Allele-specific PCR; Chad; Drug resistance; HIV-1; Subtypes; Anti-HIV Agents; Humans; Alleles; Reproducibility of Results; Mutation; Polymerase Chain Reaction/methods; Drug Resistance, Viral/genetics; HIV-1/genetics; HIV Infections/diagnosis; HIV Infections/drug therapy; Anti-HIV Agents/pharmacology; Anti-HIV Agents/therapeutic use; Drug Resistance, Viral; HIV Infections; Polymerase Chain Reaction; Virology
Abstract :
[en] Allele-Specific Polymerase Chain Reaction (ASPCR) is an affordable point-mutation assay whose validation could improve the detection of HIV-1 drug resistance mutations (DRMs) in resource-limited settings (RLS). We assessed the performance of ASPCR onforty-four non-B HIV-1 plasma samples from patients who were ARV treated in failure in N'Djamena-Chad. Viral RNA was reverse-transcribed and amplified using LightCycler® FastStart DNA MasterPLUS SYBR Green I. Detection of six major DRMs (K70R, K103N, Y181C, M184V, T215F, T215Y) was evaluated on Roche LightCycler®480 automated system (with dilutions 0.01-100%). ASPCR-results were compared to Sanger-sequencing (gold-standard). Correlations of mutation curves were excellent (R2 >0.97); all DRMs were detected with desirable mutant/wild-type threshold differences (ΔCt≥9) except K70R(ΔCtK70R=6; ΔCtK103N=13; ΔCtM184V=9; ΔCtT215F=12; ΔCtT215Y=12; ΔCtY181C=9) and positive controls were below required thresholds. Also, ASPCR reproducibility on DRMs was assessed by using dilutions of intra-assay and inter-assay coefficient of variations respectively with a threshold of less than 50(i.e.<0.50 variation) which are;: K70R (0.02-0.28 vs. 0.12-0.37), K103N (0.08-0.42 vs. 0.12-0.37), Y181C (0.12-0.39 vs. 0.31-0.37), M184V (0.13-0.39 vs. 0.23-0.42), T215F (0.05-0.43 vs. 0.04-0.45) and T215Y (0.13-0.41 vs. 0.19-0.41). DRM detection-rate by ASPCR vs Sanger was respectively: M184V (63.6% vs. 38.6%); T215F (18.1% vs. 9.1%); T215Y (6.8% vs. 2.3%); K70R (4.5% vs. 2.3%). K103N (22.7% vs. 13.6%); Y181C (13.6% vs. 11.4%). Correlations of mutation curves were excellent (R2 >0.97); all DRMs were detected with desirable mutant/wild-type threshold differences (ΔCt≥9) except K70R(ΔCtK70R=6; ΔCtK103N=13; ΔCtM184V=9; ΔCtT215F=12; ΔCtT215Y=12; ΔCtY181C=9) and positive controls were below required thresholds. Also, ASPCR reproducibility on DRMs was assessed by using dilutions of intra-assay and inter-assay coefficient of variations respectively with a threshold of less than 50(i.e.<0.50 variation) which are;: K70R (0.02-0.28 vs. 0.12-0.37), K103N (0.08-0.42 vs. 0.12-0.37), Y181C (0.12-0.39 vs. 0.31-0.37), M184V (0.13-0.39 vs. 0.23-0.42), T215F (0.05-0.43 vs. 0.04-0.45) and T215Y (0.13-0.41 vs. 0.19-0.41). DRM detection-rate by ASPCR vs Sanger was respectively: M184V (63.6% vs. 38.6%); T215F (18.1% vs. 9.1%); T215Y (6.8% vs. 2.3%); K70R (4.5% vs. 2.3%). K103N (22.7% vs. 13.6%); Y181C (13.6% vs. 11.4%). ASPCR appears more efficient for detecting DRMs on diverse HIV-1 non-B circulating in RLS like Chad.
Disciplines :
Immunology & infectious disease
Author, co-author :
Adawaye, Chatté; National Institute of Sciences and Techniques of Abeche (INSTA), Abeche, Chad, Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium. Electronic address: cadawaye@yahoo.fr
Fokam, Joseph; Virology Laboratory, Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management, Yaoundé, Cameroon, Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Buea, Cameroon, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaounde, Cameroon, National HIV Drug Resistance Surveillance and Prevention Working Group (HIVDRWG), Ministry of Public Health, Yaounde, Cameroon. Electronic address: josephfokam@gmail.com
Kamangu, Erick Ntambwe; Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo, Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
Ngwese, Derrick Tambe Ayuk; Virology Laboratory, Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management, Yaoundé, Cameroon, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaounde, Cameroon, Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
SUSIN, Fabrice ; Centre Hospitalier Universitaire de Liège - CHU > > Service de microbiologie clinique
Moussa, Ali Mahamat; AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium, Faculty of Human Health Sciences, University of N'Djamena, N'Djamena, Chad, Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
Hig-Zounet, BertinTchombou; AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium, Faculty of Human Health Sciences, University of N'Djamena, N'Djamena, Chad, Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
Mad-Toingué, Joseph; AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium, Faculty of Human Health Sciences, University of N'Djamena, N'Djamena, Chad, Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
Tidjani, Abdelsalam; AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium, Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
VAIRA, Dolorès ; Centre Hospitalier Universitaire de Liège - CHU > > Service de microbiologie clinique
Moutschen, Michel ; Université de Liège - ULiège > GIGA > GIGA I3 - Immunology & Infectious Diseases
Language :
English
Title :
Performance characteristics of Allele-Specific PCR (ASPCR) in detecting drug resistance mutations among non-B HIV-1 Variants.
Adawaye, C., Fokam, J., Kamangu, E., Alio, H.M., Chahad, A.M., Susin, F., Moussa, A.M., Bertin, T.H., Tidjani, A., Vaira, D., Moutschen, M., Virological response, HIV-1 drug resistance mutations and genetic diversity among patients on first-line antiretroviral therapy in N'Djamena, Chad: findings from a cross-sectional study. BMC Res. Notes, 10, 2017, 589, 10.1186/s13104-017-2893-1.
Ameziane, N., Bogard, M., Lamoril, J., 2006. Principes de biologie moléculaire en biologie clinique, Campus référence.
Bennett, D., McCormick, L., Kline, R., Wheeler, W., Hemmen, M., Smith, A., Zaidi, I., Donolero, T., US surveillance of HIV drug resistance at diagnosis using HIV diagnostic sera. 12th Conf. Retrovir. Opportunistic Infect., 2005, 22–25.
Brun-Vézinet, F., Costagliola, D., Ait Khaled, M., Calvez, V., Clavel, F., Clotet, B., Haubrich, R., Kempf, D., King, M., Kuritzkes, D., Lanier, R., Miller, M., Miller, V., Phillips, A., Pillay, D., Schapiro, J., Scott, J., Shafer, R., Zazzi, M., Zolopa, A., DeGruttola, V., Clinically validated genotype analysis: guiding principles and statistical concerns. Antivir. Ther., 2004.
Buckton, A.J., Harris, R.J., Pillay, D., Cane, P.A., HIV type-1 drug resistance in treatment-naive patients monitored using minority species assays: a systematic review and meta-analysis. Antivir. Ther. 16 (2011), 9–16, 10.3851/IMP1687.
Cadranel, J., Giroux Leprieur, E., Prelevement et recherche de la mutation EGFR: quoi pr?lever, quand et comment tester. Rev. Pneumol. Clin. 67 (2011), S9–S14, 10.1016/S0761-8417(11)70004-9.
Calvez, V., Costagliola, D., Descamps, D., Yvon, A., Collin, G., Cécile, A., Delaugerre, C., Damond, F., Marcelin, A.G., Matheron, S., Simon, A., Valantin, M.A., Katlama, C., Brun-Vézinet, F., Impact of stavudine phenotype and thymidine analogues mutations on viral response to stavudine plus lamivudine in ALTIS 2 ANRS trial. Antivir. Ther. 7 (2002), 211–218.
Damond, F., Descamps, D., Résistance du VIH aux antirétroviraux: évaluations virologiques des thérapeutiques. Rev. Fr. Des. Lab. 1998 (1998), 51–55, 10.1016/S0338-9898(98)80139-X.
Ekici, H., Amogne, W., Aderaye, G., Lindquist, L., Sönnerborg, A., Abdurahman, S., Minority drug-resistant HIV-1 variants in treatment Naïve East-African and Caucasian patients detected by allele-specific real-time PCR. PLoS One, 9, 2014, e111042, 10.1371/journal.pone.0111042.
Eshleman, S.H., Mracna, M., Guay, L. a, Deseyve, M., Cunningham, S., Mirochnick, M., Musoke, P., Fleming, T., Glenn Fowler, M., Mofenson, L.M., Mmiro, F., Jackson, J.B., Selection and fading of resistance mutations in women and infants receiving nevirapine to prevent HIV-1 vertical transmission (HIVNET 012). AIDS 15 (2001), 1951–1957, 10.1097/00002030-200110190-00006.
Gaudet, M., Fara, A.-G., Beritognolo, I., Sabatti, M., Allele-specific PCR in SNP genotyping. Methods Mol. Biol., 2009, 415–424, 10.1007/978-1-60327-411-1_26.
Gianella, S., Richman, D.D., Minority variants of drug-resistant HIV. J. Infect. Dis. 202 (2010), 657–666, 10.1086/655397.
Grant, R.M., Kuritzkes, D.R., Johnson, V.A., Mellors, J.W., Sullivan, J.L., Swanstrom, R., D'Aquila, R.T., Van Gorder, M., Holodniy, M., Lloyd, R.M., Reid, C., Morgan, G.F., Winslow, D.L., Accuracy of the TRUGENE HIV-1 Genotyping Kit. J. Clin. Microbiol. 41 (2003), 1586–1593, 10.1128/JCM.41.4.1586-1593.2003.
Grant, Robert M, Hecht, Frederick M, Warmerdam, Maria, Liu, Lea, Liegler, Teri, Petropoulos, Christos J, Hellmann, Nicholas S, Chesney, Margaret, Busch, Michael P, Kahn, James O, Time trends in primary Hiv-1 drug resistance among recently infected persons. Infect. Dis. Clin. Pract., 11, 2002, 268, 10.1097/00019048-200205000-00060.
Guo, D.X., Li, H.P., Li, L., Zhuang, D.M., Jiao, L.Y., Wang, Z., Bao, Z.Y., Liu, S.Y., Liu, Y.J., Li, J.Y., Allele-specific real-time PCR testing for minor HIV-1 drug resistance mutations: assay preparation and application to reveal dynamic of mutations in vivo. Chin. Med. J. 123 (2010), 3389–3395, 10.3760/cma.j.issn.0366-6999.2010.23.003.
Gutsche, B.G., Jourdain, G., Ngo-Giang-Huong, N., Le Coeur, S., Bowonwatanuwong, C., Kantipong, P., Leechanachai, P., Ariyadej, S., Leenasirimakul, P., Hammer, S., Lallemant, M., Intrapartum exposure to nevirapine and subsequent maternal responses to nevirapine-based antiretroviral therapy. Surv. Anesth. 49 (2004), 229–240, 10.1097/01.sa.0000151210.76215.69.
Halvas, E.K., Aldrovandi, G.M., Balfe, P., Beck, I.A., Boltz, V.F., Coffin, J.M., Frenkel, L.M., Hazelwood, J.D., Johnson, V.A., Kearney, M., Kovacs, A., Kuritzkes, D.R., Metzner, K.J., Nissley, D.V., Nowicki, M., Palmer, S., Ziermann, R., Zhao, R.Y., Jennings, C.L., Bremer, J., Brambilla, D., Mellors, J.W., Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency. J. Clin. Microbiol. 44 (2006), 2612–2614, 10.1128/JCM.00449-06.
Hauser, A., Mugenyi, K., Kabasinguzi, R., Bluethgen, K., Kuecherer, C., Harms, G., Kunz, A., Detection and quantification of minor human immunodeficiency virus type 1 variants harboring K103N and Y181C resistance mutations in subtype A and D isolates by allele-specific real-time PCR. Antimicrob. Agents Chemother. 53 (2009), 2965–2973, 10.1128/AAC.01672-08.
Hirsch, M.S., Günthard, H.F., Schapiro, J.M., Brun-Vézinet, F., Clotet, B., Hammer, S.M., Johnson, V.A., Kuritzkes, D.R., Mellors, J.W., Pillay, D., Yeni, P.G., Jacobsen, D.M., Richman, D.D., Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an international AIDS society–USA panel. Clin. Infect. Dis. 47 (2008), 266–285, 10.1086/589297.
Jackson, J.B., Becker-Pergola, G., Guay, L.A., Musoke, P., Mracna, M., Fowler, M.G., Mofenson, L.M., Mirochnick, M., Mmiro, F., Eshleman, S.H., Identification of the K103N resistance mutation in Ugandan women receiving nevirapine to prevent HIV-1 vertical transmission. AIDS 14 (2000), F111–F115, 10.1097/00002030-200007280-00001.
Johnson, J.A., Li, J.F., Wei, X., Lipscomb, J., Irlbeck, D., Craig, C., Smith, A., Bennett, D.E., Monsour, M., Sandstrom, P., Lanier, E.R., Heneine, W., Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naïve populations and associate with reduced treatment efficacy. PLoS Med. 5 (2008), 1112–1122, 10.1371/journal.pmed.0050158.
Johnson, V. a, Brun-Vézinet, F., Clotet, B., Günthard, H.F., Kuritzkes, D.R., Pillay, D., Schapiro, J.M., Richman, D.D., Update of the drug resistance mutations in HIV-1: December 2010. Top. HIV Med. 18 (2010), 156–163.
Kellam, P., Boucher, C. a, Larder, B. a, Fifth mutation in human immunodeficiency virus type 1 reverse transcriptase contributes to the development of high-level resistance to zidovudine. Proc. Natl. Acad. Sci. 89 (1992), 1934–1938, 10.1073/pnas.89.5.1934.
Kuritzkes, D.R., Bassett, R.L., Hazelwood, J.D., Barrett, H., Rhodes, R. a, Young, R.K., Johnson, V.A., Adult ACTG Protocol 306 370 Teams. Rate of thymidine analogue resistance mutation accumulation with zidovudine- or stavudine-based regimens. J. Acquir. Immune Defic. Syndr. 36 (2004), 600–603, 10.1097/00126334-200405010-00008.
Larder, B. a, Kellam, P., Kemp, S.D., Zidovudine resistance predicted by direct detection of mutations in DNA from HIV-infected lymphocytes. AIDS 5 (1991), 137–144, 10.1097/00002030-199102000-00002.
Lecossier, D., Shulman, N.S., Morand-Joubert, L., Shafer, R.W., Joly, V., Zolopa, A.R., Clavel, F., Hance, A.J., Detection of minority populations of HIV-1 expressing the K103N resistance mutation in patients failing nevirapine. JAIDS J. Acquir. Immune Defic. Syndr. 38 (2005), 37–42, 10.1097/00126334-200501010-00007.
Loubser, S., Balfe, P., Sherman, G., Hammer, S., Kuhn, L., Morris, L., Decay of K103N mutants in cellular DNA and plasma RNA after single-dose nevirapine to reduce mother-to-child HIV transmission. AIDS 20 (2006), 995–1002, 10.1097/01.aids.0000222071.60620.1d.
Metzner, K.J., Bonhoeffer, S., Fischer, M., Karanicolas, R., Allers, K., Joos, B., Weber, R., Hirschel, B., Kostrikis, L.G., Günthard, H.F., Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions. J. Infect. Dis. 188 (2003), 1433–1443, 10.1086/379215.
Metzner, K.J., Rauch, P., Walter, H., Boesecke, C., Zöllner, B., Jessen, H., Schewe, K., Fenske, S., Gellermann, H., Stellbrink, H.-J., Detection of minor populations of drug-resistant HIV-1 in acute seroconverters. AIDS 19 (2005), 1819–1825, 10.1097/01.aids.0000189878.97480.ed.
Palmer, S., Kearney, M., Maldarelli, F., Halvas, E.K., Bixby, C.J., Bazmi, H., Rock, D., Falloon, J., Davey, R.T., Dewar, R.L., Metcalf, J.A., Hammer, S., Mellors, J.W., Coffin, J.M., Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J. Clin. Microbiol. 43 (2005), 406–413, 10.1128/JCM.43.1.406-413.2005.
Paredes, R., Marconi, V.C., Campbell, T.B., Kuritzkes, D.R., Systematic evaluation of allele-specific real-time PCR for the detection of minor HIV-1 variants with pol and env resistance mutations. J. Virol. Methods 146 (2007), 136–146, 10.1016/j.jviromet.2007.06.012.
Peuchant, O., Thi?baut, R., Capdepont, S., Lavignolle-Aurillac, V., Neau, D., Morlat, P., Dabis, F., Fleury, H., Masquelier, B., Transmission of HIV-1 minority-resistant variants and response to first-line antiretroviral therapy. AIDS 22 (2008), 1417–1423, 10.1097/QAD.0b013e3283034953.
Reed, G.F., Lynn, F., Meade, B.D., Use of coefficient of variation in assessing variability of quantitative assays. Clin. Diagn. Lab. Immunol. 9 (2002), 1235–1239, 10.1128/CDLI.9.6.1235-1239.2002.
Richman, D.D., Havlir, D., Corbeil, J., Looney, D., Ignacio, C., Spector, S. a, Sullivan, J., Cheeseman, S., Barringer, K., Pauletti, D., Nevirapine resistance mutations of human immunodeficiency virus type 1 selected during therapy. J. Virol. 68 (1994), 1660–1666.
Roquebert, B., Damond, F., Brun-Vézinet, F., Descamps, D., HIV genetic diversity and its consequences. Pathol. Biol. (Paris). 57 (2009), 142–148, 10.1016/j.patbio.2008.04.004.
Torti, C., Pozniak, A., Nelson, M., Hertogs, K., Gazzard, B.G., Distribution of K103N and/or Y181C HIV-1 mutations by exposure to zidovudine and non-nucleoside reverse transcriptase inhibitors. J. Antimicrob. Chemother. 48 (2001), 113–116.
Ugozzoli, L., Wallace, R.B., Application of an allele-specific polymerase chain reaction to the direct determination of ABO blood group genotypes. Genomics 12 (1992), 670–674, 10.1016/0888-7543(92)90292-Z.
Wei, X., Liang, C., Götte, M., Wainberg, M. a, The M184V mutation in HIV-1 reverse transcriptase reduces the restoration of wild-type replication by attenuated viruses. AIDS 16 (2002), 2391–2398, 10.1097/00002030-200212060-00003.
Wei, X., Liang, C., Götte, M., Wainberg, M.A., Negative effect of the M184V mutation in HIV-1 reverse transcriptase on initiation of viral DNA synthesis. Virology 311 (2003), 202–212, 10.1016/S0042-6822(03)00173-9.
Whitcomb, J.M., Parkin, N.T., Chappey, C., Hellmann, N.S., Petropoulos, C.J., Broad nucleoside reverse-transcriptase inhibitor cross-resistance in human immunodeficiency virus type 1 clinical isolates. J. Infect. Dis. 188 (2003), 992–1000, 10.1086/378281.
Wu, D.Y., Ugozzoli, L., Pal, B.K., Wallace, R.B., Allele-specific enzymatic amplification of beta-globin genomic DNA for diagnosis of sickle cell anemia. Proc. Natl. Acad. Sci. 86 (1989), 2757–2760, 10.1073/pnas.86.8.2757.
Yang, M., Donaldson, A.E., Marshall, C.E., Shen, J., Iacovitti, L., Studies on the differentiation of dopaminergic traits in human neural progenitor cells in vitro and in vivo. Cell Transpl. 13 (2004), 535–547, 10.1016/j.bbi.2008.05.010.
Yeni, P., 2008. Rapport du Groupe d'Experts 2008 sur la prise en charge médicale des patients infectées par le VIH, sous la direction du Pr Patrick Yeni. Paris.
