Skip to main content
Top
Published in: European Journal of Clinical Microbiology & Infectious Diseases 5/2019

01-05-2019 | HIV Drug | Review

Nucleic acid testing and molecular characterization of HIV infections

Authors: Junpeng Zhao, Le Chang, Lunan Wang

Published in: European Journal of Clinical Microbiology & Infectious Diseases | Issue 5/2019

Login to get access

Abstract

Significant advances have been made in the molecular assays used for the detection of human immunodeficiency virus (HIV), which are crucial in preventing HIV transmission and monitoring disease progression. Molecular assays for HIV diagnosis have now reached a high degree of specificity, sensitivity and reproducibility, and have less operator involvement to minimize risk of contamination. Furthermore, analyses have been developed for the characterization of host gene polymorphisms and host responses to better identify and monitor HIV-1 infections in the clinic. Currently, molecular technologies including HIV quantitative and qualitative assays are mainly based on the polymerase chain reaction (PCR), transcription-mediated amplification (TMA), nucleic acid sequence-based amplification (NASBA), and branched chain (b) DNA methods and widely used for HIV detection and characterization, such as blood screening, point-of-care testing (POCT), pediatric diagnosis, acute HIV infection (AHI), HIV drug resistance testing, antiretroviral (AR) susceptibility testing, host genome polymorphism testing, and host response analysis. This review summarizes the development and the potential utility of molecular assays used to detect and characterize HIV infections.
Literature
3.
go back to reference Branson B, Owen SM, Bennett B, Werner BG, Pentella MA, Wesolowski LG (2014) Laboratory testing for the diagnosis of HIV infection: updated recommendations. Algorithms Branson B, Owen SM, Bennett B, Werner BG, Pentella MA, Wesolowski LG (2014) Laboratory testing for the diagnosis of HIV infection: updated recommendations. Algorithms
5.
go back to reference Viana IFT, Coelho DF, Palma ML, Nascimento EJM, Gu G, Lima LFO et al (2018) Detection of IgG3 antibodies specific to the human immunodeficiency virus type 1 (HIV-1) p24 protein as marker for recently acquired infection. Epidemiol Infect 146(10):1293–1300CrossRefPubMed Viana IFT, Coelho DF, Palma ML, Nascimento EJM, Gu G, Lima LFO et al (2018) Detection of IgG3 antibodies specific to the human immunodeficiency virus type 1 (HIV-1) p24 protein as marker for recently acquired infection. Epidemiol Infect 146(10):1293–1300CrossRefPubMed
6.
go back to reference Ou CY, Kwok S, Mitchell SW, Mack DH, Sninsky JJ, Krebs JW et al (1988) DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells. Science 239(4837):295–297CrossRefPubMed Ou CY, Kwok S, Mitchell SW, Mack DH, Sninsky JJ, Krebs JW et al (1988) DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells. Science 239(4837):295–297CrossRefPubMed
7.
go back to reference Brauer M, De Villiers JC, Mayaphi SH (2013) Evaluation of the determine fourth generation HIV rapid assay. J Virol Methods 189(1):180–183CrossRefPubMed Brauer M, De Villiers JC, Mayaphi SH (2013) Evaluation of the determine fourth generation HIV rapid assay. J Virol Methods 189(1):180–183CrossRefPubMed
8.
go back to reference Ly TD, Laperche S, Brennan C, Vallari A, Ebel A, Hunt J et al (2004) Evaluation of the sensitivity and specificity of six HIV combined p24 antigen and antibody assays. J Virol Methods 122(2):185–194CrossRefPubMed Ly TD, Laperche S, Brennan C, Vallari A, Ebel A, Hunt J et al (2004) Evaluation of the sensitivity and specificity of six HIV combined p24 antigen and antibody assays. J Virol Methods 122(2):185–194CrossRefPubMed
9.
go back to reference Zhao Y, Gou Y, Li D, Wang T, Huang X, Shi M et al (2018) Performance evaluation of a new automated fourth-generation HIV Ag/Ab combination chemiluminescence immunoassay. Clin Chem Lab Med 56(5):e115–e117CrossRefPubMed Zhao Y, Gou Y, Li D, Wang T, Huang X, Shi M et al (2018) Performance evaluation of a new automated fourth-generation HIV Ag/Ab combination chemiluminescence immunoassay. Clin Chem Lab Med 56(5):e115–e117CrossRefPubMed
10.
go back to reference Delaney KP, Wesolowski LG, Owen SM (2017) The evolution of HIV testing continues. Sex Transm Dis 44(12):747–749CrossRefPubMed Delaney KP, Wesolowski LG, Owen SM (2017) The evolution of HIV testing continues. Sex Transm Dis 44(12):747–749CrossRefPubMed
13.
go back to reference Branson BM, Stekler JD (2012) Detection of acute HIV infection: we can’t close the window. J Infect Dis 205(4):521–524CrossRefPubMed Branson BM, Stekler JD (2012) Detection of acute HIV infection: we can’t close the window. J Infect Dis 205(4):521–524CrossRefPubMed
14.
go back to reference Weber B (2006) Screening of HIV infection: role of molecular and immunological assays. Expert Rev Mol Diagn 6(3):399–411CrossRefPubMed Weber B (2006) Screening of HIV infection: role of molecular and immunological assays. Expert Rev Mol Diagn 6(3):399–411CrossRefPubMed
15.
go back to reference Galel SA, Simon TL, Williamson PC, AuBuchon JP, Waxman DA, Erickson Y et al (2018) Sensitivity and specificity of a new automated system for the detection of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus nucleic acid in blood and plasma donations. Transfusion 58(3):649–659CrossRefPubMed Galel SA, Simon TL, Williamson PC, AuBuchon JP, Waxman DA, Erickson Y et al (2018) Sensitivity and specificity of a new automated system for the detection of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus nucleic acid in blood and plasma donations. Transfusion 58(3):649–659CrossRefPubMed
16.
go back to reference Pas S, Rossen JW, Schoener D, Thamke D, Pettersson A, Babiel R et al (2010) Performance evaluation of the new Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 for quantification of human immunodeficiency virus type 1 RNA. J Clin Microbiol 48(4):1195–1200CrossRefPubMedPubMedCentral Pas S, Rossen JW, Schoener D, Thamke D, Pettersson A, Babiel R et al (2010) Performance evaluation of the new Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 for quantification of human immunodeficiency virus type 1 RNA. J Clin Microbiol 48(4):1195–1200CrossRefPubMedPubMedCentral
17.
go back to reference Schmidt M, Korn K, Nubling CM, Chudy M, Kress J, Horst HA et al (2009) First transmission of human immunodeficiency virus type 1 by a cellular blood product after mandatory nucleic acid screening in Germany. Transfusion 49(9):1836–1844CrossRefPubMed Schmidt M, Korn K, Nubling CM, Chudy M, Kress J, Horst HA et al (2009) First transmission of human immunodeficiency virus type 1 by a cellular blood product after mandatory nucleic acid screening in Germany. Transfusion 49(9):1836–1844CrossRefPubMed
18.
go back to reference Müller B, Nübling CM, Kress J, Roth WK, De Zolt S, Pichl L (2013) How safe is safe: new human immunodeficiency virus type 1 variants missed by nucleic acid testing. Transfusion 53(10pt2):2422–2430CrossRefPubMed Müller B, Nübling CM, Kress J, Roth WK, De Zolt S, Pichl L (2013) How safe is safe: new human immunodeficiency virus type 1 variants missed by nucleic acid testing. Transfusion 53(10pt2):2422–2430CrossRefPubMed
27.
go back to reference COBAS AmpliPrep/COBAS TaqMan HIV-1 Test, 48 Tests; COBAS AmpliPrep/COBAS TaqMan Wash Reagent, 5.1 L, https://www.fda.gov/downloads/ BiologicsBloodVaccines/BloodBloodProducts/Approv-edProducts/PremarketApprovalsPMAs/UCM092878.pdf COBAS AmpliPrep/COBAS TaqMan HIV-1 Test, 48 Tests; COBAS AmpliPrep/COBAS TaqMan Wash Reagent, 5.1 L, https://​www.​fda.​gov/​downloads/​ BiologicsBloodVaccines/BloodBloodProducts/Approv-edProducts/PremarketApprovalsPMAs/UCM092878.pdf
29.
go back to reference Gomes P, Palma AC, Cabanas J, Abecasis A, Carvalho AP, Ziermann R et al (2006) Comparison of the COBAS TAQMAN HIV-1 HPS with VERSANT HIV-1 RNA 3.0 assay (bDNA) for plasma RNA quantitation in different HIV-1 subtypes. J Virol Methods 135(2):223–228CrossRefPubMed Gomes P, Palma AC, Cabanas J, Abecasis A, Carvalho AP, Ziermann R et al (2006) Comparison of the COBAS TAQMAN HIV-1 HPS with VERSANT HIV-1 RNA 3.0 assay (bDNA) for plasma RNA quantitation in different HIV-1 subtypes. J Virol Methods 135(2):223–228CrossRefPubMed
31.
go back to reference Eshleman SH, John H, Priscilla S, Cunningham SP, Birgit D, Catherine B et al (2004) Performance of the Celera Diagnostics ViroSeq HIV-1 Genotyping System for sequence-based analysis of diverse human immunodeficiency virus type 1 strains. J Clin Microbiol 42(6):2711CrossRefPubMedPubMedCentral Eshleman SH, John H, Priscilla S, Cunningham SP, Birgit D, Catherine B et al (2004) Performance of the Celera Diagnostics ViroSeq HIV-1 Genotyping System for sequence-based analysis of diverse human immunodeficiency virus type 1 strains. J Clin Microbiol 42(6):2711CrossRefPubMedPubMedCentral
33.
go back to reference Robert MG, Daniel RK, Victoria AJ, John WM, John LS, Ronald S et al (2003) Accuracy of the TRUGENE HIV-1 genotyping kit. J Clin Microbiol 41(4):1586CrossRef Robert MG, Daniel RK, Victoria AJ, John WM, John LS, Ronald S et al (2003) Accuracy of the TRUGENE HIV-1 genotyping kit. J Clin Microbiol 41(4):1586CrossRef
41.
go back to reference Bourlet T, Memmi M, Saoudin H, Pozzetto B (2013) Molecular HIV screening. Expert Rev Mol Diagn 13(7):693–705CrossRefPubMed Bourlet T, Memmi M, Saoudin H, Pozzetto B (2013) Molecular HIV screening. Expert Rev Mol Diagn 13(7):693–705CrossRefPubMed
42.
go back to reference Stevens WS, Noble L, Berrie L, Sarang S, Scott LE (2009) 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 Microbiol 47(8):2465–2469CrossRefPubMedPubMedCentral Stevens WS, Noble L, Berrie L, Sarang S, Scott LE (2009) 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 Microbiol 47(8):2465–2469CrossRefPubMedPubMedCentral
43.
go back to reference Simonds RJ, Brown TM, Thea DM, Orloff SL, Steketee RW, Lee FK et al (1998) Sensitivity and specificity of a qualitative RNA detection assay to diagnose HIV infection in young infants. Perinatal AIDS Collaborative Transmission Study. Aids 12(12):1545–1549CrossRefPubMed Simonds RJ, Brown TM, Thea DM, Orloff SL, Steketee RW, Lee FK et al (1998) Sensitivity and specificity of a qualitative RNA detection assay to diagnose HIV infection in young infants. Perinatal AIDS Collaborative Transmission Study. Aids 12(12):1545–1549CrossRefPubMed
44.
go back to reference Dubrow R, Qin L, Lin H, Hernandez-Ramirez RU, Neugebauer RS, Leyden W et al (2017) Association of CD4+ T-cell count, HIV-1 RNA viral load, and antiretroviral therapy with Kaposi sarcoma risk among HIV-infected persons in the United States and Canada. J Acquir Immune Defic Syndr 75(4):382–390CrossRefPubMedPubMedCentral Dubrow R, Qin L, Lin H, Hernandez-Ramirez RU, Neugebauer RS, Leyden W et al (2017) Association of CD4+ T-cell count, HIV-1 RNA viral load, and antiretroviral therapy with Kaposi sarcoma risk among HIV-infected persons in the United States and Canada. J Acquir Immune Defic Syndr 75(4):382–390CrossRefPubMedPubMedCentral
45.
go back to reference May MT, Gompels M, Delpech V, Porter K, Orkin C, Kegg S et al (2014) Impact on life expectancy of HIV-1 positive individuals of CD4+ cell count and viral load response to antiretroviral therapy. Aids 28(8):1193–1202CrossRefPubMed May MT, Gompels M, Delpech V, Porter K, Orkin C, Kegg S et al (2014) Impact on life expectancy of HIV-1 positive individuals of CD4+ cell count and viral load response to antiretroviral therapy. Aids 28(8):1193–1202CrossRefPubMed
46.
go back to reference Mellors JW, Rinaldo CR Jr, Gupta P, White RM, Todd JA, Kingsley LA (1996) Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272(5265):1167–1170CrossRefPubMed Mellors JW, Rinaldo CR Jr, Gupta P, White RM, Todd JA, Kingsley LA (1996) Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272(5265):1167–1170CrossRefPubMed
47.
go back to reference Cozzi LA, Katzenstein TL, Ullum H, Phillips AN, Skinhøj P, Gerstoft J et al (1998) The relative prognostic value of plasma HIV RNA levels and CD4 lymphocyte counts in advanced HIV infection. Aids 12(13):1639–1643CrossRef Cozzi LA, Katzenstein TL, Ullum H, Phillips AN, Skinhøj P, Gerstoft J et al (1998) The relative prognostic value of plasma HIV RNA levels and CD4 lymphocyte counts in advanced HIV infection. Aids 12(13):1639–1643CrossRef
48.
go back to reference Abbott MA, Poiesz BJ, Byrne BC, Kwok S, Sninsky JJ, Ehrlich GD (1988) Enzymatic gene amplification: qualitative and quantitative methods for detecting proviral DNA amplified in vitro. J Infect Dis 158(6):1158–1169CrossRefPubMed Abbott MA, Poiesz BJ, Byrne BC, Kwok S, Sninsky JJ, Ehrlich GD (1988) Enzymatic gene amplification: qualitative and quantitative methods for detecting proviral DNA amplified in vitro. J Infect Dis 158(6):1158–1169CrossRefPubMed
49.
go back to reference Malek L, Sooknanan R, Compton J (1994) Nucleic acid sequence-based amplification (NASBA). Methods Mol Biol 28(28):253PubMed Malek L, Sooknanan R, Compton J (1994) Nucleic acid sequence-based amplification (NASBA). Methods Mol Biol 28(28):253PubMed
50.
go back to reference Horn T, Chang CA, Urdea MS (1997) Chemical synthesis and characterization of branched oligodeoxyribonucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays. Nucleic Acids Res 25(23):4842–4849CrossRefPubMedPubMedCentral Horn T, Chang CA, Urdea MS (1997) Chemical synthesis and characterization of branched oligodeoxyribonucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays. Nucleic Acids Res 25(23):4842–4849CrossRefPubMedPubMedCentral
51.
go back to reference Sloma CR, Germer JJ, Gerads TM, Mandrekar JN, Mitchell PS, Yao JD (2009) Comparison of the Abbott realtime human immunodeficiency virus type 1 (HIV-1) assay to the Cobas AmpliPrep/Cobas TaqMan HIV-1 test: workflow, reliability, and direct costs. J Clin Microbiol 47(4):889–895CrossRefPubMedPubMedCentral Sloma CR, Germer JJ, Gerads TM, Mandrekar JN, Mitchell PS, Yao JD (2009) Comparison of the Abbott realtime human immunodeficiency virus type 1 (HIV-1) assay to the Cobas AmpliPrep/Cobas TaqMan HIV-1 test: workflow, reliability, and direct costs. J Clin Microbiol 47(4):889–895CrossRefPubMedPubMedCentral
52.
go back to reference Schumacher W, Frick E, Kauselmann M, Maier-Hoyle V, van der Vliet R, Babiel R (2007) Fully automated quantification of human immunodeficiency virus (HIV) type 1 RNA in human plasma by the COBAS AmpliPrep/COBAS TaqMan system. J Clin Virol 38(4):304–312CrossRefPubMed Schumacher W, Frick E, Kauselmann M, Maier-Hoyle V, van der Vliet R, Babiel R (2007) Fully automated quantification of human immunodeficiency virus (HIV) type 1 RNA in human plasma by the COBAS AmpliPrep/COBAS TaqMan system. J Clin Virol 38(4):304–312CrossRefPubMed
53.
go back to reference Korn K, Weissbrich B, Henke-Gendo C, Heim A, Jauer CM, Taylor N et al (2009) Single-point mutations causing more than 100-fold underestimation of human immunodeficiency virus type 1 (HIV-1) load with the Cobas TaqMan HIV-1 real-time PCR assay. J Clin Microbiol 47(4):1238–1240CrossRefPubMedPubMedCentral Korn K, Weissbrich B, Henke-Gendo C, Heim A, Jauer CM, Taylor N et al (2009) Single-point mutations causing more than 100-fold underestimation of human immunodeficiency virus type 1 (HIV-1) load with the Cobas TaqMan HIV-1 real-time PCR assay. J Clin Microbiol 47(4):1238–1240CrossRefPubMedPubMedCentral
54.
go back to reference Tung YC, Ke LY, Lu PL, Lin KH, Lee SC, Lin YY et al (2015) Comparison of the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 test V1.0 with V2.0 in HIV-1 viral load quantification. Kaohsiung J Med Sci 31(4):188–193CrossRefPubMed Tung YC, Ke LY, Lu PL, Lin KH, Lee SC, Lin YY et al (2015) Comparison of the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 test V1.0 with V2.0 in HIV-1 viral load quantification. Kaohsiung J Med Sci 31(4):188–193CrossRefPubMed
55.
go back to reference Mourez T, Delaugerre C, Vray M, Lemee V, Simon F, Plantier JC (2015) Comparison of the bioMerieux NucliSENS EasyQ HIV-1 V2.0-HIV-1 RNA quantification assay versus Abbott RealTime HIV-1 and Roche Cobas TaqMan HIV-1 V2.0 on current epidemic HIV-1 variants. J Clin Virol 71:76–81CrossRefPubMed Mourez T, Delaugerre C, Vray M, Lemee V, Simon F, Plantier JC (2015) Comparison of the bioMerieux NucliSENS EasyQ HIV-1 V2.0-HIV-1 RNA quantification assay versus Abbott RealTime HIV-1 and Roche Cobas TaqMan HIV-1 V2.0 on current epidemic HIV-1 variants. J Clin Virol 71:76–81CrossRefPubMed
56.
go back to reference Manak MM, Hack HR, Nair SV, Worlock A, Malia JA, Peel SA et al (2016) Evaluation of Hologic Aptima HIV-1 Quant Dx assay on the Panther System on HIV subtypes. J Clin Microbiol 54(10):2575–2581CrossRefPubMedPubMedCentral Manak MM, Hack HR, Nair SV, Worlock A, Malia JA, Peel SA et al (2016) Evaluation of Hologic Aptima HIV-1 Quant Dx assay on the Panther System on HIV subtypes. J Clin Microbiol 54(10):2575–2581CrossRefPubMedPubMedCentral
57.
go back to reference Loetscher P (2017) Performance evaluation of Cobas® HIV-1, a quantitative nucleic acid test for use on the Cobas® 6800/8800 systems. Journal of HIV and AIDS 3(1) Loetscher P (2017) Performance evaluation of Cobas® HIV-1, a quantitative nucleic acid test for use on the Cobas® 6800/8800 systems. Journal of HIV and AIDS 3(1)
58.
go back to reference Wiesmann F, Ehret R, Naeth G, Daumer M, Fuhrmann J, Kaiser R et al (2018) Multicenter evaluation of two next-generation HIV-1 quantitation assays, Aptima Quant Dx and Cobas 6800, in comparison to the RealTime HIV-1 reference assay. J Clin Microbiol 56(10) Wiesmann F, Ehret R, Naeth G, Daumer M, Fuhrmann J, Kaiser R et al (2018) Multicenter evaluation of two next-generation HIV-1 quantitation assays, Aptima Quant Dx and Cobas 6800, in comparison to the RealTime HIV-1 reference assay. J Clin Microbiol 56(10)
59.
go back to reference Elbeik T, Loftus RA, Beringer S (2014) Health care industries perspective of viral load assays: the VERSANT HIV-1 RNA 3.0 assay. Expert Rev Mol Diagn 2(3):275–285CrossRef Elbeik T, Loftus RA, Beringer S (2014) Health care industries perspective of viral load assays: the VERSANT HIV-1 RNA 3.0 assay. Expert Rev Mol Diagn 2(3):275–285CrossRef
60.
go back to reference Zhang L, Jin C, Jiang Z, Tang T, Jiang Y, Pan PL (2017) Comparison of commercial HIV-1 viral load tests by using proficiency test results in China, 2013–2015. Zhonghua Liu Xing Bing Xue Za Zhi 38(9):1231–1235PubMed Zhang L, Jin C, Jiang Z, Tang T, Jiang Y, Pan PL (2017) Comparison of commercial HIV-1 viral load tests by using proficiency test results in China, 2013–2015. Zhonghua Liu Xing Bing Xue Za Zhi 38(9):1231–1235PubMed
61.
go back to reference Baumeister MA, Zhang N, Beas H, Brooks JR, Canchola JA, Cosenza C et al (2012) A sensitive branched DNA HIV-1 signal amplification viral load assay with single day turnaround. PLoS One 7(3):e33295CrossRefPubMedPubMedCentral Baumeister MA, Zhang N, Beas H, Brooks JR, Canchola JA, Cosenza C et al (2012) A sensitive branched DNA HIV-1 signal amplification viral load assay with single day turnaround. PLoS One 7(3):e33295CrossRefPubMedPubMedCentral
62.
go back to reference Xu S, Song A, Nie J, Li X, Wang Y (2010) Performance of NucliSens HIV-1 EasyQ Version 2.0 compared with six commercially available quantitative nucleic acid assays for detection of HIV-1 in China. Mol Diagn Ther 14(5):305CrossRefPubMed Xu S, Song A, Nie J, Li X, Wang Y (2010) Performance of NucliSens HIV-1 EasyQ Version 2.0 compared with six commercially available quantitative nucleic acid assays for detection of HIV-1 in China. Mol Diagn Ther 14(5):305CrossRefPubMed
64.
go back to reference Roth WK, Weber M, Seifried E (1999) Feasibility and efficacy of routine PCR screening of blood donations for hepatitis C virus, hepatitis B virus, and HIV-1 in a blood-bank setting. Lancet 353(9150):359CrossRefPubMed Roth WK, Weber M, Seifried E (1999) Feasibility and efficacy of routine PCR screening of blood donations for hepatitis C virus, hepatitis B virus, and HIV-1 in a blood-bank setting. Lancet 353(9150):359CrossRefPubMed
65.
go back to reference Susan AF, Takesha M, Julie AEN, William CM (2013) Validation of the gen-probe Aptima qualitative HIV-1 RNA assay for diagnosis of human immunodeficiency virus infection in infants. J Clin Microbiol 51(12):4137–4140CrossRef Susan AF, Takesha M, Julie AEN, William CM (2013) Validation of the gen-probe Aptima qualitative HIV-1 RNA assay for diagnosis of human immunodeficiency virus infection in infants. J Clin Microbiol 51(12):4137–4140CrossRef
66.
go back to reference Lelie PN, van Drimmelen HA, Cuypers HT, Best SJ, Stramer SL, Hyland C et al (2010) Sensitivity of HCV RNA and HIV RNA blood screening assays. Transfusion 42(5):527–536CrossRef Lelie PN, van Drimmelen HA, Cuypers HT, Best SJ, Stramer SL, Hyland C et al (2010) Sensitivity of HCV RNA and HIV RNA blood screening assays. Transfusion 42(5):527–536CrossRef
67.
go back to reference (2010) WHO Guidelines Approved by the Guidelines Review Committee. WHO Recommendations on the Diagnosis of HIV Infection in Infants and Children. World Health Organization World Health Organization., Geneva (2010) WHO Guidelines Approved by the Guidelines Review Committee. WHO Recommendations on the Diagnosis of HIV Infection in Infants and Children. World Health Organization World Health Organization., Geneva
68.
go back to reference Hamlyn E, Jones V, Porter K, Fidler S (2010) Antiretroviral treatment of primary HIV infection to reduce onward transmission. Curr Opin HIV AIDS 5(4):283–290CrossRefPubMed Hamlyn E, Jones V, Porter K, Fidler S (2010) Antiretroviral treatment of primary HIV infection to reduce onward transmission. Curr Opin HIV AIDS 5(4):283–290CrossRefPubMed
69.
go back to reference Dodd RY (2015) Transfusion-transmitted infections: testing strategies and residual risk. Isbt Science 9(1):1–5 Dodd RY (2015) Transfusion-transmitted infections: testing strategies and residual risk. Isbt Science 9(1):1–5
70.
go back to reference Shyamala V (2015) Nucleic acid technology (NAT) testing for blood screening: impact of individual donation and Mini Pool-NAT testing on analytical sensitivity, screening sensitivity and clinical sensitivity. Isbt Science 9(2):315–324CrossRef Shyamala V (2015) Nucleic acid technology (NAT) testing for blood screening: impact of individual donation and Mini Pool-NAT testing on analytical sensitivity, screening sensitivity and clinical sensitivity. Isbt Science 9(2):315–324CrossRef
71.
go back to reference Van Laethem K, Beuselinck K, Van Dooren S, De Clercq E, Desmyter J, Vandamme AM (1998) Diagnosis of human immunodeficiency virus infection by a polymerase chain reaction assay evaluated in patients harbouring strains of diverse geographical origin. J Virol Methods 70(2):153–166CrossRefPubMed Van Laethem K, Beuselinck K, Van Dooren S, De Clercq E, Desmyter J, Vandamme AM (1998) Diagnosis of human immunodeficiency virus infection by a polymerase chain reaction assay evaluated in patients harbouring strains of diverse geographical origin. J Virol Methods 70(2):153–166CrossRefPubMed
72.
go back to reference Chudy M, Weber-Schehl M, Pichl L, Jork C, Kress J, Heiden M et al (2012) Blood screening nucleic acid amplification tests for human immunodeficiency virus type 1 may require two different amplification targets. Transfusion 52(2):431–439CrossRefPubMed Chudy M, Weber-Schehl M, Pichl L, Jork C, Kress J, Heiden M et al (2012) Blood screening nucleic acid amplification tests for human immunodeficiency virus type 1 may require two different amplification targets. Transfusion 52(2):431–439CrossRefPubMed
73.
go back to reference Margaritis AR, Brown SM, Seed CR, Kiely P, D'Agostino B, Keller AJ (2007) Comparison of two automated nucleic acid testing systems for simultaneous detection of human immunodeficiency virus and hepatitis C virus RNA and hepatitis B virus DNA. Transfusion 47(10):1783–1793CrossRefPubMed Margaritis AR, Brown SM, Seed CR, Kiely P, D'Agostino B, Keller AJ (2007) Comparison of two automated nucleic acid testing systems for simultaneous detection of human immunodeficiency virus and hepatitis C virus RNA and hepatitis B virus DNA. Transfusion 47(10):1783–1793CrossRefPubMed
74.
go back to reference Assal A, Barlet V, Deschaseaux M, Dupont I, Gallian P, Guitton C et al (2009) Comparison of the analytical and operational performance of two viral nucleic acid test blood screening systems: Procleix Tigris and cobas s 201. Transfusion 49(2):289–300CrossRefPubMed Assal A, Barlet V, Deschaseaux M, Dupont I, Gallian P, Guitton C et al (2009) Comparison of the analytical and operational performance of two viral nucleic acid test blood screening systems: Procleix Tigris and cobas s 201. Transfusion 49(2):289–300CrossRefPubMed
75.
go back to reference Assal A, Barlet V, Deschaseaux M, Dupont I, Gallian P, Guitton C et al (2009) Sensitivity of two hepatitis B virus, hepatitis C virus (HCV), and human immunodeficiency virus (HIV) nucleic acid test systems relative to hepatitis B surface antigen, anti-HCV, anti-HIV, and p24/anti-HIV combination assays in seroconversion panels. Transfusion 49(2):301–310CrossRefPubMed Assal A, Barlet V, Deschaseaux M, Dupont I, Gallian P, Guitton C et al (2009) Sensitivity of two hepatitis B virus, hepatitis C virus (HCV), and human immunodeficiency virus (HIV) nucleic acid test systems relative to hepatitis B surface antigen, anti-HCV, anti-HIV, and p24/anti-HIV combination assays in seroconversion panels. Transfusion 49(2):301–310CrossRefPubMed
76.
go back to reference Grabarczyk P, van Drimmelen H, Kopacz A, Gdowska J, Liszewski G, Piotrowski D et al (2013) Head-to-head comparison of two transcription-mediated amplification assay versions for detection of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus type 1 in blood donors. Transfusion 53(10 Pt 2):2512–2524CrossRefPubMed Grabarczyk P, van Drimmelen H, Kopacz A, Gdowska J, Liszewski G, Piotrowski D et al (2013) Head-to-head comparison of two transcription-mediated amplification assay versions for detection of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus type 1 in blood donors. Transfusion 53(10 Pt 2):2512–2524CrossRefPubMed
77.
go back to reference Grabarczyk P, Koppelman M, Boland F, Sauleda S, Fabra C, Cambie G et al (2015) Inclusion of human immunodeficiency virus type 2 (HIV-2) in a multiplex transcription-mediated amplification assay does not affect detection of HIV-1 and hepatitis B and C virus genotypes: a multicenter performance evaluation study. Transfusion 55(9):2246–2255CrossRefPubMed Grabarczyk P, Koppelman M, Boland F, Sauleda S, Fabra C, Cambie G et al (2015) Inclusion of human immunodeficiency virus type 2 (HIV-2) in a multiplex transcription-mediated amplification assay does not affect detection of HIV-1 and hepatitis B and C virus genotypes: a multicenter performance evaluation study. Transfusion 55(9):2246–2255CrossRefPubMed
78.
go back to reference Heim A (2016) Evaluation of the Procleix Ultrio Elite Assay and the Panther-System for individual NAT screening of blood, hematopoietic stem cell, tissue and organ donors. Transfus Med Hemother 43(3):177–182CrossRefPubMedPubMedCentral Heim A (2016) Evaluation of the Procleix Ultrio Elite Assay and the Panther-System for individual NAT screening of blood, hematopoietic stem cell, tissue and organ donors. Transfus Med Hemother 43(3):177–182CrossRefPubMedPubMedCentral
79.
go back to reference Le Corfec E, Le Pont F, Tuckwell HC, Rouzioux C, Costagliola D (1999) Direct HIV testing in blood donations: variation of the yield with detection threshold and pool size. Transfusion 39(10):1141–1144CrossRefPubMed Le Corfec E, Le Pont F, Tuckwell HC, Rouzioux C, Costagliola D (1999) Direct HIV testing in blood donations: variation of the yield with detection threshold and pool size. Transfusion 39(10):1141–1144CrossRefPubMed
80.
go back to reference Ha J, Park Y, Kim HS (2017) Evaluation of clinical sensitivity and specificity of hepatitis B virus (HBV), hepatitis C virus, and human immunodeficiency Virus-1 by cobas MPX: detection of occult HBV infection in an HBV-endemic area. J Clin Virol 96:60–63CrossRefPubMed Ha J, Park Y, Kim HS (2017) Evaluation of clinical sensitivity and specificity of hepatitis B virus (HBV), hepatitis C virus, and human immunodeficiency Virus-1 by cobas MPX: detection of occult HBV infection in an HBV-endemic area. J Clin Virol 96:60–63CrossRefPubMed
81.
go back to reference Migueles SA, Connors M (2010) Long-term nonprogressive disease among untreated HIV-infected individuals: clinical implications of understanding immune control of HIV. Jama 304(2):194–201CrossRefPubMed Migueles SA, Connors M (2010) Long-term nonprogressive disease among untreated HIV-infected individuals: clinical implications of understanding immune control of HIV. Jama 304(2):194–201CrossRefPubMed
82.
go back to reference Mendoza D, Johnson SA, Peterson BA, Natarajan V, Salgado M, Dewar RL et al (2012) Comprehensive analysis of unique cases with extraordinary control over HIV replication. Blood 119(20):4645–4655CrossRefPubMedPubMedCentral Mendoza D, Johnson SA, Peterson BA, Natarajan V, Salgado M, Dewar RL et al (2012) Comprehensive analysis of unique cases with extraordinary control over HIV replication. Blood 119(20):4645–4655CrossRefPubMedPubMedCentral
83.
go back to reference Cock KMD, Fowler MG, Mercier E, Vincenzi ID, Saba J, Hoff E et al (2000) Prevention of mother-to-child HIV transmission in resource-poor countries: translating research into policy and practice. Jama 283(9):1175–1182CrossRefPubMed Cock KMD, Fowler MG, Mercier E, Vincenzi ID, Saba J, Hoff E et al (2000) Prevention of mother-to-child HIV transmission in resource-poor countries: translating research into policy and practice. Jama 283(9):1175–1182CrossRefPubMed
84.
go back to reference Luzuriaga K, Mofenson LM (2016) Challenges in the elimination of pediatric HIV-1 infection. N Engl J Med 374(8):761–770CrossRefPubMed Luzuriaga K, Mofenson LM (2016) Challenges in the elimination of pediatric HIV-1 infection. N Engl J Med 374(8):761–770CrossRefPubMed
85.
go back to reference Canals F, Masia M, Gutierrez F (2018) Developments in early diagnosis and therapy of HIV infection in newborns. Expert Opin Pharmacother 19(1):13–25CrossRefPubMed Canals F, Masia M, Gutierrez F (2018) Developments in early diagnosis and therapy of HIV infection in newborns. Expert Opin Pharmacother 19(1):13–25CrossRefPubMed
86.
go back to reference Stevens W, Sherman G, Downing R, Parsons LM, Ou CY, Crowley S et al (2008) Role of the laboratory in ensuring global access to ARV treatment for HIV-infected children: consensus statement on the performance of laboratory assays for early infant diagnosis. Open AIDS J 2:17–25CrossRefPubMedPubMedCentral Stevens W, Sherman G, Downing R, Parsons LM, Ou CY, Crowley S et al (2008) Role of the laboratory in ensuring global access to ARV treatment for HIV-infected children: consensus statement on the performance of laboratory assays for early infant diagnosis. Open AIDS J 2:17–25CrossRefPubMedPubMedCentral
87.
go back to reference Ou C-Y, Fiscus S, Ellenberger D, Parekh B, Korhonen C, Nkengasong J et al (2012) Early diagnosis of HIV infection in the breastfed infant. Adv Exp Med Biol 743(743):51–65CrossRefPubMed Ou C-Y, Fiscus S, Ellenberger D, Parekh B, Korhonen C, Nkengasong J et al (2012) Early diagnosis of HIV infection in the breastfed infant. Adv Exp Med Biol 743(743):51–65CrossRefPubMed
88.
go back to reference Pierce VM, Neide B, Hodinka RL (2011) Evaluation of the Gen-Probe Aptima HIV-1 RNA qualitative assay as an alternative to Western blot analysis for confirmation of HIV infection. J Clin Microbiol 49(4):1642–1645CrossRefPubMedPubMedCentral Pierce VM, Neide B, Hodinka RL (2011) Evaluation of the Gen-Probe Aptima HIV-1 RNA qualitative assay as an alternative to Western blot analysis for confirmation of HIV infection. J Clin Microbiol 49(4):1642–1645CrossRefPubMedPubMedCentral
89.
go back to reference Alvarez P, Prieto L, Martin L, Obiang J, Avedillo P, Vargas A et al (2017) Evaluation of four commercial virological assays for early infant HIV-1 diagnosis using dried blood specimens. Pediatr Res 81(1–1):80–87CrossRefPubMed Alvarez P, Prieto L, Martin L, Obiang J, Avedillo P, Vargas A et al (2017) Evaluation of four commercial virological assays for early infant HIV-1 diagnosis using dried blood specimens. Pediatr Res 81(1–1):80–87CrossRefPubMed
90.
go back to reference Ceffa S, Luhanga R, Andreotti M, Brambilla D, Erba F, Jere H et al (2016) Comparison of the Cepheid GeneXpert and Abbott M2000 HIV-1 real time molecular assays for monitoring HIV-1 viral load and detecting HIV-1 infection. J Virol Methods 229:35–39CrossRefPubMed Ceffa S, Luhanga R, Andreotti M, Brambilla D, Erba F, Jere H et al (2016) Comparison of the Cepheid GeneXpert and Abbott M2000 HIV-1 real time molecular assays for monitoring HIV-1 viral load and detecting HIV-1 infection. J Virol Methods 229:35–39CrossRefPubMed
91.
go back to reference Hsiao NY, Dunning L, Kroon M, Myer L (2016) Laboratory evaluation of the Alere q point-of-care system for early infant HIV diagnosis. PLoS One 11(3):e0152672CrossRefPubMedPubMedCentral Hsiao NY, Dunning L, Kroon M, Myer L (2016) Laboratory evaluation of the Alere q point-of-care system for early infant HIV diagnosis. PLoS One 11(3):e0152672CrossRefPubMedPubMedCentral
92.
go back to reference Koopman JS, Jacquez JA, Welch GW, Simon CP, Foxman B, Pollock SM et al (1997) The role of early HIV infection in the spread of HIV through populations. J Acquir Immune Defic Syndr Hum Retrovirol 14(3):249–258CrossRefPubMed Koopman JS, Jacquez JA, Welch GW, Simon CP, Foxman B, Pollock SM et al (1997) The role of early HIV infection in the spread of HIV through populations. J Acquir Immune Defic Syndr Hum Retrovirol 14(3):249–258CrossRefPubMed
93.
go back to reference Brenner BG, Roger M, Routy JP, Moisi D, Ntemgwa M, Matte C et al (2007) High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis 195(7):951–959CrossRefPubMed Brenner BG, Roger M, Routy JP, Moisi D, Ntemgwa M, Matte C et al (2007) High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis 195(7):951–959CrossRefPubMed
94.
go back to reference Bassett IV, Chetty S, Giddy J, Reddy S, Bishop K, Lu Z et al (2015) Screening for acute HIV infection in South Africa: finding acute and chronic disease. HIV Med 12(1):46–53CrossRef Bassett IV, Chetty S, Giddy J, Reddy S, Bishop K, Lu Z et al (2015) Screening for acute HIV infection in South Africa: finding acute and chronic disease. HIV Med 12(1):46–53CrossRef
95.
go back to reference Martin EG, Salaru G, Mohammed D, Coombs RW, Paul SM, Cadoff EM (2013) Finding those at risk: acute HIV infection in Newark, NJ. J Clin Virol 58:E24–E28CrossRefPubMedPubMedCentral Martin EG, Salaru G, Mohammed D, Coombs RW, Paul SM, Cadoff EM (2013) Finding those at risk: acute HIV infection in Newark, NJ. J Clin Virol 58:E24–E28CrossRefPubMedPubMedCentral
96.
go back to reference Emerson B, Plough K (2013) Detection of acute HIV-1 infections utilizing NAAT technology in Dallas, Texas. J Clin Virol 58(Suppl 1):e48–e53CrossRefPubMed Emerson B, Plough K (2013) Detection of acute HIV-1 infections utilizing NAAT technology in Dallas, Texas. J Clin Virol 58(Suppl 1):e48–e53CrossRefPubMed
98.
go back to reference Engel N, Pant PN (2015) Qualitative research on point-of-care testing strategies and programs for HIV. Expert Rev Mol Diagn 15(1):71CrossRefPubMed Engel N, Pant PN (2015) Qualitative research on point-of-care testing strategies and programs for HIV. Expert Rev Mol Diagn 15(1):71CrossRefPubMed
99.
go back to reference Chang M, Steinmetzer K, Raugi DN, Smith RA, Ba S, Sall F et al (2017) Detection and differentiation of HIV-2 using the point-of-care Alere q HIV-1/2 detect nucleic acid test. J Clin Virol 97:22–25CrossRefPubMedPubMedCentral Chang M, Steinmetzer K, Raugi DN, Smith RA, Ba S, Sall F et al (2017) Detection and differentiation of HIV-2 using the point-of-care Alere q HIV-1/2 detect nucleic acid test. J Clin Virol 97:22–25CrossRefPubMedPubMedCentral
100.
go back to reference Jani IV, Meggi B, Vubil A, Sitoe NE, Bhatt N, Tobaiwa O et al (2016) Evaluation of the whole-blood Alere Q NAT point-of-care RNA assay for HIV-1 viral load monitoring in a primary health care setting in Mozambique. J Clin Microbiol 54(8):2104–2108CrossRefPubMedPubMedCentral Jani IV, Meggi B, Vubil A, Sitoe NE, Bhatt N, Tobaiwa O et al (2016) Evaluation of the whole-blood Alere Q NAT point-of-care RNA assay for HIV-1 viral load monitoring in a primary health care setting in Mozambique. J Clin Microbiol 54(8):2104–2108CrossRefPubMedPubMedCentral
101.
go back to reference Scott L, Gous N, Carmona S, Stevens W (2015) Laboratory evaluation of the Liat HIV Quant (IQuum) whole-blood and plasma HIV-1 viral load assays for point-of-care testing in South Africa. J Clin Microbiol 53(5):1616–1621CrossRefPubMedPubMedCentral Scott L, Gous N, Carmona S, Stevens W (2015) Laboratory evaluation of the Liat HIV Quant (IQuum) whole-blood and plasma HIV-1 viral load assays for point-of-care testing in South Africa. J Clin Microbiol 53(5):1616–1621CrossRefPubMedPubMedCentral
102.
go back to reference Murtagh M (2013) HIV / AIDS diagnostic technology landscape. 3rd edition Murtagh M (2013) HIV / AIDS diagnostic technology landscape. 3rd edition
103.
go back to reference Pironti A, Walter H, Pfeifer N, Knops E, Lübke N, Büch J et al (2017) Determination of phenotypic resistance cutoffs from routine clinical data. J Acquir Immune Defic Syndr 74(5):e129–e137CrossRefPubMedPubMedCentral Pironti A, Walter H, Pfeifer N, Knops E, Lübke N, Büch J et al (2017) Determination of phenotypic resistance cutoffs from routine clinical data. J Acquir Immune Defic Syndr 74(5):e129–e137CrossRefPubMedPubMedCentral
104.
go back to reference Tsai HC, Chen IT, Lee SS, Chen YS (2018) HIV-1 genotypic drug resistance in patients with virological failure to single-tablet antiretroviral regimens in southern Taiwan. Infection & Drug Resistance 11:1061CrossRef Tsai HC, Chen IT, Lee SS, Chen YS (2018) HIV-1 genotypic drug resistance in patients with virological failure to single-tablet antiretroviral regimens in southern Taiwan. Infection & Drug Resistance 11:1061CrossRef
105.
go back to reference Mayers DL, Baxter JD (2017) Clinical implications of HIV-1 drug resistance. In: Mayers DL, Sobel JD, Ouellette M, Kaye KS, Marchaim D (eds) Antimicrobial drug resistance: clinical and epidemiological aspects, Volume 2. Springer International Publishing, Cham, pp 1213–1225 Mayers DL, Baxter JD (2017) Clinical implications of HIV-1 drug resistance. In: Mayers DL, Sobel JD, Ouellette M, Kaye KS, Marchaim D (eds) Antimicrobial drug resistance: clinical and epidemiological aspects, Volume 2. Springer International Publishing, Cham, pp 1213–1225
106.
go back to reference Pattery T, Verlinden Y, De Wolf H, Nauwelaers D, Van Baelen K, Van Houtte M et al (2012) Development and performance of conventional HIV-1 phenotyping (Antivirogram(R)) and genotype-based calculated phenotyping assay (virco(R)TYPE HIV-1) on protease and reverse transcriptase genes to evaluate drug resistance. Intervirology 55(2):138–146CrossRefPubMed Pattery T, Verlinden Y, De Wolf H, Nauwelaers D, Van Baelen K, Van Houtte M et al (2012) Development and performance of conventional HIV-1 phenotyping (Antivirogram(R)) and genotype-based calculated phenotyping assay (virco(R)TYPE HIV-1) on protease and reverse transcriptase genes to evaluate drug resistance. Intervirology 55(2):138–146CrossRefPubMed
107.
go back to reference Cahn P, Pozniak AL, Mingrone H, Shuldyakov A, Brites C, Andrade-Villanueva JF et al (2013) Dolutegravir versus raltegravir in antiretroviral-experienced, integrase-inhibitor-naive adults with HIV: week 48 results from the randomised, double-blind, non-inferiority SAILING study. Lancet 382(9893):700–708CrossRefPubMed Cahn P, Pozniak AL, Mingrone H, Shuldyakov A, Brites C, Andrade-Villanueva JF et al (2013) Dolutegravir versus raltegravir in antiretroviral-experienced, integrase-inhibitor-naive adults with HIV: week 48 results from the randomised, double-blind, non-inferiority SAILING study. Lancet 382(9893):700–708CrossRefPubMed
108.
go back to reference Westen GJPV, Hendriks A, Wegner JK, Ijzerman AP, Vlijmen HWTV, Bender A (2013) Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data. PLoS Comput Biol 9(2(2013-2-21)):e1002899CrossRefPubMedPubMedCentral Westen GJPV, Hendriks A, Wegner JK, Ijzerman AP, Vlijmen HWTV, Bender A (2013) Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data. PLoS Comput Biol 9(2(2013-2-21)):e1002899CrossRefPubMedPubMedCentral
109.
go back to reference Mohamed S, Penaranda G, Gonzalez D, Camus C, Khiri H, Boulmé R et al (2014) Clinical impact of ultra deep versus Sanger sequencing detection of minority mutations on HIV-1 drug resistance genotype interpretation after virological failure. Aids 14(S2):1–1 Mohamed S, Penaranda G, Gonzalez D, Camus C, Khiri H, Boulmé R et al (2014) Clinical impact of ultra deep versus Sanger sequencing detection of minority mutations on HIV-1 drug resistance genotype interpretation after virological failure. Aids 14(S2):1–1
110.
go back to reference Mekue MLC, Hélène P, Angélique NM, Donato K, Dieu LJD, François-Xavier MK et al (2015) LETTER TO THE EDITOR Performance of the ViroSeq® HIV-1 genotyping system V2.0 in Central Africa. Open Aids Journal 9(1):9–13CrossRef Mekue MLC, Hélène P, Angélique NM, Donato K, Dieu LJD, François-Xavier MK et al (2015) LETTER TO THE EDITOR Performance of the ViroSeq® HIV-1 genotyping system V2.0 in Central Africa. Open Aids Journal 9(1):9–13CrossRef
111.
go back to reference Paraschiv S, Otelea D, Baicus C, Tinischi M, Costache M, Neaga E (2009) Nucleoside reverse transcriptase inhibitor resistance mutations in subtype F1 strains isolated from heavily treated adolescents in Romania. Int J Infect Dis 13(1):81–89CrossRefPubMed Paraschiv S, Otelea D, Baicus C, Tinischi M, Costache M, Neaga E (2009) Nucleoside reverse transcriptase inhibitor resistance mutations in subtype F1 strains isolated from heavily treated adolescents in Romania. Int J Infect Dis 13(1):81–89CrossRefPubMed
112.
go back to reference Stelzl E, Proll J, Bizon B, Niklas N, Danzer M, Hackl C et al (2011) Human immunodeficiency virus type 1 drug resistance testing: evaluation of a new ultra-deep sequencing-based protocol and comparison with the TRUGENE HIV-1 genotyping kit. J Virol Methods 178(1–2):94–97CrossRefPubMed Stelzl E, Proll J, Bizon B, Niklas N, Danzer M, Hackl C et al (2011) Human immunodeficiency virus type 1 drug resistance testing: evaluation of a new ultra-deep sequencing-based protocol and comparison with the TRUGENE HIV-1 genotyping kit. J Virol Methods 178(1–2):94–97CrossRefPubMed
113.
go back to reference Duarte HA, Panpradist N, Beck IA, Lutz B, Lai J, Kanthula RM et al (2017) Current status of point-of-care testing for human immunodeficiency virus drug resistance. J Infect Dis 216(suppl_9):S824–s828CrossRefPubMedPubMedCentral Duarte HA, Panpradist N, Beck IA, Lutz B, Lai J, Kanthula RM et al (2017) Current status of point-of-care testing for human immunodeficiency virus drug resistance. J Infect Dis 216(suppl_9):S824–s828CrossRefPubMedPubMedCentral
114.
go back to reference Metzner KJ, Rauch P, Braun P, Knechten H, Ehret R, Korn K et al (2011) Prevalence of key resistance mutations K65R, K103N, and M184V as minority HIV-1 variants in chronically HIV-1 infected, treatment-naive patients. J Clin Virol 50(2):156–161CrossRefPubMed Metzner KJ, Rauch P, Braun P, Knechten H, Ehret R, Korn K et al (2011) Prevalence of key resistance mutations K65R, K103N, and M184V as minority HIV-1 variants in chronically HIV-1 infected, treatment-naive patients. J Clin Virol 50(2):156–161CrossRefPubMed
115.
go back to reference Grant RM, Liegler T, Defechereux P, Kashuba AD, Taylor D, Abdelmohsen M et al (2015) Drug resistance and plasma viral RNA level after ineffective use of oral pre-exposure prophylaxis in women. Aids 29(3):331CrossRefPubMed Grant RM, Liegler T, Defechereux P, Kashuba AD, Taylor D, Abdelmohsen M et al (2015) Drug resistance and plasma viral RNA level after ineffective use of oral pre-exposure prophylaxis in women. Aids 29(3):331CrossRefPubMed
116.
go back to reference Zhang G, Cai F, de Rivera IL, Zhou Z, Zhang J, Nkengasong J et al (2016) Simultaneous detection of major drug resistance mutations of HIV-1 subtype B viruses from dried blood spot specimens by multiplex allele-specific assay. J Clin Microbiol 54(1):220–222CrossRefPubMed Zhang G, Cai F, de Rivera IL, Zhou Z, Zhang J, Nkengasong J et al (2016) Simultaneous detection of major drug resistance mutations of HIV-1 subtype B viruses from dried blood spot specimens by multiplex allele-specific assay. J Clin Microbiol 54(1):220–222CrossRefPubMed
117.
go back to reference Clutter DS, Rojas Sanchez P, Rhee SY, Shafer RW (2016) Genetic variability of HIV-1 for drug resistance assay development. Viruses 8(2) Clutter DS, Rojas Sanchez P, Rhee SY, Shafer RW (2016) Genetic variability of HIV-1 for drug resistance assay development. Viruses 8(2)
118.
go back to reference Quinones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA (2014) Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 61(1):9–19CrossRefPubMedPubMedCentral Quinones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA (2014) Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 61(1):9–19CrossRefPubMedPubMedCentral
119.
go back to reference Thiam M, Diop-Ndiaye H, Kebe K, Vidal N, Diakhate-Lô R, Diouara AA et al (2013) Performance of the ViroSeq HIV-1 genotyping system V2.0 on HIV-1 strains circulating in Senegal. J Virol Methods 188(1–2):97–103CrossRefPubMed Thiam M, Diop-Ndiaye H, Kebe K, Vidal N, Diakhate-Lô R, Diouara AA et al (2013) Performance of the ViroSeq HIV-1 genotyping system V2.0 on HIV-1 strains circulating in Senegal. J Virol Methods 188(1–2):97–103CrossRefPubMed
120.
go back to reference Van Laethem K, Theys K, Vandamme AM (2015) HIV-1 genotypic drug resistance testing: digging deep, reaching wide? Curr Opin Virol 14:16–23CrossRefPubMed Van Laethem K, Theys K, Vandamme AM (2015) HIV-1 genotypic drug resistance testing: digging deep, reaching wide? Curr Opin Virol 14:16–23CrossRefPubMed
121.
go back to reference Johnson EO, Hancock DB, Gaddis NC, Levy JL, Page G, Novak SP et al (2015) Novel genetic locus implicated for HIV-1 acquisition with putative regulatory links to HIV replication and infectivity: a genome-wide association study. PLoS One 10(3):e0118149CrossRefPubMedPubMedCentral Johnson EO, Hancock DB, Gaddis NC, Levy JL, Page G, Novak SP et al (2015) Novel genetic locus implicated for HIV-1 acquisition with putative regulatory links to HIV replication and infectivity: a genome-wide association study. PLoS One 10(3):e0118149CrossRefPubMedPubMedCentral
122.
go back to reference McLaren PJ, Pulit SL, Gurdasani D, Bartha I, Shea PR, Pomilla C et al (2017) Evaluating the impact of functional genetic variation on HIV-1 control. J Infect Dis 216(9):1063–1069CrossRefPubMedPubMedCentral McLaren PJ, Pulit SL, Gurdasani D, Bartha I, Shea PR, Pomilla C et al (2017) Evaluating the impact of functional genetic variation on HIV-1 control. J Infect Dis 216(9):1063–1069CrossRefPubMedPubMedCentral
123.
go back to reference Skerlj RT, Bridger GJ, Kaller A, Mceachern EJ, Crawford JB, Zhou Y et al (2010) Discovery of novel small molecule orally bioavailable C-X-C chemokine receptor 4 antagonists that are potent inhibitors of T-tropic (X4) HIV-1 replication. J Med Chem 53(8):3376–3388CrossRefPubMed Skerlj RT, Bridger GJ, Kaller A, Mceachern EJ, Crawford JB, Zhou Y et al (2010) Discovery of novel small molecule orally bioavailable C-X-C chemokine receptor 4 antagonists that are potent inhibitors of T-tropic (X4) HIV-1 replication. J Med Chem 53(8):3376–3388CrossRefPubMed
124.
go back to reference Tsukamoto T (2018) Transcriptional gene silencing limits CXCR4-associated depletion of bone marrow CD34+ cells in HIV-1 infection. Aids 32(13):1737–1747CrossRefPubMed Tsukamoto T (2018) Transcriptional gene silencing limits CXCR4-associated depletion of bone marrow CD34+ cells in HIV-1 infection. Aids 32(13):1737–1747CrossRefPubMed
125.
go back to reference Liu Z, Chen S, Jin X, Wang Q, Yang K, Li C et al (2017) Genome editing of the HIV co-receptors CCR5 and CXCR4 by CRISPR-Cas9 protects CD4 + T cells from HIV-1 infection. Cell Biosci 7(1):47CrossRefPubMedPubMedCentral Liu Z, Chen S, Jin X, Wang Q, Yang K, Li C et al (2017) Genome editing of the HIV co-receptors CCR5 and CXCR4 by CRISPR-Cas9 protects CD4 + T cells from HIV-1 infection. Cell Biosci 7(1):47CrossRefPubMedPubMedCentral
126.
go back to reference D'Antoni ML, Paul RH, Mitchell BI, Kohorn L, Fischer L, Lefebvre E et al (2018) Improved cognitive performance and reduced monocyte activation in virally suppressed chronic HIV following dual CCR2 and CCR5 antagonism. J Acquir Immune Defic Syndr 79(1):1CrossRef D'Antoni ML, Paul RH, Mitchell BI, Kohorn L, Fischer L, Lefebvre E et al (2018) Improved cognitive performance and reduced monocyte activation in virally suppressed chronic HIV following dual CCR2 and CCR5 antagonism. J Acquir Immune Defic Syndr 79(1):1CrossRef
127.
go back to reference Ioannidis JPA, Rosenberg PS, Goedert JJ, Ashton LJ, Benfield TL, Buchbinder SP et al (2001) Effects of CCR5-Δ 32, CCR2-64I, and SDF-1 3′a alleles on HIV-1 disease progression: an international meta-analysis of individual-patient data. Ann Intern Med 135(9):782–795CrossRefPubMed Ioannidis JPA, Rosenberg PS, Goedert JJ, Ashton LJ, Benfield TL, Buchbinder SP et al (2001) Effects of CCR5-Δ 32, CCR2-64I, and SDF-1 3′a alleles on HIV-1 disease progression: an international meta-analysis of individual-patient data. Ann Intern Med 135(9):782–795CrossRefPubMed
128.
go back to reference Verheyen J, Thielen A, Lübke N, Dirks M, Widera M, Dittmer U, et al (2018) Rapid rebound of a preexisting CXCR4-tropic HIV variant after allogeneic transplantation with CCR5 delta32 homozygous stem cells. Clinical Infectious Diseases An Official Publication of the Infectious Diseases Society of America Verheyen J, Thielen A, Lübke N, Dirks M, Widera M, Dittmer U, et al (2018) Rapid rebound of a preexisting CXCR4-tropic HIV variant after allogeneic transplantation with CCR5 delta32 homozygous stem cells. Clinical Infectious Diseases An Official Publication of the Infectious Diseases Society of America
129.
go back to reference Mori M, Wichukchinda N, Miyahara R, Rojanawiwat A, Pathipvanich P, Maekawa T et al (2014) HLA-B*35: 05 is a protective allele with a unique structure among HIV-1 CRF01_AE-infected Thais, in whom the B*57 frequency is low. Aids 28(7):959–967CrossRefPubMed Mori M, Wichukchinda N, Miyahara R, Rojanawiwat A, Pathipvanich P, Maekawa T et al (2014) HLA-B*35: 05 is a protective allele with a unique structure among HIV-1 CRF01_AE-infected Thais, in whom the B*57 frequency is low. Aids 28(7):959–967CrossRefPubMed
130.
go back to reference Ragoussis J (2009) Genotyping technologies for genetic research. Annu Rev Genomics Hum Genet 10(1):117–133CrossRefPubMed Ragoussis J (2009) Genotyping technologies for genetic research. Annu Rev Genomics Hum Genet 10(1):117–133CrossRefPubMed
131.
go back to reference Dumoulin A, Hirsch HH (2011) Reevaluating and optimizing polyomavirus BK and JC real-time PCR assays to detect rare sequence polymorphisms. J Clin Microbiol 49(4):1382CrossRefPubMedPubMedCentral Dumoulin A, Hirsch HH (2011) Reevaluating and optimizing polyomavirus BK and JC real-time PCR assays to detect rare sequence polymorphisms. J Clin Microbiol 49(4):1382CrossRefPubMedPubMedCentral
132.
go back to reference Komninakis S, Fukumori L, Alcalde R, Cortina M, Abdala L, Brito A et al (2007) Techniques used to identify the Brazilian variant of HIV-1 subtype B. Braz J Med Biol Res 40(3):301CrossRefPubMed Komninakis S, Fukumori L, Alcalde R, Cortina M, Abdala L, Brito A et al (2007) Techniques used to identify the Brazilian variant of HIV-1 subtype B. Braz J Med Biol Res 40(3):301CrossRefPubMed
133.
go back to reference Devadas K, Biswas S, Haleyurgirisetty M, Wood O, Ragupathy V, Lee S et al (2016) Analysis of host gene expression profile in HIV-1 and HIV-2 infected T-cells. PLoS One 11(1):e0147421CrossRefPubMedPubMedCentral Devadas K, Biswas S, Haleyurgirisetty M, Wood O, Ragupathy V, Lee S et al (2016) Analysis of host gene expression profile in HIV-1 and HIV-2 infected T-cells. PLoS One 11(1):e0147421CrossRefPubMedPubMedCentral
135.
go back to reference Julia D, Nienke V, Tendai M, Bregje DBA, Otto SA, Hazenberg MD et al (2016) Reconciling longitudinal naive T-cell and TREC dynamics during HIV-1 infection. PLoS One 11(3):e0152513CrossRef Julia D, Nienke V, Tendai M, Bregje DBA, Otto SA, Hazenberg MD et al (2016) Reconciling longitudinal naive T-cell and TREC dynamics during HIV-1 infection. PLoS One 11(3):e0152513CrossRef
136.
go back to reference Touloumi G, Pantazis N, Karafoulidou A, Mandalaki T, Goedert JJ, Kostrikis LG et al (2004) Changes in T cell receptor excision DNA circle (TREC) levels in HIV type 1-infected subjects pre- and post-highly active antiretroviral therapy. Aids Research & Human Retroviruses 20(1):47–54CrossRef Touloumi G, Pantazis N, Karafoulidou A, Mandalaki T, Goedert JJ, Kostrikis LG et al (2004) Changes in T cell receptor excision DNA circle (TREC) levels in HIV type 1-infected subjects pre- and post-highly active antiretroviral therapy. Aids Research & Human Retroviruses 20(1):47–54CrossRef
138.
go back to reference Jones RB, Mueller S, O'Connor R, Rimpel K, Sloan DD, Karel D et al (2016) A subset of latency-reversing agents expose HIV-infected resting CD4+ T-cells to recognition by cytotoxic T-lymphocytes. PLoS Pathog 12(4):e1005545CrossRefPubMedPubMedCentral Jones RB, Mueller S, O'Connor R, Rimpel K, Sloan DD, Karel D et al (2016) A subset of latency-reversing agents expose HIV-infected resting CD4+ T-cells to recognition by cytotoxic T-lymphocytes. PLoS Pathog 12(4):e1005545CrossRefPubMedPubMedCentral
139.
go back to reference Yucha RW, Hobbs KS, Hanhauser E, Hogan LE, Nieves W, Ozen MO et al (2017) High-throughput characterization of HIV-1 reservoir reactivation using a single-cell-in-droplet PCR assay. Ebiomedicine 20(C):217–229CrossRefPubMedPubMedCentral Yucha RW, Hobbs KS, Hanhauser E, Hogan LE, Nieves W, Ozen MO et al (2017) High-throughput characterization of HIV-1 reservoir reactivation using a single-cell-in-droplet PCR assay. Ebiomedicine 20(C):217–229CrossRefPubMedPubMedCentral
140.
go back to reference Hancock G, Morónlópez S, Kopycinski J, Puertas MC, Giannoulatou E, Rose A et al (2017) Evaluation of the immunogenicity and impact on the latent HIV-1 reservoir of a conserved region vaccine, MVA.HIVconsv, in antiretroviral therapy-treated subjects. Journal of the International Aids Society 20(1):1CrossRef Hancock G, Morónlópez S, Kopycinski J, Puertas MC, Giannoulatou E, Rose A et al (2017) Evaluation of the immunogenicity and impact on the latent HIV-1 reservoir of a conserved region vaccine, MVA.HIVconsv, in antiretroviral therapy-treated subjects. Journal of the International Aids Society 20(1):1CrossRef
141.
go back to reference Mothe B, Climent N, Plana M, Rosà M, Luis J, Nez J et al (2015) Safety and immunogenicity of a modified vaccinia Ankara-based HIV-1 vaccine (MVA-B) in HIV-1-infected patients alone or in combination with a drug to reactivate latent HIV-1. J Antimicrob Chemother 70(6):1833–1842PubMed Mothe B, Climent N, Plana M, Rosà M, Luis J, Nez J et al (2015) Safety and immunogenicity of a modified vaccinia Ankara-based HIV-1 vaccine (MVA-B) in HIV-1-infected patients alone or in combination with a drug to reactivate latent HIV-1. J Antimicrob Chemother 70(6):1833–1842PubMed
142.
go back to reference Goo L, Jalalianlechak Z, Richardson BA, Overbaugh J (2012) A combination of broadly neutralizing HIV-1 monoclonal antibodies targeting distinct epitopes effectively neutralizes variants found in early infection. J Virol 86(19):10857–10861CrossRefPubMedPubMedCentral Goo L, Jalalianlechak Z, Richardson BA, Overbaugh J (2012) A combination of broadly neutralizing HIV-1 monoclonal antibodies targeting distinct epitopes effectively neutralizes variants found in early infection. J Virol 86(19):10857–10861CrossRefPubMedPubMedCentral
144.
go back to reference Stahl T, Böhme MU, Kröger N, Fehse B (2015) Digital PCR to assess hematopoietic chimerism after allogeneic stem cell transplantation. Exp Hematol 43(6):462–468.e461CrossRefPubMed Stahl T, Böhme MU, Kröger N, Fehse B (2015) Digital PCR to assess hematopoietic chimerism after allogeneic stem cell transplantation. Exp Hematol 43(6):462–468.e461CrossRefPubMed
145.
go back to reference Rosas-Umbert M, Mothe B, Noguera-Julian M, Bellido R, Puertas MC, Carrillo J et al (2017) Virological and immunological outcome of treatment interruption in HIV-1-infected subjects vaccinated with MVA-B. PLoS One 12(9):e0184929CrossRefPubMedPubMedCentral Rosas-Umbert M, Mothe B, Noguera-Julian M, Bellido R, Puertas MC, Carrillo J et al (2017) Virological and immunological outcome of treatment interruption in HIV-1-infected subjects vaccinated with MVA-B. PLoS One 12(9):e0184929CrossRefPubMedPubMedCentral
146.
go back to reference Maria JB, Enrique M-G, Florencia P, Zhengyu O, Hong S, Jonathan ZL et al (2014) Long-term antiretroviral treatment initiated at primary HIV-1 infection affects the size, composition, and decay kinetics of the reservoir of HIV-1-infected CD4 T cells. J Virol 88(17):10056–10065CrossRef Maria JB, Enrique M-G, Florencia P, Zhengyu O, Hong S, Jonathan ZL et al (2014) Long-term antiretroviral treatment initiated at primary HIV-1 infection affects the size, composition, and decay kinetics of the reservoir of HIV-1-infected CD4 T cells. J Virol 88(17):10056–10065CrossRef
147.
go back to reference Chaillon A, Gianella S, Lada SM, Perez-Santiago J, Jordan P, Ignacio C et al (2017) Size, composition, and evolution of HIV DNA populations during early antiretroviral therapy and intensification with Maraviroc. J Virol 92(3):JVI.01589–JVI.01517CrossRef Chaillon A, Gianella S, Lada SM, Perez-Santiago J, Jordan P, Ignacio C et al (2017) Size, composition, and evolution of HIV DNA populations during early antiretroviral therapy and intensification with Maraviroc. J Virol 92(3):JVI.01589–JVI.01517CrossRef
148.
go back to reference Bosman KJ, Nijhuis M, van Ham PM, Wensing AM, Vervisch K, Vandekerckhove L et al (2015) Comparison of digital PCR platforms and semi-nested qPCR as a tool to determine the size of the HIV reservoir. Sci Rep 5(2):13811CrossRefPubMedPubMedCentral Bosman KJ, Nijhuis M, van Ham PM, Wensing AM, Vervisch K, Vandekerckhove L et al (2015) Comparison of digital PCR platforms and semi-nested qPCR as a tool to determine the size of the HIV reservoir. Sci Rep 5(2):13811CrossRefPubMedPubMedCentral
149.
150.
go back to reference Strain MC, Lada SM, Luong T, Rought SE, Gianella S, Terry VH et al (2013) Highly precise measurement of HIV DNA by droplet digital PCR. PLoS One 8(4):e55943CrossRefPubMedPubMedCentral Strain MC, Lada SM, Luong T, Rought SE, Gianella S, Terry VH et al (2013) Highly precise measurement of HIV DNA by droplet digital PCR. PLoS One 8(4):e55943CrossRefPubMedPubMedCentral
151.
go back to reference Henrich TJ, Gallien S, Li JZ, Pereyra F, Kuritzkes DR (2012) Low-level detection and quantitation of cellular HIV-1 DNA and 2-LTR circles using droplet digital PCR. J Virol Methods 186(1–2):68–72CrossRefPubMedPubMedCentral Henrich TJ, Gallien S, Li JZ, Pereyra F, Kuritzkes DR (2012) Low-level detection and quantitation of cellular HIV-1 DNA and 2-LTR circles using droplet digital PCR. J Virol Methods 186(1–2):68–72CrossRefPubMedPubMedCentral
152.
go back to reference Ho Y, Shan L, Hosmane Nina N, Wang J, Laskey Sarah B, Rosenbloom Daniel IS et al (2013) Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell 155(3):540–551CrossRefPubMedPubMedCentral Ho Y, Shan L, Hosmane Nina N, Wang J, Laskey Sarah B, Rosenbloom Daniel IS et al (2013) Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell 155(3):540–551CrossRefPubMedPubMedCentral
153.
go back to reference Samson M, Labbe O, Mollereau C, Vassart G, Parmentier M (1996) Molecular cloning and functional expression of a new human CC-chemokine receptor gene. Biochemistry 35(11):3362–3367CrossRefPubMed Samson M, Labbe O, Mollereau C, Vassart G, Parmentier M (1996) Molecular cloning and functional expression of a new human CC-chemokine receptor gene. Biochemistry 35(11):3362–3367CrossRefPubMed
154.
go back to reference Hutter G, Nowak D, Mossner M, Ganepola S, Mussig A, Allers K et al (2009) Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. N Engl J Med 360(7):692–698CrossRefPubMed Hutter G, Nowak D, Mossner M, Ganepola S, Mussig A, Allers K et al (2009) Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. N Engl J Med 360(7):692–698CrossRefPubMed
155.
go back to reference Soriano V (2017) Hot news: gene therapy with CRISPR/Cas9 coming to age for HIV cure. AIDS Rev 19(3):167–172PubMed Soriano V (2017) Hot news: gene therapy with CRISPR/Cas9 coming to age for HIV cure. AIDS Rev 19(3):167–172PubMed
156.
go back to reference Zulfiqar HF, Javed A, Sumbal, Afroze B, Ali Q, Akbar K et al (2017) HIV diagnosis and treatment through advanced technologies. Front Public Health 5:32CrossRefPubMedPubMedCentral Zulfiqar HF, Javed A, Sumbal, Afroze B, Ali Q, Akbar K et al (2017) HIV diagnosis and treatment through advanced technologies. Front Public Health 5:32CrossRefPubMedPubMedCentral
157.
158.
go back to reference Wang Z, Pan Q, Gendron P, Zhu W, Guo F, Cen S et al (2016) CRISPR/Cas9-derived mutations both inhibit HIV-1 replication and accelerate viral escape. Cell Rep 15(3):481–489CrossRefPubMed Wang Z, Pan Q, Gendron P, Zhu W, Guo F, Cen S et al (2016) CRISPR/Cas9-derived mutations both inhibit HIV-1 replication and accelerate viral escape. Cell Rep 15(3):481–489CrossRefPubMed
159.
go back to reference Hütter G, Bodor J, Ledger S, Boyd M, Millington M, Tsie M et al (2015) CCR5 targeted cell therapy for HIV and prevention of viral escape. Viruses 7(8):4186–4203CrossRefPubMedPubMedCentral Hütter G, Bodor J, Ledger S, Boyd M, Millington M, Tsie M et al (2015) CCR5 targeted cell therapy for HIV and prevention of viral escape. Viruses 7(8):4186–4203CrossRefPubMedPubMedCentral
Metadata
Title
Nucleic acid testing and molecular characterization of HIV infections
Authors
Junpeng Zhao
Le Chang
Lunan Wang
Publication date
01-05-2019
Publisher
Springer Berlin Heidelberg
Published in
European Journal of Clinical Microbiology & Infectious Diseases / Issue 5/2019
Print ISSN: 0934-9723
Electronic ISSN: 1435-4373
DOI
https://doi.org/10.1007/s10096-019-03515-0

Other articles of this Issue 5/2019

European Journal of Clinical Microbiology & Infectious Diseases 5/2019 Go to the issue
Live Webinar | 27-06-2024 | 18:00 (CEST)

Keynote webinar | Spotlight on medication adherence

Live: Thursday 27th June 2024, 18:00-19:30 (CEST)

WHO estimates that half of all patients worldwide are non-adherent to their prescribed medication. The consequences of poor adherence can be catastrophic, on both the individual and population level.

Join our expert panel to discover why you need to understand the drivers of non-adherence in your patients, and how you can optimize medication adherence in your clinics to drastically improve patient outcomes.

Prof. Kevin Dolgin
Prof. Florian Limbourg
Prof. Anoop Chauhan
Developed by: Springer Medicine
Obesity Clinical Trial Summary

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.

Developed by: Springer Medicine