Skip to main content
Journal of Virology logoLink to Journal of Virology
. 1995 Apr;69(4):2557–2564. doi: 10.1128/jvi.69.4.2557-2564.1995

Conservation of an intact human immunodeficiency virus type 1 vif gene in vitro and in vivo.

P Sova 1, M van Ranst 1, P Gupta 1, R Balachandran 1, W Chao 1, S Itescu 1, G McKinley 1, D J Volsky 1
PMCID: PMC188933  PMID: 7884906

Abstract

Replication of vif-negative human immunodeficiency virus type 1 (HIV-1) is attenuated in certain cell lines and highly impaired in peripheral blood lymphocytes in vitro. To determine whether intact vif is positively selected during natural HIV-1 infection and to determine vif sequence variability, we employed PCR amplification, cloning, and sequencing to investigate the vif region of replicating virus in short-term-passage HIV-1 primary isolates from five asymptomatic individuals and from five persons with AIDS. A total of 46 vif clones were obtained and analyzed. Recombinant proviruses were constructed from selected vif clones from one patient and found to be fully infectious. We found that 38 of the 46 clones sequenced carried open vif reading frames and that there was a low degree of heterogeneity of vif genes within isolates from the same individual and among isolates from different donors. The cysteines previously found to be essential for vif protein function were conserved in all clones. A phylogenetic tree constructed from all available vif nucleotide sequences resulted in a virus grouping similar to those of gag and env. Direct sequencing of vif amplified by PCR from uncultured lymphocytes of 15 individuals at various stages of progression toward AIDS demonstrated vif open reading frames in 13 of 15 samples tested. There was no obvious correlation between disease status and the presence of an intact vif within this sample group at the time of sample procurement. The conservation of the vif open reading frame in vitro and in vivo and its limited variability following virus transmission in vitro are consistent with a role for vif in natural HIV-1 infection.

Full Text

The Full Text of this article is available as a PDF (310.9 KB).

Selected References

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

  1. Akari H., Sakuragi J., Takebe Y., Tomonaga K., Kawamura M., Fukasawa M., Miura T., Shinjo T., Hayami M. Biological characterization of human immunodeficiency virus type 1 and type 2 mutants in human peripheral blood mononuclear cells. Arch Virol. 1992;123(1-2):157–167. doi: 10.1007/BF01317146. [DOI] [PubMed] [Google Scholar]
  2. Alizon M., Wain-Hobson S., Montagnier L., Sonigo P. Genetic variability of the AIDS virus: nucleotide sequence analysis of two isolates from African patients. Cell. 1986 Jul 4;46(1):63–74. doi: 10.1016/0092-8674(86)90860-3. [DOI] [PubMed] [Google Scholar]
  3. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  4. Bairoch A. PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res. 1992 May 11;20 (Suppl):2013–2018. doi: 10.1093/nar/20.suppl.2013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Balachandran R., Thampatty P., Enrico A., Rinaldo C., Gupta P. Human immunodeficiency virus isolates from asymptomatic homosexual men and from AIDS patients have distinct biologic and genetic properties. Virology. 1991 Jan;180(1):229–238. doi: 10.1016/0042-6822(91)90027-9. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Fisher A. G., Ensoli B., Ivanoff L., Chamberlain M., Petteway S., Ratner L., Gallo R. C., Wong-Staal F. The sor gene of HIV-1 is required for efficient virus transmission in vitro. Science. 1987 Aug 21;237(4817):888–893. doi: 10.1126/science.3497453. [DOI] [PubMed] [Google Scholar]
  8. Fouchier R. A., Groenink M., Kootstra N. A., Tersmette M., Huisman H. G., Miedema F., Schuitemaker H. Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J Virol. 1992 May;66(5):3183–3187. doi: 10.1128/jvi.66.5.3183-3187.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gabuzda D. H., Lawrence K., Langhoff E., Terwilliger E., Dorfman T., Haseltine W. A., Sodroski J. Role of vif in replication of human immunodeficiency virus type 1 in CD4+ T lymphocytes. J Virol. 1992 Nov;66(11):6489–6495. doi: 10.1128/jvi.66.11.6489-6495.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Groenink M., Andeweg A. C., Fouchier R. A., Broersen S., van der Jagt R. C., Schuitemaker H., de Goede R. E., Bosch M. L., Huisman H. G., Tersmette M. Phenotype-associated env gene variation among eight related human immunodeficiency virus type 1 clones: evidence for in vivo recombination and determinants of cytotropism outside the V3 domain. J Virol. 1992 Oct;66(10):6175–6180. doi: 10.1128/jvi.66.10.6175-6180.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Itescu S., Brancato L. J., Winchester R. A sicca syndrome in HIV infection: association with HLA-DR5 and CD8 lymphocytosis. Lancet. 1989 Aug 26;2(8661):466–468. doi: 10.1016/s0140-6736(89)92085-0. [DOI] [PubMed] [Google Scholar]
  12. Itescu S., Rose S., Dwyer E., Winchester R. Certain HLA-DR5 and -DR6 major histocompatibility complex class II alleles are associated with a CD8 lymphocytic host response to human immunodeficiency virus type 1 characterized by low lymphocyte viral strain heterogeneity and slow disease progression. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11472–11476. doi: 10.1073/pnas.91.24.11472. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Keys B., Karis J., Fadeel B., Valentin A., Norkrans G., Hagberg L., Chiodi F. V3 sequences of paired HIV-1 isolates from blood and cerebrospinal fluid cluster according to host and show variation related to the clinical stage of disease. Virology. 1993 Oct;196(2):475–483. doi: 10.1006/viro.1993.1503. [DOI] [PubMed] [Google Scholar]
  14. Kishi M., Nishino Y., Sumiya M., Ohki K., Kimura T., Goto T., Nakai M., Kakinuma M., Ikuta K. Cells surviving infection by human immunodeficiency virus type 1: vif or vpu mutants produce non-infectious or markedly less cytopathic viruses. J Gen Virol. 1992 Jan;73(Pt 1):77–87. doi: 10.1099/0022-1317-73-1-77. [DOI] [PubMed] [Google Scholar]
  15. Korber B., Myers G. Signature pattern analysis: a method for assessing viral sequence relatedness. AIDS Res Hum Retroviruses. 1992 Sep;8(9):1549–1560. doi: 10.1089/aid.1992.8.1549. [DOI] [PubMed] [Google Scholar]
  16. Kusumi K., Conway B., Cunningham S., Berson A., Evans C., Iversen A. K., Colvin D., Gallo M. V., Coutre S., Shpaer E. G. Human immunodeficiency virus type 1 envelope gene structure and diversity in vivo and after cocultivation in vitro. J Virol. 1992 Feb;66(2):875–885. doi: 10.1128/jvi.66.2.875-885.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Louwagie J., McCutchan F. E., Peeters M., Brennan T. P., Sanders-Buell E., Eddy G. A., van der Groen G., Fransen K., Gershy-Damet G. M., Deleys R. Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes. AIDS. 1993 Jun;7(6):769–780. doi: 10.1097/00002030-199306000-00003. [DOI] [PubMed] [Google Scholar]
  18. Ma X. Y., Sakai K., Sinangil F., Golub E., Volsky D. J. Interaction of a noncytopathic human immunodeficiency virus type 1 (HIV-1) with target cells: efficient virus entry followed by delayed expression of its RNA and protein. Virology. 1990 May;176(1):184–194. doi: 10.1016/0042-6822(90)90243-k. [DOI] [PubMed] [Google Scholar]
  19. Ma X. Y., Sova P., Chao W., Volsky D. J. Cysteine residues in the Vif protein of human immunodeficiency virus type 1 are essential for viral infectivity. J Virol. 1994 Mar;68(3):1714–1720. doi: 10.1128/jvi.68.3.1714-1720.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. McNearney T., Hornickova Z., Markham R., Birdwell A., Arens M., Saah A., Ratner L. Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease. Proc Natl Acad Sci U S A. 1992 Nov 1;89(21):10247–10251. doi: 10.1073/pnas.89.21.10247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Michaels F. H., Hattori N., Gallo R. C., Franchini G. The human immunodeficiency virus type 1 (HIV-1) vif protein is located in the cytoplasm of infected cells and its effect on viral replication is equivalent in HIV-2. AIDS Res Hum Retroviruses. 1993 Oct;9(10):1025–1030. doi: 10.1089/aid.1993.9.1025. [DOI] [PubMed] [Google Scholar]
  22. O'Marro S. D., Armstrong J. A., Asuncion C., Gueverra L., Ho M. The effect of combinations of ampligen and zidovudine or dideoxyinosine against human immunodeficiency viruses in vitro. Antiviral Res. 1992 Feb;17(2):169–177. doi: 10.1016/0166-3542(92)90050-f. [DOI] [PubMed] [Google Scholar]
  23. Oberste M. S., Gonda M. A. Conservation of amino-acid sequence motifs in lentivirus Vif proteins. Virus Genes. 1992 Jan;6(1):95–102. doi: 10.1007/BF01703760. [DOI] [PubMed] [Google Scholar]
  24. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  26. Sakai K., Dewhurst S., Ma X. Y., Volsky D. J. Differences in cytopathogenicity and host cell range among infectious molecular clones of human immunodeficiency virus type 1 simultaneously isolated from an individual. J Virol. 1988 Nov;62(11):4078–4085. doi: 10.1128/jvi.62.11.4078-4085.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Sakai K., Ma X. Y., Gordienko I., Volsky D. J. Recombinational analysis of a natural noncytopathic human immunodeficiency virus type 1 (HIV-1) isolate: role of the vif gene in HIV-1 infection kinetics and cytopathicity. J Virol. 1991 Nov;65(11):5765–5773. doi: 10.1128/jvi.65.11.5765-5773.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Salminen M., Nykänen A., Brummer-Korvenkontio H., Kantanen M. L., Liitsola K., Leinikki P. Molecular epidemiology of HIV-1 based on phylogenetic analysis of in vivo gag p7/p9 direct sequences. Virology. 1993 Jul;195(1):185–194. doi: 10.1006/viro.1993.1359. [DOI] [PubMed] [Google Scholar]
  29. Sodroski J., Goh W. C., Rosen C., Tartar A., Portetelle D., Burny A., Haseltine W. Replicative and cytopathic potential of HTLV-III/LAV with sor gene deletions. Science. 1986 Mar 28;231(4745):1549–1553. doi: 10.1126/science.3006244. [DOI] [PubMed] [Google Scholar]
  30. Sova P., Volsky D. J. Efficiency of viral DNA synthesis during infection of permissive and nonpermissive cells with vif-negative human immunodeficiency virus type 1. J Virol. 1993 Oct;67(10):6322–6326. doi: 10.1128/jvi.67.10.6322-6326.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Strebel K., Daugherty D., Clouse K., Cohen D., Folks T., Martin M. A. The HIV 'A' (sor) gene product is essential for virus infectivity. Nature. 1987 Aug 20;328(6132):728–730. doi: 10.1038/328728a0. [DOI] [PubMed] [Google Scholar]
  32. Van de Peer Y., De Wachter R. TREECON: a software package for the construction and drawing of evolutionary trees. Comput Appl Biosci. 1993 Apr;9(2):177–182. doi: 10.1093/bioinformatics/9.2.177. [DOI] [PubMed] [Google Scholar]
  33. Wain-Hobson S., Vartanian J. P., Henry M., Chenciner N., Cheynier R., Delassus S., Martins L. P., Sala M., Nugeyre M. T., Guétard D. LAV revisited: origins of the early HIV-1 isolates from Institut Pasteur. Science. 1991 May 17;252(5008):961–965. doi: 10.1126/science.2035026. [DOI] [PubMed] [Google Scholar]
  34. Wieland U., Hartmann J., Suhr H., Salzberger B., Eggers H. J., Kühn J. E. In vivo genetic variability of the HIV-1 vif gene. Virology. 1994 Aug 15;203(1):43–51. doi: 10.1006/viro.1994.1453. [DOI] [PubMed] [Google Scholar]
  35. von Schwedler U., Song J., Aiken C., Trono D. Vif is crucial for human immunodeficiency virus type 1 proviral DNA synthesis in infected cells. J Virol. 1993 Aug;67(8):4945–4955. doi: 10.1128/jvi.67.8.4945-4955.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES