Darko.qxp 13/11/07 11:17 Page 23
Update on the Diagnosis and Monitoring of HIV-1 Infection
Genotype assays are used more commonly than phenotypic assays because changes. All of the standard genotyping assays listed above are limited in
they are easier to run, cost-effective, and have faster turnaround times. In their ability to detect emerging resistance in mixed viral populations. The
addition, they detect mutations before they are phenotypically expressed. lower limit of detection of mixed mutations in most of these assays is in the
However, accurate interpretation relies on the analyst’s knowledge of 20–25% range. Several research methods, such as the Oligo-Ligase assay
complex mutations and mutational interactions. Moreover, mutations are (OLA), Ty-1 HIV-RT assay, and Single Genome Sequencing (SGS) assay, are
not always consistent with the results derived from phenotypic assays. currently employed in clinical trials. These assays are capable of detecting
Currently, several types of genotypic and phenotypic assays exist for testing. emerging resistance mutations in the 2–5% range.
37,41–43
An emerging
The TruGene™ HIV-1 genotyping kit and OpenGene DNA sequencing system powerful genotypic way of determining HIV-1 drug resistance is the use of
(Visible Genetics/Bayer Diagnostics) and ViroSeq™ HIV-1 Genotyping microarray technology. Affymetrix Inc. has developed specific DNA chips
systems with the 3700 Genetic Analyzer (Celera Diagnostics/Applied that can be used to detect all the possible gene mutations conferring drug
Biosystems/Abbott Laboratories) are FDA-approved. Both offer an integrated resistance to either RT or PR inhibitors. Although rapid, this test is limited by
software algorithm to give the clinician information about which gene its high cost and instrument set-up.
38–40
mutations of RT and PR are most likely to confer resistance to a specific drug
regimen. Another method, the INNO-LiPATM HIV-1 RT assay Conclusion
(Innogenetics/Bayer Diagnostics), is a reverse hybridization method that uses The development of tests such as microarray chips, PCR tests, and rapid
easy-to-read strips to determine specific viral gene codon changes that tests attests to the great advances that have been made in HIV diagnostics,
confer drug resistance. However, the test identifies only the gene mutations and provide hope for better and faster detection and monitoring of HIV.
that have been targeted by certain oligonucleotides applied on the strip. The goal is to keep ahead of a rapidly changing virus. With the aid of
Another method that uses the DNA repair enzyme Cleavase™ in the recent changes in screening, surveillance, and mandatory testing
Invader™ assay (Third Wave) could potentially detect all viral gene recommendations, management of HIV may be able to keep up with the
mutations, but is unable to provide specific information on gene codon ever-mutating virus. ■
1. UNAIDS, AIDS Epidemic update: Special report on HIV/AIDS, Dec 16. Gueudin M, Plantier JC, Lemee V, et al., Evaluation of the Roche 31. Butcher A, Spadoro J, Using PCR for the Detection of HIV
2006. Bobas TaqMan and Abbott RealTime Extraction–Quantification Infection, Clin Imm Newsletter v12, 1992:73–6.
2. Branson BM, Point-of-care rapid tests for HIV antibodies, J Lab Systems for HIV-1 subtypes, JAIDS, 2007;44(5):500–5. 32. Coffin J, HIV population dynamics in vivo:implications for genetic
Med, 2003;27:288–95. 17. Lin H-H, Gaschen BK, Collie, et al., L Genetic characterization of variation, pathogenesis, and therapy, Science, 1995;267:483–9.
3. Constantine NT, Saville R, Dax EM, Retroviral Testing and Quality diverse HIV-1 strains in an immigrant population living in New 33. Larder A, et al., HIV with reduced sensitivity to zidovudine (AZT)
Assurance: Essentials for Laboratory Diagnosis, Malloy Printers, 2005. York City, JAIDS, 2006;41(4):399–404. isolated during prolonged therapy, Science, 1989;243:1731–4.
4. Phillips A, CASCADE Collaboration, Short-term risk of AIDS 18. Barletta, JM, Edelman, DC, Constantine, NT Lowering the detection 34. Cohen CJ, Hunt S, Sension M, et al., A randomized trial assessing
according to current CD4 cell count and viral load in antiretroviral limits of HIV-1 viral load using real-time immuno-PCR for HIV-1 p24 the impact of phenotypic resistance testing on antiretroviral
drug-naive individuals and those treated in the monotherapy era, antigen, Am J Clin Pathol, 122:20–27. therapy, AIDS, 2002;16(4):579–88.
AIDS, 2004;18:51–8. 19. Schüpbach J, Böni, Flepp M, et al., Antiretroviral treatment 35. De Luca A, Di Giambenedetto S, et al., Three-year clinical
5. Napravnik S, et al., Gender difference in HIV RNA levels: a meta- monitoring with an improved HIV-1 p24 antigen test: an inexpensive outcomes of resistance genotyping and expert advice: extended
analysis of published studies, J Acquir Immune Defic Syndr, alternative to tests for viral RNA, J Med Viro, 2001;65:225–32. follow-up of the Argenta trial, Antivir Ther, 2006;11(3):321–7.
2002;31:11–19. 20. Schupbach J, Measurement of HIV-1 p24 antigen by signal 36. Winters MA, Shafer RW, Jellinger RA, et al., HIV type 1 reverse
6. Bartlett JG, Gallant JE, Medical Management of HIV Infection, amplification-boosted ELISA of heat-denatured plasma is a simple transcriptase genotype and drug susceptibility changes in infected
Baltimore: Johns Hopkins University, 2003. and inexpensive alternative to tests for viral RNA, AIDS Rev, individuals receiving dideoxyinosine monotherapy for 1 to 2 years,
7. Marschner IC, Collier AC, et al., Use of changes in plasma levels of 2002;4:83–92. Antimicrob Agents Chemother, 1997;41:757–62.
human immunodeficiency virus type 1 RNA to assess the clinical 21. Zhao RY, From single cell gene-based diagnostics to diagnostic 37. Kearney M, Palmer S, et al., Comparison of single-genome
benefit of antiretroviral therapy, J Infect Dis, 1998;177:40–47. genomics: current applications and future perspectives, Clin Lab sequencing with standard genotype analysis for detection of HIV-1
8. Albrecht H, et al., Highly active antiretroviral therapy significantly Sci, 2005;18(4):254–62. drug resistance mutations, 12th International HIV Drug Resistance
improves the prognosis of patients with HIV-associated progressive 22. Finan JE, Zhao RY, From molecular diagnostics to personalized Workshop, Cabo San Lucas, Mexico, June 10–14, 2003, Abstract 86.
multifocal leukoencephalopathy, AIDS, 1998;12:1149–54. testing, Pharmacogenomics, 2007;8(1):85–99. 38. Vahey M, et al., Performance of the Affymetrix GeneChip HIV PRT
9. de Mendoza, C, Soriano V, Perez-Olmeda M, et al., Different 23. Chun,TW, Stuyver l, Mizell SB, et al., Presence of an inducible HIV- 440 Platform for Antiretroviral Drug Resistance Genotyping of
outcomes in patients achieving complete or partial viral load 1 latent reservoir during highly active antiretroviral therapy, Proc Human Immunodeficiency Virus Type 1 Clades and Viral Isolates with
suppression on antiretroviral therapy, J Hum Virol, 1999;2;344–9 Natl Acad Sci USA, 1997;94:13193–7. Length Polymorphisms, J Clin Microbiol Aug, 1999;37(8):2533–7.
10. JC Guatelli, KM Whitfield, et al., Isothermal, In Vitro Amplification 24. Finzi D, Hermankova M, Pierson T, et al., Identification of a 39. Wilson JW, Bean P, Robins T, et al., Comparative Evaluation of
of Nucleic Acids by a Multienzyme Reaction Modeled After reservoir for HIV-1 in patient on highly active antiretroviral Three Human Immunodeficiency Virus Genotyping Systems: the
Retroviral Replication, Proc Natl Acad of Sci U S A, 1990;87:1874–8. therapy, Science, 1997;278:1295–1300. HIV-GenotypR Method, the HIV PRT GeneChip Assay, and the HIV-
11. Urdea MS, Horn T, Fultz TJ, et al., Branched DNA amplification 25. Finzi D, Blankson J, Siliciano JD, et al., Latent infection of CD4+ T 1 RT Line Probe Assay, J Clin Microbiol Aug, 2000;38(8):3022–8.
multimers for the sensitive, direct detection of human hepatitis cells provides a mechanism for lifelong persistence of HIV-1, even in 40. Wilson JW, Update on antiretroviral drug resistance testing:
viruses, Nucleic Acids Symp Ser, 1991;(24):197–200. patients on effective combination therapy, Nat Med, 1999;5:512–17. combining laboratory technology with patient care, AIDS Read,
12. Ginnocchio CC, HIV-1 viral load testing: methods and clinical 26. Bennett JM, Kaye S, Berry N, Tedder RS, A quantitative PCR 2003;13(1);25–30, 35–8.
applications, Lab Med, 2001;32:42–52. method for the assay of HIV-1 provirus load in peripheral blood 41. Nissley DV, Halvas E, Garfinkel D, et al., Detection of rare drug-
13. McClernon DR, Vavro C, St. Clair M, Evaluation of a Real-Time mononuclear cells, J Virol Methods, 1991:83:11–20. resistant HIV-1 reverse transcriptase variants using a sensitive
Nucleic Acid Sequence-Based Amplification Assay Using Molecular 27. Christopherson C, Kidane Y, Conway B, et al., PCR-based assay to phenotypic assay, 12th International HIV Drug Resistance Workshop,
Beacons for Detection of Human Immunodeficiency Virus Type 1, quantify human immunodeficiency virus type 1 DNA in peripheral Cabo San Lucas, Mexico, June 10–14, 2003, Abstract 93.
J Clin Microbiol, 2006;44(6):2280–82. blood mononuclear cells, J Clin Microbiol, 2000;38:630–34. 42. Beck IA, Mahalanabis M, Pepper G, et al., Rapid and sensitive
14. Yeghiazarian T, et al., Quantification of Human Immunodeficiency 28. Guenthner PC, Hart CE, Quantitative, competitive PCR assay for Oligonucleotide Ligation Assay for Detection of Mutations in Human
Virus Type 1 RNA Levels in Plasma by Using Small-Volume-Format HIV-I using a microplate-based detection system, Biotechniques, Immunodeficiency Virus Type 1 Associated with High Level Resistance
Branched-DNA Assays, J Clin Microbiol, 1998;36(7):2096–8. 1998;24:810–16. to Protease Inhibitors, J Clin Micro,2002;V40/4:1413–19.
15. Swanson P, et al., Comparative performance of three viral load assays 29. Izopet J, et al., Quantification of HIV-1 proviral DNA by a standardized 43. Vahey M, Nau ME, Barrick S, et al., Performance of Affymetrix Gene
on human immunodeficiency virus type 1 (HIV-1) isolates representing colorimetric PCR-based assay, J MedVirol, 1998:54:54–9. Chip HIV PRT 440 Platform for Antiretroviral Drug Resistance
group M (subtypes A to G) and group O: LCx HIV RNA quantitative, 30. Zhao Y, Yu M, Miller JW, et al., Quantification of human Genotyping of Human Immunodeficiency Virus Type 1 Clades and
AMPLICOR HIV-1 MONITOR version 1.5, and Quantiplex HIV-1 RNA immunodeficiency virus type 1 proviral DNA by using TaqMan Viral Isolates with Length Polymorphisms, J Clin Micro,
version 3.0, J Clin Microbiol, 2001;39(3):862–70. technology, J Clin Microbiol, 2002;40:675–8. 1999;V37/8:2533–7.
US INFECTIOUS DISEASE 2007 23