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. 1996 Apr;9(2):135–147. doi: 10.1128/cmr.9.2.135

Clinical use of quantitative molecular methods in studying human immunodeficiency virus type 1 infection.

M Clementi 1, S Menzo 1, P Bagnarelli 1, A Valenza 1, S Paolucci 1, R Sampaolesi 1, A Manzin 1, P E Varaldo 1
PMCID: PMC172887  PMID: 8964032

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Selected References

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  1. Acosta E. P., Fletcher C. V. Agents for treating human immunodeficiency virus infection. Am J Hosp Pharm. 1994 Sep 15;51(18):2251–2287. [PubMed] [Google Scholar]
  2. Albert J., Gaines H., Sönnerborg A., Nyström G., Pehrson P. O., Chiodi F., von Sydow M., Moberg L., Lidman K., Christensson B. Isolation of human immunodeficiency virus (HIV) from plasma during primary HIV infection. J Med Virol. 1987 Sep;23(1):67–73. doi: 10.1002/jmv.1890230108. [DOI] [PubMed] [Google Scholar]
  3. Alimenti A., Luzuriaga K., Sullivan J. L., Van den Borre C., Zissis G., Levy J. Quantitation of HIV-1 in whole blood of infected children. AIDS. 1994 Jul;8(7):895–900. doi: 10.1097/00002030-199407000-00005. [DOI] [PubMed] [Google Scholar]
  4. Arendrup M., Nielsen C., Hansen J. E., Pedersen C., Mathiesen L., Nielsen J. O. Autologous HIV-1 neutralizing antibodies: emergence of neutralization-resistant escape virus and subsequent development of escape virus neutralizing antibodies. J Acquir Immune Defic Syndr. 1992;5(3):303–307. [PubMed] [Google Scholar]
  5. Arens M., Joseph T., Nag S., Miller J. P., Powderly W. G., Ratner L. Alterations in spliced and unspliced HIV-1-specific RNA detection in peripheral blood mononuclear cells of individuals with varying CD4-positive lymphocyte counts. AIDS Res Hum Retroviruses. 1993 Dec;9(12):1257–1263. doi: 10.1089/aid.1993.9.1257. [DOI] [PubMed] [Google Scholar]
  6. Arrigo S. J., Weitsman S., Rosenblatt J. D., Chen I. S. Analysis of rev gene function on human immunodeficiency virus type 1 replication in lymphoid cells by using a quantitative polymerase chain reaction method. J Virol. 1989 Nov;63(11):4875–4881. doi: 10.1128/jvi.63.11.4875-4881.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Asjö B., Morfeldt-Månson L., Albert J., Biberfeld G., Karlsson A., Lidman K., Fenyö E. M. Replicative capacity of human immunodeficiency virus from patients with varying severity of HIV infection. Lancet. 1986 Sep 20;2(8508):660–662. [PubMed] [Google Scholar]
  8. Bagnarelli P., Menzo S., Manzin A., Giacca M., Varaldo P. E., Clementi M. Detection of human immunodeficiency virus type 1 genomic RNA in plasma samples by reverse-transcription polymerase chain reaction. J Med Virol. 1991 Jun;34(2):89–95. doi: 10.1002/jmv.1890340204. [DOI] [PubMed] [Google Scholar]
  9. Bagnarelli P., Menzo S., Manzin A., Varaldo P. E., Montroni M., Giacca M., Clementi M. Detection of human immunodeficiency virus type 1 transcripts in peripheral blood lymphocytes by the polymerase chain reaction. J Virol Methods. 1991 Apr;32(1):31–39. doi: 10.1016/0166-0934(91)90182-y. [DOI] [PubMed] [Google Scholar]
  10. Bagnarelli P., Menzo S., Valenza A., Manzin A., Giacca M., Ancarani F., Scalise G., Varaldo P. E., Clementi M. Molecular profile of human immunodeficiency virus type 1 infection in symptomless patients and in patients with AIDS. J Virol. 1992 Dec;66(12):7328–7335. doi: 10.1128/jvi.66.12.7328-7335.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Bagnarelli P., Menzo S., Valenza A., Paolucci S., Petroni S., Scalise G., Sampaolesi R., Manzin A., Varaldo P. E., Clementi M. Quantitative molecular monitoring of human immunodeficiency virus type 1 activity during therapy with specific antiretroviral compounds. J Clin Microbiol. 1995 Jan;33(1):16–23. doi: 10.1128/jcm.33.1.16-23.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Bagnarelli P., Valenza A., Menzo S., Manzin A., Scalise G., Varaldo P. E., Clementi M. Dynamics of molecular parameters of human immunodeficiency virus type 1 activity in vivo. J Virol. 1994 Apr;68(4):2495–2502. doi: 10.1128/jvi.68.4.2495-2502.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Barré-Sinoussi F., Chermann J. C., Rey F., Nugeyre M. T., Chamaret S., Gruest J., Dauguet C., Axler-Blin C., Vézinet-Brun F., Rouzioux C. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science. 1983 May 20;220(4599):868–871. doi: 10.1126/science.6189183. [DOI] [PubMed] [Google Scholar]
  14. Baumberger C., Kinloch-de-Loës S., Yerly S., Hirschel B., Perrin L. High levels of circulating RNA in patients with symptomatic HIV-1 infection. AIDS. 1993 Nov;7 (Suppl 2):S59–S64. doi: 10.1097/00002030-199311002-00013. [DOI] [PubMed] [Google Scholar]
  15. Becker-André M., Hahlbrock K. Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a PCR aided transcript titration assay (PATTY). Nucleic Acids Res. 1989 Nov 25;17(22):9437–9446. doi: 10.1093/nar/17.22.9437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Berry N., Ariyoshi K., Jobe O., Ngum P. T., Corrah T., Wilkins A., Whittle H., Tedder R. HIV type 2 proviral load measured by quantitative polymerase chain reaction correlates with CD4+ lymphopenia in HIV type 2-infected individuals. AIDS Res Hum Retroviruses. 1994 Aug;10(8):1031–1037. doi: 10.1089/aid.1994.10.1031. [DOI] [PubMed] [Google Scholar]
  17. Besnard N. C., Andre P. M. Automated quantitative determination of hepatitis C virus viremia by reverse transcription-PCR. J Clin Microbiol. 1994 Aug;32(8):1887–1893. doi: 10.1128/jcm.32.8.1887-1893.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Boucher C. A., Tersmette M., Lange J. M., Kellam P., de Goede R. E., Mulder J. W., Darby G., Goudsmit J., Larder B. A. Zidovudine sensitivity of human immunodeficiency viruses from high-risk, symptom-free individuals during therapy. Lancet. 1990 Sep 8;336(8715):585–590. doi: 10.1016/0140-6736(90)93391-2. [DOI] [PubMed] [Google Scholar]
  19. Boucher C. A., van Leeuwen R., Kellam P., Schipper P., Tijnagel J., Lange J. M., Larder B. A. Effects of discontinuation of zidovudine treatment on zidovudine sensitivity of human immunodeficiency virus type 1 isolates. Antimicrob Agents Chemother. 1993 Jul;37(7):1525–1530. doi: 10.1128/aac.37.7.1525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Bruisten S., van Gemen B., Koppelman M., Rasch M., van Strijp D., Schukkink R., Beyer R., Weigel H., Lens P., Huisman H. Detection of HIV-1 distribution in different blood fractions by two nucleic acid amplification assays. AIDS Res Hum Retroviruses. 1993 Mar;9(3):259–265. doi: 10.1089/aid.1993.9.259. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Burger H., Weiser B., Flaherty K., Gulla J., Nguyen P. N., Gibbs R. A. Evolution of human immunodeficiency virus type 1 nucleotide sequence diversity among close contacts. Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11236–11240. doi: 10.1073/pnas.88.24.11236. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Burns D. P., Desrosiers R. C. Envelope sequence variation, neutralizing antibodies, and primate lentivirus persistence. Curr Top Microbiol Immunol. 1994;188:185–219. doi: 10.1007/978-3-642-78536-8_11. [DOI] [PubMed] [Google Scholar]
  24. Busso M., Resnick L. Development of an assay that detects transcriptionally competent human immunodeficiency virus type one particles. J Virol Methods. 1994 Apr;47(1-2):129–139. doi: 10.1016/0166-0934(94)90072-8. [DOI] [PubMed] [Google Scholar]
  25. Byrnes V. W., Sardana V. V., Schleif W. A., Condra J. H., Waterbury J. A., Wolfgang J. A., Long W. J., Schneider C. L., Schlabach A. J., Wolanski B. S. Comprehensive mutant enzyme and viral variant assessment of human immunodeficiency virus type 1 reverse transcriptase resistance to nonnucleoside inhibitors. Antimicrob Agents Chemother. 1993 Aug;37(8):1576–1579. doi: 10.1128/aac.37.8.1576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. Chakrabarti L., Cumont M. C., Montagnier L., Hurtrel B. Variable course of primary simian immunodeficiency virus infection in lymph nodes: relation to disease progression. J Virol. 1994 Oct;68(10):6634–6643. doi: 10.1128/jvi.68.10.6634-6643.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Chakrabarti L., Isola P., Cumont M. C., Claessens-Maire M. A., Hurtrel M., Montagnier L., Hurtrel B. Early stages of simian immunodeficiency virus infection in lymph nodes. Evidence for high viral load and successive populations of target cells. Am J Pathol. 1994 Jun;144(6):1226–1237. [PMC free article] [PubMed] [Google Scholar]
  29. Cheng-Mayer C., Seto D., Tateno M., Levy J. A. Biologic features of HIV-1 that correlate with virulence in the host. Science. 1988 Apr 1;240(4848):80–82. doi: 10.1126/science.2832945. [DOI] [PubMed] [Google Scholar]
  30. Chevret S., Kirstetter M., Mariotti M., Lefrère F., Frottier J., Lefrère J. J. Provirus copy number to predict disease progression in asymptomatic human immunodeficiency virus type 1 infection. J Infect Dis. 1994 Apr;169(4):882–885. doi: 10.1093/infdis/169.4.882. [DOI] [PubMed] [Google Scholar]
  31. Clementi M., Bagnarelli P., Manzin A., Menzo S. Competitive polymerase chain reaction and analysis of viral activity at the molecular level. Genet Anal Tech Appl. 1994;11(1):1–6. doi: 10.1016/1050-3862(94)90002-7. [DOI] [PubMed] [Google Scholar]
  32. Clementi M., Bagnarelli P., Menzo S., Valenza A., Manzin A., Varaldo P. E. Clearance of HIV-1 viraemia after seroconversion. Lancet. 1993 Jan 30;341(8840):315–316. doi: 10.1016/0140-6736(93)92678-m. [DOI] [PubMed] [Google Scholar]
  33. Clementi M., Manzin A., Bagnarelli P., Menzo S., Varaldo P. E., Carloni G. Human immunodeficiency virus type 1 and hepatitis B virus transcription in peripheral blood lymphocytes from co-infected subjects. Arch Virol. 1992;126(1-4):1–9. doi: 10.1007/BF01309679. [DOI] [PubMed] [Google Scholar]
  34. Clementi M., Menzo S., Bagnarelli P., Manzin A., Valenza A., Varaldo P. E. Quantitative PCR and RT-PCR in virology. PCR Methods Appl. 1993 Feb;2(3):191–196. doi: 10.1101/gr.2.3.191. [DOI] [PubMed] [Google Scholar]
  35. Clementi M., Menzo S., Manzin A., Bagnarelli P. Quantitative molecular methods in virology. Arch Virol. 1995;140(9):1523–1539. doi: 10.1007/BF01322527. [DOI] [PubMed] [Google Scholar]
  36. Coffin J. M. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science. 1995 Jan 27;267(5197):483–489. doi: 10.1126/science.7824947. [DOI] [PubMed] [Google Scholar]
  37. Delassus S., Cheynier R., Wain-Hobson S. Nonhomogeneous distribution of human immunodeficiency virus type 1 proviruses in the spleen. J Virol. 1992 Sep;66(9):5642–5645. doi: 10.1128/jvi.66.9.5642-5645.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Dewar R. L., Highbarger H. C., Sarmiento M. D., Todd J. A., Vasudevachari M. B., Davey R. T., Jr, Kovacs J. A., Salzman N. P., Lane H. C., Urdea M. S. Application of branched DNA signal amplification to monitor human immunodeficiency virus type 1 burden in human plasma. J Infect Dis. 1994 Nov;170(5):1172–1179. doi: 10.1093/infdis/170.5.1172. [DOI] [PubMed] [Google Scholar]
  39. Dickover R. E., Dillon M., Gillette S. G., Deveikis A., Keller M., Plaeger-Marshall S., Chen I., Diagne A., Stiehm E. R., Bryson Y. Rapid increases in load of human immunodeficiency virus correlate with early disease progression and loss of CD4 cells in vertically infected infants. J Infect Dis. 1994 Nov;170(5):1279–1284. doi: 10.1093/infdis/170.5.1279. [DOI] [PubMed] [Google Scholar]
  40. Dimitrov D. S., Martin M. A. HIV results in the frame. CD4+ cell turnover. Nature. 1995 May 18;375(6528):194–198. doi: 10.1038/375194b0. [DOI] [PubMed] [Google Scholar]
  41. Dormont J. Future treatment strategies in HIV infection. AIDS. 1994 Sep;8 (Suppl 3):S31–S33. doi: 10.1097/00002030-199409001-00007. [DOI] [PubMed] [Google Scholar]
  42. Dropulić B., Jeang K. T. Gene therapy for human immunodeficiency virus infection: genetic antiviral strategies and targets for intervention. Hum Gene Ther. 1994 Aug;5(8):927–939. doi: 10.1089/hum.1994.5.8-927. [DOI] [PubMed] [Google Scholar]
  43. Embretson J., Zupancic M., Ribas J. L., Burke A., Racz P., Tenner-Racz K., Haase A. T. Massive covert infection of helper T lymphocytes and macrophages by HIV during the incubation period of AIDS. Nature. 1993 Mar 25;362(6418):359–362. doi: 10.1038/362359a0. [DOI] [PubMed] [Google Scholar]
  44. Epstein L. G., Kuiken C., Blumberg B. M., Hartman S., Sharer L. R., Clement M., Goudsmit J. HIV-1 V3 domain variation in brain and spleen of children with AIDS: tissue-specific evolution within host-determined quasispecies. Virology. 1991 Feb;180(2):583–590. doi: 10.1016/0042-6822(91)90072-j. [DOI] [PubMed] [Google Scholar]
  45. Evans L. A., McHugh T. M., Stites D. P., Levy J. A. Differential ability of human immunodeficiency virus isolates to productively infect human cells. J Immunol. 1987 May 15;138(10):3415–3418. [PubMed] [Google Scholar]
  46. Farzadegan H., Polis M. A., Wolinsky S. M., Rinaldo C. R., Jr, Sninsky J. J., Kwok S., Griffith R. L., Kaslow R. A., Phair J. P., Polk B. F. Loss of human immunodeficiency virus type 1 (HIV-1) antibodies with evidence of viral infection in asymptomatic homosexual men. A report from the Multicenter AIDS Cohort Study. Ann Intern Med. 1988 Jun;108(6):785–790. doi: 10.7326/0003-4819-108-6-785. [DOI] [PubMed] [Google Scholar]
  47. Fauci A. S. Multifactorial nature of human immunodeficiency virus disease: implications for therapy. Science. 1993 Nov 12;262(5136):1011–1018. doi: 10.1126/science.8235617. [DOI] [PubMed] [Google Scholar]
  48. Fauci A. S., Schnittman S. M., Poli G., Koenig S., Pantaleo G. NIH conference. Immunopathogenic mechanisms in human immunodeficiency virus (HIV) infection. Ann Intern Med. 1991 Apr 15;114(8):678–693. doi: 10.7326/0003-4819-114-8-678. [DOI] [PubMed] [Google Scholar]
  49. Fauci A. S. The human immunodeficiency virus: infectivity and mechanisms of pathogenesis. Science. 1988 Feb 5;239(4840):617–622. doi: 10.1126/science.3277274. [DOI] [PubMed] [Google Scholar]
  50. Fenyö E. M. Antigenic variation of primate lentiviruses in humans and experimentally infected macaques. Immunol Rev. 1994 Aug;140:131–146. doi: 10.1111/j.1600-065x.1994.tb00868.x. [DOI] [PubMed] [Google Scholar]
  51. Ferre F., Marchese A., Duffy P. C., Lewis D. E., Wallace M. R., Beecham H. J., Burnett K. G., Jensen F. C., Carlo D. J. Quantitation of HIV viral burden by PCR in HIV seropositive Navy personnel representing Walter Reed stages 1 to 6. AIDS Res Hum Retroviruses. 1992 Feb;8(2):269–275. doi: 10.1089/aid.1992.8.269. [DOI] [PubMed] [Google Scholar]
  52. Ferre F. Quantitative or semi-quantitative PCR: reality versus myth. PCR Methods Appl. 1992 Aug;2(1):1–9. doi: 10.1101/gr.2.1.1. [DOI] [PubMed] [Google Scholar]
  53. Fisher A. G., Ensoli B., Looney D., Rose A., Gallo R. C., Saag M. S., Shaw G. M., Hahn B. H., Wong-Staal F. Biologically diverse molecular variants within a single HIV-1 isolate. Nature. 1988 Aug 4;334(6181):444–447. doi: 10.1038/334444a0. [DOI] [PubMed] [Google Scholar]
  54. Fox C. H., Tenner-Rácz K., Rácz P., Firpo A., Pizzo P. A., Fauci A. S. Lymphoid germinal centers are reservoirs of human immunodeficiency virus type 1 RNA. J Infect Dis. 1991 Dec;164(6):1051–1057. doi: 10.1093/infdis/164.6.1051. [DOI] [PubMed] [Google Scholar]
  55. Furuta R. A., Kubota S., Maki M., Miyazaki Y., Hattori T., Hatanaka M. Use of a human immunodeficiency virus type 1 Rev mutant without nucleolar dysfunction as a candidate for potential AIDS therapy. J Virol. 1995 Mar;69(3):1591–1599. doi: 10.1128/jvi.69.3.1591-1599.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Förster E. An improved general method to generate internal standards for competitive PCR. Biotechniques. 1994 Jan;16(1):18–20. [PubMed] [Google Scholar]
  57. Gause W. C., Adamovicz J. The use of the PCR to quantitate gene expression. PCR Methods Appl. 1994 Jun;3(6):S123–S135. doi: 10.1101/gr.3.6.s123. [DOI] [PubMed] [Google Scholar]
  58. Gillespie D., Hubbell H. R., Carter W. A., Midgette P., Elsasser W., Mullaney R., Strayer D. R. Synergistic inhibition of AZT-resistant HIV by AZT combined with poly(I):poly(C12U), without synergistic toxicity to bone marrow progenitor cell elements. In Vivo. 1994 May-Jun;8(3):375–381. [PubMed] [Google Scholar]
  59. Gilliland G., Perrin S., Blanchard K., Bunn H. F. Analysis of cytokine mRNA and DNA: detection and quantitation by competitive polymerase chain reaction. Proc Natl Acad Sci U S A. 1990 Apr;87(7):2725–2729. doi: 10.1073/pnas.87.7.2725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Graziosi C., Pantaleo G., Butini L., Demarest J. F., Saag M. S., Shaw G. M., Fauci A. S. Kinetics of human immunodeficiency virus type 1 (HIV-1) DNA and RNA synthesis during primary HIV-1 infection. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6405–6409. doi: 10.1073/pnas.90.14.6405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Greene W. C. The molecular biology of human immunodeficiency virus type 1 infection. N Engl J Med. 1991 Jan 31;324(5):308–317. doi: 10.1056/NEJM199101313240506. [DOI] [PubMed] [Google Scholar]
  62. Gretch D., Corey L., Wilson J., dela Rosa C., Willson R., Carithers R., Jr, Busch M., Hart J., Sayers M., Han J. Assessment of hepatitis C virus RNA levels by quantitative competitive RNA polymerase chain reaction: high-titer viremia correlates with advanced stage of disease. J Infect Dis. 1994 Jun;169(6):1219–1225. doi: 10.1093/infdis/169.6.1219. [DOI] [PubMed] [Google Scholar]
  63. Guatelli J. C., Whitfield K. M., Kwoh D. Y., Barringer K. J., Richman D. D., Gingeras T. R. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc Natl Acad Sci U S A. 1990 Mar;87(5):1874–1878. doi: 10.1073/pnas.87.5.1874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Gupta P., Ding M., Cottrill M., Rinaldo C., Kingsley L., Wolinsky S., Mellors J. Quantitation of human immunodeficiency virus type 1 DNA and RNA by a novel internally controlled PCR assay. J Clin Microbiol. 1995 Jun;33(6):1670–1673. doi: 10.1128/jcm.33.6.1670-1673.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Hammer S. M., Kessler H. A., Saag M. S. Issues in combination antiretroviral therapy: a review. J Acquir Immune Defic Syndr. 1994;7 (Suppl 2):S24–S37. [PubMed] [Google Scholar]
  66. Hart C., Schochetman G., Spira T., Lifson A., Moore J., Galphin J., Sninsky J., Ou C. Y. Direct detection of HIV RNA expression in seropositive subjects. Lancet. 1988 Sep 10;2(8611):596–599. doi: 10.1016/s0140-6736(88)90639-3. [DOI] [PubMed] [Google Scholar]
  67. Henco K., Heibey M. Quantitative PCR: the determination of template copy numbers by temperature gradient gel electrophoresis (TGGE). Nucleic Acids Res. 1990 Nov 25;18(22):6733–6734. doi: 10.1093/nar/18.22.6733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. Ho D. D., Neumann A. U., Perelson A. S., Chen W., Leonard J. M., Markowitz M. Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature. 1995 Jan 12;373(6510):123–126. doi: 10.1038/373123a0. [DOI] [PubMed] [Google Scholar]
  69. Holodniy M., Mole L., Margolis D., Moss J., Dong H., Boyer E., Urdea M., Kolberg J., Eastman S. Determination of human immunodeficiency virus RNA in plasma and cellular viral DNA genotypic zidovudine resistance and viral load during zidovudine-didanosine combination therapy. J Virol. 1995 Jun;69(6):3510–3516. doi: 10.1128/jvi.69.6.3510-3516.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  70. Jackson J. B., Kwok S. Y., Sninsky J. J., Hopsicker J. S., Sannerud K. J., Rhame F. S., Henry K., Simpson M., Balfour H. H., Jr Human immunodeficiency virus type 1 detected in all seropositive symptomatic and asymptomatic individuals. J Clin Microbiol. 1990 Jan;28(1):16–19. doi: 10.1128/jcm.28.1.16-19.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  71. Jackson J. B., MacDonald K. L., Cadwell J., Sullivan C., Kline W. E., Hanson M., Sannerud K. J., Stramer S. L., Fildes N. J., Kwok S. Y. Absence of HIV infection in blood donors with indeterminate western blot tests for antibody to HIV-1. N Engl J Med. 1990 Jan 25;322(4):217–222. doi: 10.1056/NEJM199001253220402. [DOI] [PubMed] [Google Scholar]
  72. Johnson V. A. Combination therapy: more effective control of HIV type 1? AIDS Res Hum Retroviruses. 1994 Aug;10(8):907–912. doi: 10.1089/aid.1994.10.907. [DOI] [PubMed] [Google Scholar]
  73. Jurriaans S., Van Gemen B., Weverling G. J., Van Strijp D., Nara P., Coutinho R., Koot M., Schuitemaker H., Goudsmit J. The natural history of HIV-1 infection: virus load and virus phenotype independent determinants of clinical course? Virology. 1994 Oct;204(1):223–233. doi: 10.1006/viro.1994.1526. [DOI] [PubMed] [Google Scholar]
  74. Kato N., Yokosuka O., Hosoda K., Ito Y., Ohto M., Omata M. Quantification of hepatitis C virus by competitive reverse transcription-polymerase chain reaction: increase of the virus in advanced liver disease. Hepatology. 1993 Jul;18(1):16–20. [PubMed] [Google Scholar]
  75. Katz R. A., Skalka A. M. The retroviral enzymes. Annu Rev Biochem. 1994;63:133–173. doi: 10.1146/annurev.bi.63.070194.001025. [DOI] [PubMed] [Google Scholar]
  76. Kellam P., Boucher C. A., Larder B. A. Fifth mutation in human immunodeficiency virus type 1 reverse transcriptase contributes to the development of high-level resistance to zidovudine. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1934–1938. doi: 10.1073/pnas.89.5.1934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  77. Kellogg D. E., Sninsky J. J., Kwok S. Quantitation of HIV-1 proviral DNA relative to cellular DNA by the polymerase chain reaction. Anal Biochem. 1990 Sep;189(2):202–208. doi: 10.1016/0003-2697(90)90108-l. [DOI] [PubMed] [Google Scholar]
  78. Koken S. E., van Wamel J. L., Goudsmit J., Berkhout B., Geelen J. L. Natural variants of the HIV-1 long terminal repeat: analysis of promoters with duplicated DNA regulatory motifs. Virology. 1992 Dec;191(2):968–972. doi: 10.1016/0042-6822(92)90274-s. [DOI] [PubMed] [Google Scholar]
  79. 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]
  80. Kwoh D. Y., Davis G. R., Whitfield K. M., Chappelle H. L., DiMichele L. J., Gingeras T. R. Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proc Natl Acad Sci U S A. 1989 Feb;86(4):1173–1177. doi: 10.1073/pnas.86.4.1173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  81. Lafeuillade A., Tamalet C., Pellegrino P., de Micco P., Vignoli C., Quilichini R. Correlation between surrogate markers, viral load, and disease progression in HIV-1 infection. J Acquir Immune Defic Syndr. 1994 Oct;7(10):1028–1033. [PubMed] [Google Scholar]
  82. Landgraf A., Reckmann B., Pingoud A. Quantitative analysis of polymerase chain reaction (PCR) products using primers labeled with biotin and a fluorescent dye. Anal Biochem. 1991 Mar 2;193(2):231–235. doi: 10.1016/0003-2697(91)90014-k. [DOI] [PubMed] [Google Scholar]
  83. Larder B. A., Darby G., Richman D. D. HIV with reduced sensitivity to zidovudine (AZT) isolated during prolonged therapy. Science. 1989 Mar 31;243(4899):1731–1734. doi: 10.1126/science.2467383. [DOI] [PubMed] [Google Scholar]
  84. Larder B. A., Kellam P., Kemp S. D. Zidovudine resistance predicted by direct detection of mutations in DNA from HIV-infected lymphocytes. AIDS. 1991 Feb;5(2):137–144. doi: 10.1097/00002030-199102000-00002. [DOI] [PubMed] [Google Scholar]
  85. Larder B. A., Kemp S. D. Multiple mutations in HIV-1 reverse transcriptase confer high-level resistance to zidovudine (AZT). Science. 1989 Dec 1;246(4934):1155–1158. doi: 10.1126/science.2479983. [DOI] [PubMed] [Google Scholar]
  86. Lazar J. G. Advanced methods in PCR product detection. PCR Methods Appl. 1994 Aug;4(1):S1–14. doi: 10.1101/gr.4.1.s1. [DOI] [PubMed] [Google Scholar]
  87. Lee S. W., Gallardo H. F., Gilboa E., Smith C. Inhibition of human immunodeficiency virus type 1 in human T cells by a potent Rev response element decoy consisting of the 13-nucleotide minimal Rev-binding domain. J Virol. 1994 Dec;68(12):8254–8264. doi: 10.1128/jvi.68.12.8254-8264.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  88. Lemp G. F., Payne S. F., Rutherford G. W., Hessol N. A., Winkelstein W., Jr, Wiley J. A., Moss A. R., Chaisson R. E., Chen R. T., Feigal D. W., Jr Projections of AIDS morbidity and mortality in San Francisco. JAMA. 1990 Mar 16;263(11):1497–1501. [PubMed] [Google Scholar]
  89. Levy J. A. HIV pathogenesis and long-term survival. AIDS. 1993 Nov;7(11):1401–1410. doi: 10.1097/00002030-199311000-00001. [DOI] [PubMed] [Google Scholar]
  90. Levy J. A. Pathogenesis of human immunodeficiency virus infection. Microbiol Rev. 1993 Mar;57(1):183–289. doi: 10.1128/mr.57.1.183-289.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  91. 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]
  92. Lin H. J., Myers L. E., Yen-Lieberman B., Hollinger F. B., Henrard D., Hooper C. J., Kokka R., Kwok S., Rasheed S., Vahey M. Multicenter evaluation of quantification methods for plasma human immunodeficiency virus type 1 RNA. J Infect Dis. 1994 Sep;170(3):553–562. doi: 10.1093/infdis/170.3.553. [DOI] [PubMed] [Google Scholar]
  93. Lisziewicz J., Sun D., Trapnell B., Thomson M., Chang H. K., Ensoli B., Peng B. An autoregulated dual-function antitat gene for human immunodeficiency virus type 1 gene therapy. J Virol. 1995 Jan;69(1):206–212. doi: 10.1128/jvi.69.1.206-212.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  94. Malley S. D., Grange J. M., Hamedi-Sangsari F., Vila J. R. Synergistic anti-human immunodeficiency virus type 1 effect of hydroxamate compounds with 2',3'-dideoxyinosine in infected resting human lymphocytes. Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11017–11021. doi: 10.1073/pnas.91.23.11017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  95. Markowitz M., Mo H., Kempf D. J., Norbeck D. W., Bhat T. N., Erickson J. W., Ho D. D. Selection and analysis of human immunodeficiency virus type 1 variants with increased resistance to ABT-538, a novel protease inhibitor. J Virol. 1995 Feb;69(2):701–706. doi: 10.1128/jvi.69.2.701-706.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  96. Mathez D., Paul D., de Bélilovsky C., Sultan Y., Deleuze J., Gorin I., Saurin W., Decker R., Leibowitch J. Productive human immunodeficiency virus infection levels correlate with AIDS-related manifestations in the patient. Proc Natl Acad Sci U S A. 1990 Oct;87(19):7438–7442. doi: 10.1073/pnas.87.19.7438. [DOI] [PMC free article] [PubMed] [Google Scholar]
  97. McKeating J. A., Gow J., Goudsmit J., Pearl L. H., Mulder C., Weiss R. A. Characterization of HIV-1 neutralization escape mutants. AIDS. 1989 Dec;3(12):777–784. doi: 10.1097/00002030-198912000-00001. [DOI] [PubMed] [Google Scholar]
  98. McKnight A., Weiss R. A., Shotton C., Takeuchi Y., Hoshino H., Clapham P. R. Change in tropism upon immune escape by human immunodeficiency virus. J Virol. 1995 May;69(5):3167–3170. doi: 10.1128/jvi.69.5.3167-3170.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  99. Menzo S., Bagnarelli P., Giacca M., Manzin A., Varaldo P. E., Clementi M. Absolute quantitation of viremia in human immunodeficiency virus infection by competitive reverse transcription and polymerase chain reaction. J Clin Microbiol. 1992 Jul;30(7):1752–1757. doi: 10.1128/jcm.30.7.1752-1757.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  100. Meyerhans A., Cheynier R., Albert J., Seth M., Kwok S., Sninsky J., Morfeldt-Månson L., Asjö B., Wain-Hobson S. Temporal fluctuations in HIV quasispecies in vivo are not reflected by sequential HIV isolations. Cell. 1989 Sep 8;58(5):901–910. doi: 10.1016/0092-8674(89)90942-2. [DOI] [PubMed] [Google Scholar]
  101. Michael N. L., Mo T., Merzouki A., O'Shaughnessy M., Oster C., Burke D. S., Redfield R. R., Birx D. L., Cassol S. A. Human immunodeficiency virus type 1 cellular RNA load and splicing patterns predict disease progression in a longitudinally studied cohort. J Virol. 1995 Mar;69(3):1868–1877. doi: 10.1128/jvi.69.3.1868-1877.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  102. Michael N. L., Vahey M., Burke D. S., Redfield R. R. Viral DNA and mRNA expression correlate with the stage of human immunodeficiency virus (HIV) type 1 infection in humans: evidence for viral replication in all stages of HIV disease. J Virol. 1992 Jan;66(1):310–316. doi: 10.1128/jvi.66.1.310-316.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  103. Michaelis B. A., Levy J. A. Recovery of human immunodeficiency virus from serum. JAMA. 1987 Mar 13;257(10):1327–1327. doi: 10.1001/jama.1987.03390100065011. [DOI] [PubMed] [Google Scholar]
  104. Miller C. J., Marthas M., Torten J., Alexander N. J., Moore J. P., Doncel G. F., Hendrickx A. G. Intravaginal inoculation of rhesus macaques with cell-free simian immunodeficiency virus results in persistent or transient viremia. J Virol. 1994 Oct;68(10):6391–6400. doi: 10.1128/jvi.68.10.6391-6400.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  105. Mita E., Hayashi N., Kanazawa Y., Hagiwara H., Ueda K., Kasahara A., Fusamoto H., Kamada T. Hepatitis C virus genotype and RNA titer in the progression of type C chronic liver disease. J Hepatol. 1994 Sep;21(3):468–473. doi: 10.1016/s0168-8278(05)80330-7. [DOI] [PubMed] [Google Scholar]
  106. Molina J. M., Ferchal F., Chevret S., Barateau V., Poirot C., Morinet F., Modai J. Quantification of HIV-1 virus load under zidovudine therapy in patients with symptomatic HIV infection: relation to disease progression. AIDS. 1994 Jan;8(1):27–33. doi: 10.1097/00002030-199401000-00005. [DOI] [PubMed] [Google Scholar]
  107. Mosier D. E. HIV results in the frame. CD4+ cell turnover. Nature. 1995 May 18;375(6528):193–198. doi: 10.1038/375193b0. [DOI] [PubMed] [Google Scholar]
  108. Mulder J., McKinney N., Christopherson C., Sninsky J., Greenfield L., Kwok S. Rapid and simple PCR assay for quantitation of human immunodeficiency virus type 1 RNA in plasma: application to acute retroviral infection. J Clin Microbiol. 1994 Feb;32(2):292–300. doi: 10.1128/jcm.32.2.292-300.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  109. Murakawa G. J., Zaia J. A., Spallone P. A., Stephens D. A., Kaplan B. E., Wallace R. B., Rossi J. J. Direct detection of HIV-1 RNA from AIDS and ARC patient samples. DNA. 1988 May;7(4):287–295. doi: 10.1089/dna.1988.7.287. [DOI] [PubMed] [Google Scholar]
  110. Nara P., Smit L., Dunlop N., Hatch W., Merges M., Waters D., Kelliher J., Krone W., Goudsmit J. Evidence for rapid selection and deletion of HIV-1 subpopulations in vivo by V3-specific neutralizing antibody: a model of humoral-associated selection. Dev Biol Stand. 1990;72:315–341. [PubMed] [Google Scholar]
  111. Natarajan V., Plishka R. J., Scott E. W., Lane H. C., Salzman N. P. An internally controlled virion PCR for the measurement of HIV-1 RNA in plasma. PCR Methods Appl. 1994 Jun;3(6):346–350. doi: 10.1101/gr.3.6.346. [DOI] [PubMed] [Google Scholar]
  112. Newton C. R., Graham A., Heptinstall L. E., Powell S. J., Summers C., Kalsheker N., Smith J. C., Markham A. F. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 1989 Apr 11;17(7):2503–2516. doi: 10.1093/nar/17.7.2503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  113. Nunberg J. H., Schleif W. A., Boots E. J., O'Brien J. A., Quintero J. C., Hoffman J. M., Emini E. A., Goldman M. E. Viral resistance to human immunodeficiency virus type 1-specific pyridinone reverse transcriptase inhibitors. J Virol. 1991 Sep;65(9):4887–4892. doi: 10.1128/jvi.65.9.4887-4892.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  114. Oka S., Urayama K., Hirabayashi Y., Ohnishi K., Goto H., Mitamura K., Kimura S., Shimada K. Quantitative analysis of human immunodeficiency virus type-1 DNA in asymptomatic carriers using the polymerase chain reaction. Biochem Biophys Res Commun. 1990 Feb 28;167(1):1–8. doi: 10.1016/0006-291x(90)91721-4. [DOI] [PubMed] [Google Scholar]
  115. Ottmann M., Innocenti P., Thenadey M., Micoud M., Pelloquin F., Seigneurin J. M. The polymerase chain reaction for the detection of HIV-1 genomic RNA in plasma from infected individuals. J Virol Methods. 1991 Feb-Mar;31(2-3):273–283. doi: 10.1016/0166-0934(91)90165-v. [DOI] [PubMed] [Google Scholar]
  116. Ou C. Y., Kwok S., Mitchell S. W., Mack D. H., Sninsky J. J., Krebs J. W., Feorino P., Warfield D., Schochetman G. DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells. Science. 1988 Jan 15;239(4837):295–297. doi: 10.1126/science.3336784. [DOI] [PubMed] [Google Scholar]
  117. Pachl C., Todd J. A., Kern D. G., Sheridan P. J., Fong S. J., Stempien M., Hoo B., Besemer D., Yeghiazarian T., Irvine B. Rapid and precise quantification of HIV-1 RNA in plasma using a branched DNA signal amplification assay. J Acquir Immune Defic Syndr Hum Retrovirol. 1995 Apr 15;8(5):446–454. doi: 10.1097/00042560-199504120-00003. [DOI] [PubMed] [Google Scholar]
  118. Pantaleo G., Fauci A. S. Tracking HIV during disease progression. Curr Opin Immunol. 1994 Aug;6(4):600–604. doi: 10.1016/0952-7915(94)90148-1. [DOI] [PubMed] [Google Scholar]
  119. Pantaleo G., Graziosi C., Butini L., Pizzo P. A., Schnittman S. M., Kotler D. P., Fauci A. S. Lymphoid organs function as major reservoirs for human immunodeficiency virus. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9838–9842. doi: 10.1073/pnas.88.21.9838. [DOI] [PMC free article] [PubMed] [Google Scholar]
  120. Pantaleo G., Graziosi C., Demarest J. F., Butini L., Montroni M., Fox C. H., Orenstein J. M., Kotler D. P., Fauci A. S. HIV infection is active and progressive in lymphoid tissue during the clinically latent stage of disease. Nature. 1993 Mar 25;362(6418):355–358. doi: 10.1038/362355a0. [DOI] [PubMed] [Google Scholar]
  121. Pantaleo G., Graziosi C., Demarest J. F., Cohen O. J., Vaccarezza M., Gantt K., Muro-Cacho C., Fauci A. S. Role of lymphoid organs in the pathogenesis of human immunodeficiency virus (HIV) infection. Immunol Rev. 1994 Aug;140:105–130. doi: 10.1111/j.1600-065x.1994.tb00867.x. [DOI] [PubMed] [Google Scholar]
  122. Pantaleo G., Graziosi C., Fauci A. S. New concepts in the immunopathogenesis of human immunodeficiency virus infection. N Engl J Med. 1993 Feb 4;328(5):327–335. doi: 10.1056/NEJM199302043280508. [DOI] [PubMed] [Google Scholar]
  123. Pantaleo G., Graziosi C., Fauci A. S. The role of lymphoid organs in the pathogenesis of HIV infection. Semin Immunol. 1993 Jun;5(3):157–163. doi: 10.1006/smim.1993.1019. [DOI] [PubMed] [Google Scholar]
  124. 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]
  125. Pedroza Martins L., Chenciner N., Wain-Hobson S. Complex intrapatient sequence variation in the V1 and V2 hypervariable regions of the HIV-1 gp 120 envelope sequence. Virology. 1992 Dec;191(2):837–845. doi: 10.1016/0042-6822(92)90259-r. [DOI] [PubMed] [Google Scholar]
  126. Piatak M., Jr, Luk K. C., Williams B., Lifson J. D. Quantitative competitive polymerase chain reaction for accurate quantitation of HIV DNA and RNA species. Biotechniques. 1993 Jan;14(1):70–81. [PubMed] [Google Scholar]
  127. Piatak M., Jr, Saag M. S., Yang L. C., Clark S. J., Kappes J. C., Luk K. C., Hahn B. H., Shaw G. M., Lifson J. D. High levels of HIV-1 in plasma during all stages of infection determined by competitive PCR. Science. 1993 Mar 19;259(5102):1749–1754. doi: 10.1126/science.8096089. [DOI] [PubMed] [Google Scholar]
  128. Poli G., Biswas P., Fauci A. S. Interferons in the pathogenesis and treatment of human immunodeficiency virus infection. Antiviral Res. 1994 Jul;24(2-3):221–233. doi: 10.1016/0166-3542(94)90069-8. [DOI] [PubMed] [Google Scholar]
  129. Reimann K. A., Tenner-Racz K., Racz P., Montefiori D. C., Yasutomi Y., Lin W., Ransil B. J., Letvin N. L. Immunopathogenic events in acute infection of rhesus monkeys with simian immunodeficiency virus of macaques. J Virol. 1994 Apr;68(4):2362–2370. doi: 10.1128/jvi.68.4.2362-2370.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  130. Richman D. D., Bozzette S. A. The impact of the syncytium-inducing phenotype of human immunodeficiency virus on disease progression. J Infect Dis. 1994 May;169(5):968–974. doi: 10.1093/infdis/169.5.968. [DOI] [PubMed] [Google Scholar]
  131. Richman D., Shih C. K., Lowy I., Rose J., Prodanovich P., Goff S., Griffin J. Human immunodeficiency virus type 1 mutants resistant to nonnucleoside inhibitors of reverse transcriptase arise in tissue culture. Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11241–11245. doi: 10.1073/pnas.88.24.11241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  132. Rogers M. F., Ou C. Y., Rayfield M., Thomas P. A., Schoenbaum E. E., Abrams E., Krasinski K., Selwyn P. A., Moore J., Kaul A. Use of the polymerase chain reaction for early detection of the proviral sequences of human immunodeficiency virus in infants born to seropositive mothers. New York City Collaborative Study of Maternal HIV Transmission and Montefiore Medical Center HIV Perinatal Transmission Study Group. N Engl J Med. 1989 Jun 22;320(25):1649–1654. doi: 10.1056/NEJM198906223202503. [DOI] [PubMed] [Google Scholar]
  133. Roos M. T., Lange J. M., de Goede R. E., Coutinho R. A., Schellekens P. T., Miedema F., Tersmette M. Viral phenotype and immune response in primary human immunodeficiency virus type 1 infection. J Infect Dis. 1992 Mar;165(3):427–432. doi: 10.1093/infdis/165.3.427. [DOI] [PubMed] [Google Scholar]
  134. Rossi J. J., Elkins D., Zaia J. A., Sullivan S. Ribozymes as anti-HIV-1 therapeutic agents: principles, applications, and problems. AIDS Res Hum Retroviruses. 1992 Feb;8(2):183–189. doi: 10.1089/aid.1992.8.183. [DOI] [PubMed] [Google Scholar]
  135. Saag M. S. Evolving understanding of the immunopathogenesis of HIV. AIDS Res Hum Retroviruses. 1994 Aug;10(8):887–892. doi: 10.1089/aid.1994.10.887. [DOI] [PubMed] [Google Scholar]
  136. Saag M. S., Hahn B. H., Gibbons J., Li Y., Parks E. S., Parks W. P., Shaw G. M. Extensive variation of human immunodeficiency virus type-1 in vivo. Nature. 1988 Aug 4;334(6181):440–444. doi: 10.1038/334440a0. [DOI] [PubMed] [Google Scholar]
  137. Saag M. S., Hammer S. M., Lange J. M. Pathogenicity and diversity of HIV and implications for clinical management: a review. J Acquir Immune Defic Syndr. 1994;7 (Suppl 2):S2–S11. [PubMed] [Google Scholar]
  138. Saksela K., Muchmore E., Girard M., Fultz P., Baltimore D. High viral load in lymph nodes and latent human immunodeficiency virus (HIV) in peripheral blood cells of HIV-1-infected chimpanzees. J Virol. 1993 Dec;67(12):7423–7427. doi: 10.1128/jvi.67.12.7423-7427.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  139. 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]
  140. Sarmati L., Ercoli L., Parisi S. G., Rocchi G., Giannini G., Galluzzo C., Vella S., Andreoni M. High rate of HIV isolation from plasma of asymptomatic patients through polyethylene glycol (PEG) treatment. J Acquir Immune Defic Syndr. 1994 Jan;7(1):10–14. [PubMed] [Google Scholar]
  141. Scadden D. T., Wang Z., Groopman J. E. Quantitation of plasma human immunodeficiency virus type 1 RNA by competitive polymerase chain reaction. J Infect Dis. 1992 Jun;165(6):1119–1123. doi: 10.1093/infdis/165.6.1119. [DOI] [PubMed] [Google Scholar]
  142. Schnittman S. M., Greenhouse J. J., Lane H. C., Pierce P. F., Fauci A. S. Frequent detection of HIV-1-specific mRNAs in infected individuals suggests ongoing active viral expression in all stages of disease. AIDS Res Hum Retroviruses. 1991 Apr;7(4):361–367. doi: 10.1089/aid.1991.7.361. [DOI] [PubMed] [Google Scholar]
  143. 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]
  144. Schuitemaker H., Koot M., Kootstra N. A., Dercksen M. W., de Goede R. E., van Steenwijk R. P., Lange J. M., Schattenkerk J. K., Miedema F., Tersmette M. Biological phenotype of human immunodeficiency virus type 1 clones at different stages of infection: progression of disease is associated with a shift from monocytotropic to T-cell-tropic virus population. J Virol. 1992 Mar;66(3):1354–1360. doi: 10.1128/jvi.66.3.1354-1360.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  145. Schwiebert R., Fultz P. N. Immune activation and viral burden in acute disease induced by simian immunodeficiency virus SIVsmmPBj14: correlation between in vitro and in vivo events. J Virol. 1994 Sep;68(9):5538–5547. doi: 10.1128/jvi.68.9.5538-5547.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  146. Seshamma T., Bagasra O., Oakes J. W., Pomerantz R. J. A quantitative reverse transcriptase-polymerase chain reaction for HIV-1-specific RNA species. J Virol Methods. 1992 Dec 1;40(3):331–345. doi: 10.1016/0166-0934(92)90091-q. [DOI] [PubMed] [Google Scholar]
  147. 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]
  148. Simmonds P., Zhang L. Q., McOmish F., Balfe P., Ludlam C. A., Brown A. J. Discontinuous sequence change of human immunodeficiency virus (HIV) type 1 env sequences in plasma viral and lymphocyte-associated proviral populations in vivo: implications for models of HIV pathogenesis. J Virol. 1991 Nov;65(11):6266–6276. doi: 10.1128/jvi.65.11.6266-6276.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  149. Singer-Sam J., Robinson M. O., Bellvé A. R., Simon M. I., Riggs A. D. Measurement by quantitative PCR of changes in HPRT, PGK-1, PGK-2, APRT, MTase, and Zfy gene transcripts during mouse spermatogenesis. Nucleic Acids Res. 1990 Mar 11;18(5):1255–1259. doi: 10.1093/nar/18.5.1255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  150. Sprent J., Tough D. HIV results in the frame. CD4+ cell turnover. Nature. 1995 May 18;375(6528):194–198. doi: 10.1038/375194a0. [DOI] [PubMed] [Google Scholar]
  151. St Clair M. H., Martin J. L., Tudor-Williams G., Bach M. C., Vavro C. L., King D. M., Kellam P., Kemp S. D., Larder B. A. Resistance to ddI and sensitivity to AZT induced by a mutation in HIV-1 reverse transcriptase. Science. 1991 Sep 27;253(5027):1557–1559. doi: 10.1126/science.1716788. [DOI] [PubMed] [Google Scholar]
  152. Stretcher B. Management of antiretroviral drug therapy in human immunodeficiency virus infection. Crit Rev Clin Lab Sci. 1994;31(2):169–196. doi: 10.3109/10408369409084676. [DOI] [PubMed] [Google Scholar]
  153. Stålbom B. M., Torvén A., Lundberg L. G. Application of capillary electrophoresis to the post-polymerase chain reaction analysis of rat mRNA for gastric H+,K(+)-ATPase. Anal Biochem. 1994 Feb 15;217(1):91–97. doi: 10.1006/abio.1994.1087. [DOI] [PubMed] [Google Scholar]
  154. Tsoukas C. M., Bernard N. F. Markers predicting progression of human immunodeficiency virus-related disease. Clin Microbiol Rev. 1994 Jan;7(1):14–28. doi: 10.1128/cmr.7.1.14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  155. Urdea M. S., Wilber J. C., Yeghiazarian T., Todd J. A., Kern D. G., Fong S. J., Besemer D., Hoo B., Sheridan P. J., Kokka R. Direct and quantitative detection of HIV-1 RNA in human plasma with a branched DNA signal amplification assay. AIDS. 1993 Nov;7 (Suppl 2):S11–S14. doi: 10.1097/00002030-199311002-00004. [DOI] [PubMed] [Google Scholar]
  156. Vary C. P. Triple-helical capture assay for quantification of polymerase chain reaction products. Clin Chem. 1992 May;38(5):687–694. [PubMed] [Google Scholar]
  157. Verhofstede C., Reniers S., Van Wanzeele F., Plum J. Evaluation of proviral copy number and plasma RNA level as early indicators of progression in HIV-1 infection: correlation with virological and immunological markers of disease. AIDS. 1994 Oct;8(10):1421–1427. doi: 10.1097/00002030-199410000-00008. [DOI] [PubMed] [Google Scholar]
  158. Warren W., Wheat T., Knudsen P. Rapid analysis and quantitation of PCR products by high-performance liquid chromatography. Biotechniques. 1991 Aug;11(2):250–255. [PubMed] [Google Scholar]
  159. 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]
  160. 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]
  161. Woffendin C., Yang Z. Y., Udaykumar, Xu L., Yang N. S., Sheehy M. J., Nabel G. J. Nonviral and viral delivery of a human immunodeficiency virus protective gene into primary human T cells. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11581–11585. doi: 10.1073/pnas.91.24.11581. [DOI] [PMC free article] [PubMed] [Google Scholar]
  162. Wu D. Y., Wallace R. B. The ligation amplification reaction (LAR)--amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics. 1989 May;4(4):560–569. doi: 10.1016/0888-7543(89)90280-2. [DOI] [PubMed] [Google Scholar]
  163. Yu M., Leavitt M. C., Maruyama M., Yamada O., Young D., Ho A. D., Wong-Staal F. Intracellular immunization of human fetal cord blood stem/progenitor cells with a ribozyme against human immunodeficiency virus type 1. Proc Natl Acad Sci U S A. 1995 Jan 31;92(3):699–703. doi: 10.1073/pnas.92.3.699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  164. Yu M., Poeschla E., Yamada O., Degrandis P., Leavitt M. C., Heusch M., Yees J. K., Wong-Staal F., Hampel A. In vitro and in vivo characterization of a second functional hairpin ribozyme against HIV-1. Virology. 1995 Jan 10;206(1):381–386. doi: 10.1016/s0042-6822(95)80053-0. [DOI] [PubMed] [Google Scholar]
  165. Yun Z., Lundeberg J., Johansson B., Hedrum A., Weiland O., Uhlén M., Sönnerborg A. Colorimetric detection of competitive PCR products for quantification of hepatitis C viremia. J Virol Methods. 1994 Apr;47(1-2):1–13. doi: 10.1016/0166-0934(94)90061-2. [DOI] [PubMed] [Google Scholar]
  166. Zhang H., Bagasra O., Niikura M., Poiesz B. J., Pomerantz R. J. Intravirion reverse transcripts in the peripheral blood plasma on human immunodeficiency virus type 1-infected individuals. J Virol. 1994 Nov;68(11):7591–7597. doi: 10.1128/jvi.68.11.7591-7597.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  167. Zhang L. Q., MacKenzie P., Cleland A., Holmes E. C., Brown A. J., Simmonds P. Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J Virol. 1993 Jun;67(6):3345–3356. doi: 10.1128/jvi.67.6.3345-3356.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  168. Zhou C., Bahner I. C., Larson G. P., Zaia J. A., Rossi J. J., Kohn E. B. Inhibition of HIV-1 in human T-lymphocytes by retrovirally transduced anti-tat and rev hammerhead ribozymes. Gene. 1994 Nov 4;149(1):33–39. doi: 10.1016/0378-1119(94)90409-x. [DOI] [PubMed] [Google Scholar]
  169. Zhu T., Mo H., Wang N., Nam D. S., Cao Y., Koup R. A., Ho D. D. Genotypic and phenotypic characterization of HIV-1 patients with primary infection. Science. 1993 Aug 27;261(5125):1179–1181. doi: 10.1126/science.8356453. [DOI] [PubMed] [Google Scholar]
  170. van Gemen B., van Beuningen R., Nabbe A., van Strijp D., Jurriaans S., Lens P., Kievits T. A one-tube quantitative HIV-1 RNA NASBA nucleic acid amplification assay using electrochemiluminescent (ECL) labelled probes. J Virol Methods. 1994 Sep;49(2):157–167. doi: 10.1016/0166-0934(94)90040-x. [DOI] [PubMed] [Google Scholar]

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