4 cytoplasmic tail. Proc Natl Acad Sci U S A. 1995 Jan 17;92(2):349–353. doi: 10.1073/pnas.92.2.349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. 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]
  37. 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]
  38. Skowronski J., Parks D., Mariani R. Altered T cell activation and development in transgenic mice expressing the HIV-1 nef gene. EMBO J. 1993 Feb;12(2):703–713. doi: 10.1002/j.1460-2075.1993.tb05704.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. 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]
  40. 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. Viral dynamics in human immunodeficiency virus type 1 infection. Nature. 1995 Jan 12;373(6510):117–122. doi: 10.1038/373117a0. [DOI] [PubMed] [Google Scholar]
  41. 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]

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