Human Immunodeficiency Virus Type 1

  • Angela M. Caliendo


Human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2), the causative agents of the acquired immunodeficiency syndrome (AIDS), are RNA viruses belonging to the genus Lentivirus of the family Retroviridae. Like all retroviruses, replication involves reverse transcription of the RNA genome into a double-stranded DNA molecule, with subsequent integration into the host genome. This integrated retroviral DNA is referred to as the provirus. Due to this complex replicative cycle, molecular assays used in the diagnosis and management of HIV-1 infection may target either HIV-1 RNA or proviral DNA.


Human Immunodeficiency Virus Type Resistance Testing Phenotypic Assay Viral Load Testing Line Probe Assay 
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  1. 1.
    Connor R, Ho D, Kuritzkes DR, Richman D. Human Immunodeficiency Virus. In: Clinical Virology, 1st ed. Richman DD, Whitley RJ, and Hayden FG (eds.) Churchill Livingstone, New York; 1997:707–754.Google Scholar
  2. 2.
    Yeni PG, Hammer SM, Hirsch MS, et al. Treatment for adult HIV infection: 2004 recommendations of the International AIDS Society-USA Panel. JAMA. 2004;292:251–265.PubMedCrossRefGoogle Scholar
  3. 3.
    Mellors JW, Kingsley LA, Rinaldo CR Jr, et al. Quantitation of HIV-1 RNA in plasma predicts outcome after seroconversion. Ann Intern Med. 1995;122:573–579.PubMedGoogle Scholar
  4. 4.
    O’Brien TR, Blattner WA, Waters D, et al. Serum HIV-1 RNA levels and time to development of AIDS in the Multicenter Hemophilia Cohort Study. JAMA. 1996;276:105–110.PubMedCrossRefGoogle Scholar
  5. 5.
    Mellors JW, Rinaldo CR Jr, Gupta P, White RM, Todd JA, Kingsley LA. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science. 1996;272:1167–1170.PubMedCrossRefGoogle Scholar
  6. 6.
    Eron JJ, Benoit SL, Jemsek J, et al. Treatment with lamivudine, zidovudine, or both in HIV-positive patients with 200 to 500 CD4+ cells per cubic millimeter. N Eng J Med. 1995;333:1662–1669.CrossRefGoogle Scholar
  7. 7.
    Hammer SM, Squires KE, Hughes MD, et al. A controlled trial of two nucleoside analogues plus indinavir in persons with human immunodeficiency virus infection and CD4 counts of 200 per cubic millimeter or less. N Eng J Med. 1997;337:725–739.CrossRefGoogle Scholar
  8. 8.
    Cameron DW, Heath-Chiozzi M, Danner S, et al. Randomised placebo-controlled trial of ritonavir in advanced HIV-1 disease. The Advanced HIV Disease Ritonavir Study Group. Lancet. 1998;351:543–549.PubMedCrossRefGoogle Scholar
  9. 9.
    Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, Markowitz M. Rapid turnover of plasma virions and CD 4+ lymphocytes in HIV-1 infection. Nature. 1995;373:123–126.PubMedCrossRefGoogle Scholar
  10. 10.
    Wei X, Ghosh SK, Taylor ME, et al. Viral dynamics in human immunodeficiency virus type 1 infection. Nature. 1995;373:117–122.PubMedCrossRefGoogle Scholar
  11. 11.
    Raboud JM, Montaner JS, Conway B, et al. Suppression of plasma viral load below 20 copies/ml is required to achieve a long-term response to therapy. AIDS. 1998;12:1619–1624.PubMedCrossRefGoogle Scholar
  12. 12.
    Saag MS, Holodniy M, Kuritzkes DR, et al. HIV viral load markers in clinical practice. Nature Med. 1996;2:625–629.PubMedCrossRefGoogle Scholar
  13. 13.
    Kahn JO, Walker BD. Acute human immunodeficiency virus type 1 infection. N Eng J Med. 1998;339:32–39.CrossRefGoogle Scholar
  14. 14.
    Daar ES, Little S, Pitt J, et al. Diagnosis of primary HIV-1 infection. Los Angeles County Primary HIV Infection Recruitment Network. Ann Intern Med. 2001;134:25–29.PubMedGoogle Scholar
  15. 15.
    Young NL, Shaffer N, Chaowanachan T, et al. Early diagnosis of HIV-1-infected infants in Thailand using RNA and DNA PCR assays sensitive to non-B subtypes. J Acquir Immune Defic Syndr. 2000;24:401–407.PubMedGoogle Scholar
  16. 16.
    Cunningham CK, Charbonneau TT, Song K, et al. Comparison of human immunodeficiency virus 1 DNA polymerase chain reaction and qualitative and quantitative RNA polymerase chain reaction in human immunodeficiency virus 1-exposed infants. Pediatr Infect Dis J. 1999;18:30–35.PubMedCrossRefGoogle Scholar
  17. 17.
    Steketee RW, Abrams EJ, Thea DM, et al. Early detection of perinatal human immunodeficiency virus (HIV) type 1 infection using HIV RNA amplification and detection. J Infect Dis. 1997;175:707–711.PubMedGoogle Scholar
  18. 18.
    Centers for Disease Control. 1994 Revised classification system for human immunodeficiency virus infection in children less than 13 years of age. MMWR Morb Mortal Wkly Rep. 1994;43:(RR-12):1–11.Google Scholar
  19. 19.
    Durant J, Clevenbergh P, Halfon P, et al. Drug-resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet. 1999;353:2195–2199.PubMedCrossRefGoogle Scholar
  20. 20.
    Clevenbergh P, Durant J, Halfon P, et al. Persisting long-term benefit of genotype-guided treatment for HIV-infected patients failing HAART. The VIRADAPT study: week 48 follow-up. Antivir Ther. 2000;5:65–70.PubMedGoogle Scholar
  21. 21.
    Baxter JD, Mayers DL, Wentworth DN, et al. A randomized study of antiretroviral management based on plasma genotypic antiretroviral resistance testing in patients failing therapy. AIDS. 2000;14:F83–F93.PubMedCrossRefGoogle Scholar
  22. 22.
    Tural C, Ruiz L, Holtzer C, et al. Clinical utility of HIV-1 genotyping and expert advice—the Havana trial. AIDS. 2002;16:209–218.PubMedCrossRefGoogle Scholar
  23. 23.
    Weinstein MC, Goldie SJ, Losina E, et al. Use of genotypic resistance testing to guide HIV therapy: clinical impact and cost-effectiveness. Ann Intern Med. 2001;134:440–450.PubMedGoogle Scholar
  24. 24.
    Cohen CJ, Hunt S, Sension M, et al. A randomized trial assessing the impact of phenotypic resistance testing on antiretroviral therapy. AIDS. 2002;16:579–588.PubMedCrossRefGoogle Scholar
  25. 25.
    Meynard J-L, Vray M, Morand-Joubert L, et al. Phenotypic or genotypic resistance testing for choosing antiretroviral therapy after treatment failure: a randomized trial. AIDS. 2002;16:727–736.PubMedCrossRefGoogle Scholar
  26. 26.
    Miller V. HIV drug resistance: overview of clinical data. J HIV Ther. 2001;6:68–72.PubMedGoogle Scholar
  27. 27.
    Haubrich RH, Kemper CA, Hellmann NS, et al. A randomized, prospective study of phenotype susceptibility testing versus standard of care to manage antiretroviral therapy: CCTG 575. AIDS. 2005;19:295–302.PubMedGoogle Scholar
  28. 28.
    Hirsch MS, Conway B, D’Aquila RT, et al. Antiretroviral drug resistance testing in adults with human immunodeficiency virus type 1: 2003 recommendations of an International AIDS Society-USA panel. Clin Infect Dis. 2003;37:113–128.PubMedCrossRefGoogle Scholar
  29. 29.
    Erice A, Brambilla D, Bremer J, et al. Performance characteristics of the QUANTIPLEX HIV-1 RNA 3.0 assay for detection and quantitation of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol. 2000;38:2837–2845.PubMedGoogle Scholar
  30. 30.
    Sun R, Ku J, Jayakar H, et al. Ultrasensitive reverse transcription-PCR assay for quantitation of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol. 1998;36:2964–2969.PubMedGoogle Scholar
  31. 31.
    Witt DJ, Kemper M, Stead A, Ginocchio C, Caliendo AM. Relationship of incremental specimen volumes and enhanced detection of human immunodeficiency virus type 1 RNA with nucleic acid amplification technology. J Clin Microbiol. 2000;38:85–89.PubMedGoogle Scholar
  32. 32.
    Parekh B, Phillips S, Granade TC, Baggs J, Hu DJ, Respess R. Impact of HIV type 1 subtype variation on viral RNA quantitation. AIDS Res Hum Retroviruses. 1999;15:133–142.PubMedCrossRefGoogle Scholar
  33. 33.
    Jagodzinski LL, Wiggins DL, McManis JL, et al. Use of calibrated viral load standards for group M subtypes of human immunodeficiency virus type 1 to assess the performance of viral RNA quantitation tests. J Clin Microbiol. 2000;38:1247–1249.PubMedGoogle Scholar
  34. 34.
    Pasquier C, Sandres K, Salama G, Puel J, Izopet J. Using RT-PCR and bDNA assays to measure non-clade B HIV-1 subtype RNA. J Virol Methods. 1999;81:123–129.PubMedCrossRefGoogle Scholar
  35. 35.
    Nkengasong JN, Bile C, Kalou M, et al. Quantification of RNA in HIV Type 1 subtypes D and G by NucliSens and Amplicor Assays in Abidjan, Ivory Coast. AIDS Res Hum Retroviruses. 1999;15:495–498.PubMedCrossRefGoogle Scholar
  36. 36.
    Abravaya K, Esping C, Hoenle R, et al. Performance of a multiplex qualitative PCR LCx assay for detection of human immunodeficiency virus type 1 (HIV-1) group M subtypes, group O, and HIV-2. J Clin Microbiol. 2000;38:716–723.PubMedGoogle Scholar
  37. 37.
    Nolte FS, Boysza J, Thurmond C, Clark WS, Lennox JL. Clinical comparison of an enhanced-sensitivity branched-DNA assay and reverse transcription-PCR for quantitation of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol. 1998;36:716–720.PubMedGoogle Scholar
  38. 38.
    Segondy M, Izopet J, Pellegrin I, et al. Comparison of the Quantiplex HIV-1 RNA 2.0 assay with the Amplicor HIV-1 monitor 1.0 assay for quantitation of levels of human immunodeficiency virus type 1 RNA in plasma of patients receiving stavudine-didanosine combination therapy. J Clin Microbiol. 1998;36:3392–3395.PubMedGoogle Scholar
  39. 39.
    Dyer JR, Pilcher CD, Shepard R, Schock J, Eron JJ, Fiscus SA. Comparison of NucliSens and Roche Monitor assays for quantitation of levels of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol. 1999;37:447–449.PubMedGoogle Scholar
  40. 40.
    Elbeik T, Charlebois E, Nassos P, et al. Quantitative and cost comparison of ultrasensitive human immunodeficiency virus type 1 RNA viral load assays: Bayer bDNA quantiplex versions 3.0 and 2.0 and Roche PCR Amplicor Monitor version 1.5. J Clin Microbiol. 2000;38:1113–1120.PubMedGoogle Scholar
  41. 41.
    Triques K, Coste J, Perret JL, et al. Efficiencies of four versions of the AMPLICOR HIV-1 MONITOR test for quantification of different subtypes of human immunodeficiency virus type 1. J Clin Microbiol. 1999;37:110–116.PubMedGoogle Scholar
  42. 42.
    Ginocchio CC, Wang XP, Kaplan MH, et al. Effects of specimen collection, processing, and storage conditions on stability of human immunodeficiency virus type 1 RNA levels in plasma. J Clin Microbiol. 1997;35:2886–2893.PubMedGoogle Scholar
  43. 43.
    Sebire K, McGavin K, Land S, Middleton T, Birch C. Stability of human immunodeficiency virus RNA in blood specimens as measured by a commercial PCR-based assay. J Clin Microbiol. 1998;36:493–498.PubMedGoogle Scholar
  44. 44.
    Lew J, Reichelderfer P, Fowler M, et al. Determinations of levels of human immunodeficiency virus type 1 RNA in plasma: reassessment of parameters affecting assay outcome. TUBE Meeting Workshop Attendees. Technology Utilization for HIV-1 Blood Evaluation and Standardization in Pediatrics. J Clin Microbiol. 1998;36:1471–1479.PubMedGoogle Scholar
  45. 45.
    Boom R, Sol C, Salimans M, Jansen C, Wertheim-van Dillen PM, van der Noordaa J. Rapid and simple method for purification of nucleic acids. J Clin Microbiol. 1990;28:495–503.PubMedGoogle Scholar
  46. 46.
    Holodniy M, Rainen L, Herman S, Yen-Lieberman B. Stability of plasma human immunodeficiency virus load in VACUTAINER PPT plasma preparation tubes during overnight shipment. J Clin Microbiol. 2000;38:323–326.PubMedGoogle Scholar
  47. 47.
    Cassol S, Gill MJ, Pilon R, et al. Quantification of human immunodeficiency virus type 1 DNA from dried plasma spots collected on filter paper. J Clin Microbiol. 1997;35:2795–2801.PubMedGoogle Scholar
  48. 48.
    Fiscus SA, Brambilla D, Grosso L, Schock J, Cronin M. Quantitation of human immunodeficiency virus type 1 RNA in plasma by using blood dried on filter paper. J Clin Microbiol. 1998;36:258–260.PubMedGoogle Scholar
  49. 49.
    Bremer J, Nowicki M, Beckner S, et al. Comparison of two amplification technologies for detection and quantitation of human immunodeficiency virus type 1 RNA in the female genital tract. J Clin Microbiol. 2000;38:2665–2669.PubMedGoogle Scholar
  50. 50.
    Kozal MJ, Shah N, Shen N, et al. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat Med. 1996;2:753–759.PubMedCrossRefGoogle Scholar
  51. 51.
    Gunthard HF, Wong JK, Ignacio CC, Havlir DV, Richman DD. Comparative performance of high-density oligonucleotide sequencing and dideoxynucleotide sequencing of HIV type 1 pol from clinical samples. AIDS Res Hum Retroviruses. 1998;14:869–876.PubMedCrossRefGoogle Scholar
  52. 52.
    Hanna GJ, Johnson VA, Kuritzkes DR, et al. Comparison of sequencing by hybridization and cycle sequencing for genotyping of human immunodeficiency virus type 1 reverse transcriptase. J Clin Microbiol. 2000;38:2715–2721.PubMedGoogle Scholar
  53. 53.
    Wilson JW, Bean P, Robins T, Graziano F, Persing DH. Comparative evaluation of three human immunodeficiency virus genotyping systems: the HIV-Genotype R method, the HIV PRT GeneChip assay, and the HIV-1 RT line probe assay. J Clin Microbiol. 2000;38:3022–3028.PubMedGoogle Scholar
  54. 54.
    Stuyver L, Wyseur A, Rombout A. Line probe assay for rapid detection of drug-selected mutations in the human immunodeficiency virus type 1 reverse transcriptase gene. Antimicrob Agents Chemother. 1997;41:284–291.PubMedGoogle Scholar
  55. 55.
    Servais J, Lambert C, Fontaine E, et al. Comparison of DNA sequencing and a line probe assay for detection of human immunodeficiency virus type 1 drug resistance mutations in patients failing highly active antiretroviral therapy. J Clin Microbiol. 2001;39:454–459.PubMedCrossRefGoogle Scholar
  56. 56.
    Erali M, Page S, Reimer LG, Hillyard DR. Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods. J Clin Microbiol. 2001;39:2157–2165.PubMedCrossRefGoogle Scholar
  57. 57.
    Petropoulos CJ, Parkin NT, Limoli KL. A novel phenotypic drug susceptibility assay for human immunodeficiency virus type 1. Antimicrob Agents Chemother. 2000;44:920–928.PubMedCrossRefGoogle Scholar
  58. 58.
    Hertogs K, de Bethune MP, Miler V, et al. A rapid method for simultaneous detection of phenotypic resistance to inhibitors of protease and reverse transcriptase in recombinant human immunodeficiency virus type 1 isolates from patients treated with antiretroviral drugs. Antimicrob Agents Chemother. 1998;42:269–276.PubMedCrossRefGoogle Scholar
  59. 59.
    Mracna M, Becker-Pergola G, Dileanis J, et al. Performance of the Applied Biosystems ViroSeq HIV-1 genotyping system for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda. J Clin Microbiol. 2001;39:4323–4327.PubMedCrossRefGoogle Scholar
  60. 60.
    Rozenbaum W, Charpentier C, Delphin N, et al. Comparative performance evaluation of a kit-based HIV-1 genotyping assay and a laboratory developed “home-brew” genotyping assay with samples of varying viral loads and non-B subtypes of group M virus [abstract 171]. Antiviral Therapy, 5th International Workshop on HIV Drug Resistance & Treatment Strategies. Scottsdale, AZ; 2001;6:130.Google Scholar
  61. 61.
    Brambilla D, Leung S, Lew J, et al. Absolute copy number and relative change in determinations of human immunodeficiency virus type 1 RNA in plasma: effect of an external standard on kit comparisons. J Clin Microbiol. 1998;36:311–314.PubMedGoogle Scholar
  62. 62.
    Donovan RM, Bush CE, Markowitz NP, Baxa DM, Saravolatz LD. Changes in virus load markers during AIDS-associated opportunistic diseases in human immunodeficiency virus-infected persons. J Infect Dis. 1996;174:401–403.PubMedGoogle Scholar
  63. 63.
    O’Brien WA, Grovit-Ferbas K, Namazi A, et al. Human immunodeficiency virus-type 1 replication can be increased in peripheral blood of seropositive patients after influenza vaccination. Blood. 1995;86:1082–1089.PubMedGoogle Scholar
  64. 64.
    Staprans SI, Hamilton BL, Follansbee SE, et al. Activation of virus replication after vaccination of HIV-1-infected individuals. J Exp Med. 1995;182:1727–1737.PubMedCrossRefGoogle Scholar
  65. 65.
    Hirsch MS, Conway B, D’Aquila RT, et al. Antiretroviral drug resistance testing in adults with HIV infection. JAMA. 1998;279:1984–1991.PubMedCrossRefGoogle Scholar
  66. 66.
    D’Aquila RT. Incorporating antiretroviral resistance testing into clinical practice. Medscape HIV/AIDS CME Circle. Web MD Medscape Health Network. 2002. Available at: Scholar
  67. 67.
    Parkin N, Chappey C, Maroldo L, Bates M, Hellmann NS, Petropoulos CJ. Phenotypic and genotypic HIV-1 drug resistance assays provide complementary information. J Acquir Immune Defic Syndr. 2002;31:128–136.PubMedGoogle Scholar
  68. 68.
    Van Houtte M. Update on resistance testing. J HIV Ther. 2001;6:61–64.PubMedGoogle Scholar
  69. 69.
    Devereux HL, Youle M, Johnson MA, Loveday C. Rapid decline in detectability of HIV-1 drug resistance mutations after stopping therapy. AIDS. 1999;13:F123–F127.PubMedCrossRefGoogle Scholar
  70. 70.
    Keulen W, Brambilla D, Buimer M, et al. A study on HIV-1 genotyping proficiency in 125 laboratories, using the ENVA-3 panel [abstract 166]. Antiviral Therapy, 5th International Workshop on HIV Drug Resistance & Treatment Strategies. Scottsdale, AZ; 2001;6:127.Google Scholar
  71. 71.
    Wensing AM, Keulen W, Buimer M, Brambilla D, Schuurman R, Boucher C. Analysis of the world-wide evaluation study on HIV-1 genotype interpretation: ENVA-3 [abstract 133]. Antiviral Therapy, 5th International Workshop on HIV Drug Resistance & Treatment Strategies, Scottsdale, AZ; 2001;6:101.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Angela M. Caliendo
    • 1
  1. 1.Department of Pathology and Laboratory MedicineEmory University HospitalAtlantaUSA

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