Advanced search
Publication Cover
Emerging Microbes & Infections Volume 1, 2012 - Issue 1
Submit an article Journal homepage
685
Views
12
CrossRef citations to date
0
Altmetric
Reviews

Past, present and future molecular diagnosis and characterization of human immunodeficiency virus infections

Yi-Wei Tang1 Memorial Sloan-Kettering Cancer Center, New York, NY10065 , USACorrespondence[email protected]
&
Chin-Yih Ou2 Centers for Disease Control and Prevention, Atlanta, GA30333 , USA
Pages 1-8 | Received 02 Mar 2012, Accepted 21 May 2012, Published online: 25 Jan 2019

  • Branson BM.State of the art for diagnosis of HIV infection. Clin Infect Dis2007;45( Suppl 4): S221–S225.
  • Tang YW, Persing DH.Diagnostic microbiology. In: Schaechter M (ed.) Encyclopedia of microbiology. 3rd ed. Oxford: Elsevier Press, 2009: 308–320.
  • Ou CY, Kwok S, Mitchell SW et al.DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells. Science1988;239( 4837): 295–297.
  • Branson BM, Stekler JD.Detection of acute HIV infection: we can't close the window. J Infect Dis2012;205: 521–524.
  • Bentsen C, McLaughlin L, Mitchell E et al.Performance evaluation of the Bio-Rad Laboratories GS HIV Combo Ag/Ab EIA, a 4th generation HIV assay for the simultaneous detection of HIV p24 antigen and antibodies to HIV-1 (groups M and O) and HIV-2 in human serum or plasma. J Clin Virol2011;52( Suppl 1): S57–S61.
  • Chavez P, Wesolowski L, Patel P, Delaney K, Owen SM.Evaluation of the performance of the Abbott ARCHITECT HIV Ag/Ab Combo Assay. J Clin Virol2011;52( Suppl 1): S51–S55.
  • Branson BM.The future of HIV testing. J Acquir Immune Defic Syndr2010;55( Suppl 2): S102–S105.
  • Fiebig EW, Wright DJ, Rawal BD et al.Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS2003;17: 1871–1879.
  • Giachetti C, Linnen JM, Kolk DP et al.Highly sensitive multiplex assay for detection of human immunodeficiency virus type 1 and hepatitis C virus RNA. J Clin Microbiol2002;40: 2408–2419.
  • Resino S, Resino R, Maria Bellon J et al.Clinical outcomes improve with highly active antiretroviral therapy in vertically HIV type-1-infected children. Clin Infect Dis2006;43: 243–252.
  • van Rossum AM, Fraaij PL, de Groot R.Efficacy of highly active antiretroviral therapy in HIV-1 infected children. Lancet Infect Dis2002;2: 93–102.
  • Sherman GG, Cooper PA, Coovadia AH et al.Polymerase chain reaction for diagnosis of human immunodeficiency virus infection in infancy in low resource settings. Pediatr Infect Dis J2005;24: 993–997.
  • Rouet F, Montcho C, Rouzioux C et al.Early diagnosis of paediatric HIV-1 infection among African breast-fed children using a quantitative plasma HIV RNA assay. AIDS2001;15: 1849–1856.
  • Stevens WS, Noble L, Berrie L, Sarang S, Scott LE.Ultra-high-throughput, automated nucleic acid detection of human immunodeficiency virus (HIV) for infant infection diagnosis using the Gen-Probe Aptima HIV-1 screening assay. J Clin Microbiol2009;47: 2465–2469.
  • Owen SM, Yang C, Spira T et al.Alternative algorithms for human immunodeficiency virus infection diagnosis using tests that are licensed in the United States. J Clin Microbiol2008;46: 1588–1595.
  • Okonji JA, Basavaraju SV, Mwangi J et al.Comparison of HIV-1 detection in plasma specimens and dried blood spots using the Roche COBAS Ampliscreen HIV-1 test in Kisumu, Kenya. J Virol Methods2012;179: 21–25.
  • Ford N, Nachega JB, Engel ME, Mills EJ.Directly observed antiretroviral therapy: a systematic review and meta-analysis of randomised clinical trials. Lancet2009;374: 2064–2071.
  • Mellors JW, Munoz A, Giorgi JV et al.Plasma viral load and CD4+ lymphocytes as prognostic markers of HIV-1 infection. Ann Intern Med1997;126: 946–954.
  • Kitchen CM, Kitchen SG, Dubin JA, Gottlieb MS.Initial virological and immunologic response to highly active antiretroviral therapy predicts long-term clinical outcome. Clin Infect Dis2001;33: 466–472.
  • Church D, Gregson D, Lloyd T et al.Comparison of the RealTime HIV-1, COBAS TaqMan 48 v1.0, Easy Q v1.2, and Versant v3.0 assays for determination of HIV-1 viral loads in a cohort of Canadian patients with diverse HIV subtype infections. J Clin Microbiol2011;49: 118–124.
  • Barth RE, van der Loeff MF, Schuurman R, Hoepelman AI, Wensing AM.Virological follow-up of adult patients in antiretroviral treatment programmes in sub-Saharan Africa: a systematic review. Lancet Infect Dis2010;10: 155–166.
  • Stevens W, Erasmus L, Moloi M, Taleng T, Sarang S.Performance of a novel human immunodeficiency virus (HIV) type 1 total nucleic acid-based real-time PCR assay using whole blood and dried blood spots for diagnosis of HIV in infants. J Clin Microbiol2008;46: 3941–3945.
  • Garrido C, Zahonero N, Corral A, Arredondo M, Soriano V, de Mendoza C.Correlation between human immunodeficiency virus type 1 (HIV-1) RNA measurements obtained with dried blood spots and those obtained with plasma by use of Nuclisens EasyQ HIV-1 and Abbott RealTime HIV load tests. J Clin Microbiol2009;47: 1031–1036.
  • Tang YW, Huong JT, Lloyd RM Jr, Spearman P, Haas DW.Comparison of human immunodeficiency virus type 1 RNA sequence heterogeneity in cerebrospinal fluid and plasma. J Clin Microbiol2000;38: 4637–4639.
  • Rebeiro PF, Kheshti A, Bebawy SS et al.Increased detectability of plasma HIV-1 RNA after introduction of a new assay and altered specimen-processing procedures. Clin Infect Dis2008;47: 1354–1357.
  • Salimnia H, Moore EC, Crane LR, Macarthur RD, Fairfax MR.Discordance between viral loads determined by Roche COBAS AMPLICOR human immunodeficiency virus type 1 monitor (version 1.5). Standard and ultrasensitive assays caused by freezing patient plasma in centrifuged becton-dickinson vacutainer brand plasma preparation tubes. J Clin Microbiol2005;43: 4635–4639.
  • Zhang Q, Wang L, Jiang Y et al.Early infant human immunodeficiency virus type 1 detection suitable for resource-limited settings with multiple circulating subtypes by use of nested three-monoplex DNA PCR and dried blood spots. J Clin Microbiol2008;46: 721–726.
  • Lin HJ, Pedneault L, Hollinger FB.Intra-assay performance characteristics of five assays for quantification of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol1998;36: 835–839.
  • Revets H, Marissens D, de Wit S et al.Comparative evaluation of NASBA HIV-1 RNA QT, AMPLICOR-HIV monitor, and QUANTIPLEX HIV RNA assay, three methods for quantification of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol1996;34: 1058–1064.
  • Scott LE, Noble LD, Moloi J, Erasmus L, Venter WD, Stevens W.Evaluation of the Abbott m2000 RealTime human immunodeficiency virus type 1 (HIV-1) assay for HIV load monitoring in South Africa compared to the Roche Cobas AmpliPrep-Cobas Amplicor, Roche Cobas AmpliPrep-Cobas TaqMan HIV-1, and BioMerieux NucliSENS EasyQ HIV-1 assays. J Clin Microbiol2009;47: 2209–2217.
  • Swanson P, Huang S, Abravaya K et al.Evaluation of performance across the dynamic range of the Abbott RealTime HIV-1 assay as compared to VERSANT HIV-1 RNA 3.0 and AMPLICOR HIV-1 MONITOR v1.5 using serial dilutions of 39 group M and O viruses. J Virol Methods2007;141: 49–57.
  • Bourlet T, Signori-Schmuck A, Roche L et al.HIV-1 load comparison using four commercial real-time assays. J Clin Microbiol2011;49: 292–297.
  • Sire JM, Vray M, Merzouk M et al.Comparative RNA quantification of HIV-1 group M and non-M with the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 v2.0 and Abbott Real-Time HIV-1 PCR assays. J Acquir Immune Defic Syndr2011;56: 239–243.
  • Huang S, Salituro J, Tang N et al.Thermodynamically modulated partially double-stranded linear DNA probe design for homogeneous real-time PCR. Nucleic Acids Res2007;35: e101.
  • Luft LM, Gill MJ, Church DL.HIV-1 viral diversity and its implications for viral load testing: review of current platforms. Int J Infect Dis2011;15: e661–e670.
  • Cobb BR, Vaks JE, Do T, Vilchez RA.Evolution in the sensitivity of quantitative HIV-1 viral load tests. J Clin Virol2011;52( Suppl 1): S77–S82.
  • Wood E, Yip B, Hogg RS et al.Full suppression of viral load is needed to achieve an optimal CD4 cell count response among patients on triple drug antiretroviral therapy. AIDS2000;14: 1955–1960.
  • Shafer RW.Genotypic testing for human immunodeficiency virus type 1 drug resistance. Clin Microbiol Rev2002;15: 247–277.
  • 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. CPCRA 046 Study Team for the Terry Beirn Community Programs for Clinical Research on AIDS. AIDS2000;14: F83–F93.
  • Cunningham S, Ank B, Lewis D et al.Performance of the applied biosystems ViroSeq human immunodeficiency virus type 1 (HIV-1) genotyping system for sequence-based analysis of HIV-1 in pediatric plasma samples. J Clin Microbiol2001;39: 1254–1257.
  • Durant J, Clevenbergh P, Halfon P et al.Drug-resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet1999;353: 2195–2199.
  • Dunn DT, Coughlin K, Cane PA.Genotypic resistance testing in routine clinical care. Curr Opin HIV AIDS2011;6: 251–257.
  • Hammer SM, Eron JJ Jr, Reiss P et al.Antiretroviral treatment of adult HIV infection: 2008 recommendations of the International AIDS Society-USA panel. JAMA2008;300: 555–570.
  • Sturmer M, Berger A, Preiser W.HIV-1 genotyping: comparison of two commercially available assays. Expert Rev Mol Diagn2004;4: 281–291.
  • 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 Microbiol2001;39: 2157–2165.
  • Aghokeng AF, Mpoudi-Ngole E, Chia JE, Edoul EM, Delaporte E, Peeters M.High failure rate of the ViroSeq HIV-1 genotyping system for drug resistance testing in Cameroon, a country with broad HIV-1 genetic diversity. J Clin Microbiol2011;49: 1635–1641.
  • Yang C, McNulty A, Diallo K et al.Development and application of a broadly sensitive dried-blood-spot-based genotyping assay for global surveillance of HIV-1 drug resistance. J Clin Microbiol2010;48: 3158–3164.
  • Palmer S, Kearney M, Maldarelli F et al.Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J Clin Microbiol2005;43: 406–413.
  • Halvas EK, Aldrovandi GM, Balfe P et al.Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency. J Clin Microbiol2006;44: 2612–2614.
  • Toni TA, Brenner BG, Asahchop EL, Ntemgwa M, Moisi D, Wainberg MA.Development of an allele-specific PCR for detection of the K65R resistance mutation in patients infected with subtype C human immunodeficiency virus type 1. Antimicrob Agents Chemother2010;54: 907–911.
  • van Laethem K, de Munter P, Schrooten Y et al.No response to first-line tenofovir+lamivudine+efavirenz despite optimization according to baseline resistance testing: impact of resistant minority variants on efficacy of low genetic barrier drugs. J Clin Virol2007;39: 43–47.
  • Hedskog C, Mild M, Jernberg J et al.Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing. PLoS One2010;5: e11345.
  • Simen BB, Simons JF, Hullsiek KH et al.Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis2009;199: 693–701.
  • Gianella S, Delport W, Pacold ME et al.Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants. J Virol2011;85: 8359–8367.
  • Call SA, Saag MS, Westfall AO et al.Phenotypic drug susceptibility testing predicts long-term virologic suppression better than treatment history in patients with human immunodeficiency virus infection. J Infect Dis2001;183: 401–408.
  • Hertogs K, de Bethune MP, Miller 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 Chemother1998;42: 269–276.
  • Petropoulos CJ, Parkin NT, Limoli KL et al.A novel phenotypic drug susceptibility assay for human immunodeficiency virus type 1. Antimicrob Agents Chemother2000;44: 920–928.
  • Munoz M, Carmona R, Perez-Alvarez L et al.Analysis of discrepancies in the interpretation of antiretroviral drug resistance results in HIV-1 infected patients of Basque Country, Spain. J Clin Virol2005;33: 224–229.
  • Perez-Elias MJ, Garcia-Arota I, Munoz V et al.Phenotype or virtual phenotype for choosing antiretroviral therapy after failure: a prospective, randomized study. Antivir Ther2003;8: 577–584.
  • Cooper DA, Steigbigel RT, Gatell JM et al.Subgroup and resistance analyses of raltegravir for resistant HIV-1 infection. N Engl J Med2008;359: 355–365.
  • Veazey RS, Ketas TA, Klasse PJ et al.Tropism-independent protection of macaques against vaginal transmission of three SHIVs by the HIV-1 fusion inhibitor T-1249. Proc Natl Acad Sci USA2008;105: 10531–10536.
  • Westby M, Lewis M, Whitcomb J et al.Emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants in a minority of HIV-1-infected patients following treatment with the CCR5 antagonist maraviroc is from a pretreatment CXCR4-using virus reservoir. J Virol2006;80: 4909–4920.
  • Recordon-Pinson P, Soulie C, Flandre P et al.Evaluation of the genotypic prediction of HIV-1 coreceptor use versus a phenotypic assay and correlation with the virological response to maraviroc: the ANRS GenoTropism study. Antimicrob Agents Chemother2010;54: 3335–3340.
  • Low AJ, Swenson LC, Harrigan PR.HIV coreceptor phenotyping in the clinical setting. AIDS Rev2008;10: 143–151.
  • MacArthur RD, Novak RM.Reviews of anti-infective agents: maraviroc: the first of a new class of antiretroviral agents. Clin Infect Dis2008;47: 236–241.
  • Wilkin TJ, Goetz MB, Leduc R et al.Reanalysis of coreceptor tropism in HIV-1-infected adults using a phenotypic assay with enhanced sensitivity. Clin Infect Dis2011;52: 925–928.
  • Lee-Lewandrowski E, Lewandrowski K.Perspectives on cost and outcomes for point-of-care testing. Clin Lab Med2009;29: 479–489.
  • Blyth CC, Booy R, Dwyer DE.Point of care testing: diagnosis outside the virology laboratory. Methods Mol Biol2011;665: 415–433.
  • Campbell S, Fedoriw Y.HIV testing near the patient: changing the face of HIV testing. Clin Lab Med2009;29: 491–501.
  • Lee HH, Dineva MA, Chua YL, Ritchie AV, Ushiro-Lumb I, Wisniewski CA.Simple amplification-based assay: a nucleic acid-based point-of-care platform for HIV-1 testing. J Infect Dis2010;201( Suppl 1): S65–S72.
  • An L, Tang W, Ranalli TA, Kim HJ, Wytiaz J, Kong H.Characterization of a thermostable UvrD helicase and its participation in helicase-dependent amplification. J Biol Chem2005;280: 28952–28958.
  • Vincent M, Xu Y, Kong H.Helicase-dependent isothermal DNA amplification. EMBO Rep2004;5: 795–800.
  • Goldmeyer J, Li H, McCormac M et al.Identification of Staphylococcus aureus and determination of methicillin resistance directly from positive blood cultures by isothermal amplification and a disposable detection device. J Clin Microbiol2008;46: 1534–1536.
  • Tang W, Chow WH, Li Y, Kong H, Tang YW, Lemieux B.Nucleic acid assay system for tier II labs and moderately complex clinics to detect HIV in low-resource settings. J Infect Dis2010;201( Suppl): S46–S51.
  • Tang YW, Procop GW, Persing DH.Molecular diagnostics of infectious diseases. Clin Chem1997;43: 2021–2038.
  • Jangam SR, Yamada DH, McFall SM, Kelso DM.Rapid, point-of-care extraction of human immunodeficiency virus type 1 proviral DNA from whole blood for detection by real-time PCR. J Clin Microbiol2009;47: 2363–2368.
  • Guttikonda S, Wang W, Suresh M.Molecular zipper assays: a simple homosandwich with the sensitivity of PCR. J Pharm Pharm Sci2004;7: 7–16.
  • Panhotra BR, Hassan ZU, Joshi CS, Bahrani A.Visual detection of multiple viral amplicons by dipstick assay: its application in screening of blood donors a welcome tool for the limited resource settings. J Clin Microbiol2005;43: 6218.
  • Raja S, Ching J, Xi L et al.Technology for automated, rapid, and quantitative PCR or reverse transcription-PCR clinical testing. Clin Chem2005;51: 882–890.
  • Hsia CC, Chizhikov VE, Yang AX et al.Microarray multiplex assay for the simultaneous detection and discrimination of hepatitis B, hepatitis C, and human immunodeficiency type-1 viruses in human blood samples. Biochem Biophys Res Commun2007;356: 1017–1023.
  • Miller MB, Tang YW.Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev2009;22: 611–633.
  • Lee SH, Kim SW, Kang JY, Ahn CH.A polymer lab-on-a-chip for reverse transcription (RT)-PCR based point-of-care clinical diagnostics. Lab Chip2008;8: 2121–2127.
  • Sista R, Hua Z, Thwar P et al.Development of a digital microfluidic platform for point of care testing. Lab Chip2008;8: 2091–2104.
  • Rouet F, Rouzioux C.The measurement of HIV-1 viral load in resource-limited settings: how and where? Clin Lab2007;53: 135–148.
  • Calmy A, Ford N, Hirschel B et al.HIV viral load monitoring in resource-limited regions: optional or necessary? Clin Infect Dis2007;44: 128–134.
  • Fiscus SA, Cheng B, Crowe SM et al.HIV-1 viral load assays for resource-limited settings. PLoS Med2006;3: e417.
  • Tanriverdi S, Chen L, Chen S.A rapid and automated sample-to-result HIV load test for near-patient application. J Infect Dis2010;201( Suppl 1): S52–S58.
  • Greengrass V, Lohman B, Morris L et al.Assessment of the low-cost Cavidi ExaVir Load assay for monitoring HIV viral load in pediatric and adult patients. J Acquir Immune Defic Syndr2009;52: 387–390.
  • Lambert JS, Harris DR, Stiehm ER et al.Performance characteristics of HIV-1 culture and HIV-1 DNA and RNA amplification assays for early diagnosis of perinatal HIV-1 infection. J Acquir Immune Defic Syndr2003;34: 512–519.
  • Napravnik S, Cachafeiro A, Stewart P, Eron JJ Jr, Fiscus SA.HIV-1 viral load and phenotypic antiretroviral drug resistance assays based on reverse transcriptase activity in comparison to amplification based HIV-1 RNA and genotypic assays. J Clin Virol2010;47: 18–22.
  • Fellay J, Shianna KV, Telenti A, Goldstein DB.Host genetics and HIV-1: the final phase? PLoS Pathog2010;6: e1001033.
  • Vannberg FO, Chapman SJ, Hill AV.Human genetic susceptibility to intracellular pathogens. Immunol Rev2011;240: 105–116.
  • Telenti A, Goldstein DB.Genomics meets HIV-1. Nat Rev Microbiol2006;4: 865–873.
  • Pine SO, McElrath MJ, Bochud PY.Polymorphisms in Toll-like receptor 4 and Toll-like receptor 9 influence viral load in a seroincident cohort of HIV-1-infected individuals. AIDS2009;23: 2387–2395.
  • Ramsuran V, Kulkarni H, He W et al.Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women. Clin Infect Dis2011;52: 1248–1256.
  • Carrington M, O'Brien SJ.The influence of HLA genotype on AIDS. Annu Rev Med2003;54: 535–551.
  • Gonzalez E, Kulkarni H, Bolivar H et al.The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science2005;307: 1434–1440.
  • Bleiber G, May M, Martinez R et al.Use of a combined ex vivo/in vivo population approach for screening of human genes involved in the human immunodeficiency virus type 1 life cycle for variants influencing disease progression. J Virol2005;79: 12674–12680.
  • Fellay J, Marzolini C, Meaden ER et al.Response to antiretroviral treatment in HIV-1-infected individuals with allelic variants of the multidrug resistance transporter 1: a pharmacogenetics study. Lancet2002;359: 30–36.
  • Haas DW, Smeaton LM, Shafer RW et al.Pharmacogenetics of long-term responses to antiretroviral regimens containing Efavirenz and/or Nelfinavir: an Adult Aids Clinical Trials Group Study. J Infect Dis2005;192: 1931–1942.
  • Tsuchiya K, Gatanaga H, Tachikawa N et al.Homozygous CYP2B6 *6 (Q172H and K262R) correlates with high plasma efavirenz concentrations in HIV-1 patients treated with standard efavirenz-containing regimens. Biochem Biophys Res Commun2004;319: 1322–1326.
  • Pereyra F, Jia X, McLaren PJ et al.The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science2010;330: 1551–1557.
  • Kerr JR, Kaushik N, Fear D, Baldwin DA, Nuwaysir EF, Adcock IM.Single-nucleotide polymorphisms associated with symptomatic infection and differential human gene expression in healthy seropositive persons each implicate the cytoskeleton, integrin signaling, and oncosuppression in the pathogenesis of human parvovirus B19 infection. J Infect Dis2005;192: 276–286.
  • Pavy N, Pelgas B, Beauseigle S et al.Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. BMC Genomics2008;9: 21.
  • Chehab FF, Kan YW.Detection of specific DNA sequences by fluorescence amplification: a color complementation assay. Proc Natl Acad Sci USA1989;86: 9178–9182.
  • Saiki RK, Walsh PS, Levenson CH, Erlich HA.Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc Natl Acad Sci USA1989;86: 6230–6234.
  • Kornher JS, Livak KJ.Mutation detection using nucleotide analogs that alter electrophoretic mobility. Nuc Acids Res1989;17: 7779–7784.
  • Alves AM, Carr FJ.Dot blot detection of point mutations with adjacently hybridising synthetic oligonucleotide probes. Nuc Acids Res1988;16: 8723.
  • Landegren U, Kaiser R, Sanders J, Hood L.A ligase-mediated gene detection technique. Science1988;241: 1077–1080.
  • Kwok PY.Approaches to allele frequency determination. Pharmacogenomics2000;1: 231–235.
  • Shi MM.Technologies for individual genotyping: detection of genetic polymorphisms in drug targets and disease genes. Am J Pharmacogenomics2002;2: 197–205.
  • Margulies M, Egholm M, Altman WE et al.Genome sequencing in microfabricated high-density picolitre reactors. Nature2005;437: 376–380.
  • Douek DC, McFarland RD, Keiser PH et al.Changes in thymic function with age and during the treatment of HIV infection. Nature1998;396: 690–695.
  • Hatzakis A, Touloumi G, Karanicolas R et al.Effect of recent thymic emigrants on progression of HIV-1 disease. Lancet2000;355: 599–604.
  • Ribeiro RM, de Boer RJ.The contribution of the thymus to the recovery of peripheral naive T-cell numbers during antiretroviral treatment for HIV infection. J Acquir Immune Defic Syndr2008;49: 1–8.
  • Dion ML, Bordi R, Zeidan J et al.Slow disease progression and robust therapy-mediated CD4+ T-cell recovery are associated with efficient thymopoiesis during HIV-1 infection. Blood2007;109: 2912–2920.
  • Haugaard SB, Andersen O, Pedersen SB et al.Depleted skeletal muscle mitochondrial DNA, hyperlactatemia, and decreased oxidative capacity in HIV-infected patients on highly active antiretroviral therapy. J Med Virol2005;77: 29–38.
  • Swartz MN.Mitochondrial toxicity—new adverse drug effects. N Engl J Med1995;333: 1146–1148.
  • Cote HC, Brumme ZL, Craib KJ et al.Changes in mitochondrial DNA as a marker of nucleoside toxicity in HIV-infected patients. N Engl J Med2002;346: 811–820.
  • Casula M, Weverling GJ, Wit FW et al.Mitochondrial DNA and RNA increase in peripheral blood mononuclear cells from HIV-1-infected patients randomized to receive stavudine-containing or stavudine-sparing combination therapy. J Infect Dis2005;192: 1794–1800.
  • Garrabou G, Moren C, Gallego-Escuredo JM et al.Genetic and functional mitochondrial assessment of HIV-infected patients developing HAART-related hyperlactatemia. J Acquir Immune Defic Syndr2009;52: 443–451.
  • Miro O, Lopez S, Rodriguez de la Concepcion M et al.Upregulatory mechanisms compensate for mitochondrial DNA depletion in asymptomatic individuals receiving stavudine plus didanosine. J Acquir Immune Defic Syndr2004;37: 1550–1555.
  • Lin CH, Sloan DD, Dang CH et al.Assessment of mitochondrial toxicity by analysis of mitochondrial protein expression in mononuclear cells. Cytometry B Clin Cytom2009;76: 181–190.
  • Wang Z, Trillo-Pazos G, Kim SY et al.Effects of human immunodeficiency virus type 1 on astrocyte gene expression and function: potential role in neuropathogenesis. J Neurovirol2004;10 ( Suppl 1): 25–32.
  • Giri MS, Nebozhyn M, Showe L, Montaner LJ.Microarray data on gene modulation by HIV-1 in immune cells: 2000–2006. J Leukoc Biol2006;80: 1031–1043.
  • Rotger M, Dalmau J, Rauch A et al.Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque. J Clin Invest2011;121: 2391–2400.
  • Wang Z, Gerstein M, Snyder M.RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet2009;10: 57–63.
  • Cirulli ET, Singh A, Shianna KV et al.Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. Genome Biol2011;11: R57.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.