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Volumn 31, Issue 6, 2015, Pages 658-668

Primer ID informs next-generation sequencing platforms and reveals preexisting drug resistance mutations in the HIV-1 reverse transcriptase coding domain

Author keywords

[No Author keywords available]

Indexed keywords

EFAVIRENZ; NEVIRAPINE; NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE INHIBITOR; PRIMER DNA; REVERSE TRANSCRIPTASE, HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84930239847     PISSN: 08892229     EISSN: 19318405     Source Type: Journal    
DOI: 10.1089/aid.2014.0031     Document Type: Article
Times cited : (40)

References (37)
  • 1
    • 77953913629 scopus 로고    scopus 로고
    • AIDS-defining opportunistic illnesses in US patients, 1994-2007: A cohort study
    • Buchacz K, Baker RK, Palella FJ Jr, et al.: AIDS-defining opportunistic illnesses in US patients, 1994-2007: A cohort study. AIDS 2010;24(10):1549-1559.
    • (2010) AIDS , vol.24 , Issue.10 , pp. 1549-1559
    • Buchacz, K.1    Baker, R.K.2    Palella, F.J.3
  • 2
    • 0037072066 scopus 로고    scopus 로고
    • Prognosis of HIV-1-infected patients starting highly active antiretroviral therapy: A collaborative analysis of prospective studies
    • Egger M, May M, Chene G, et al.: Prognosis of HIV-1-infected patients starting highly active antiretroviral therapy: A collaborative analysis of prospective studies. Lancet 2002;360(9327):119-129.
    • (2002) Lancet , vol.360 , Issue.9327 , pp. 119-129
    • Egger, M.1    May, M.2    Chene, G.3
  • 3
    • 84867520947 scopus 로고    scopus 로고
    • Improvement in the health of HIV-infected persons in care: Reducing disparities
    • Moore RD, Keruly JC, and Bartlett JG: Improvement in the health of HIV-infected persons in care: Reducing disparities. Clin Infect Dis 2012;55(9):1242-1251.
    • (2012) Clin Infect Dis , vol.55 , Issue.9 , pp. 1242-1251
    • Moore, R.D.1    Keruly, J.C.2    Bartlett, J.G.3
  • 4
    • 1442355578 scopus 로고    scopus 로고
    • HIV drug resistance
    • Clavel F and Hance AJ: HIV drug resistance. N Engl J Med 2004;350(10):1023-1035.
    • (2004) N Engl J Med , vol.350 , Issue.10 , pp. 1023-1035
    • Clavel, F.1    Hance, A.J.2
  • 5
    • 46349112103 scopus 로고    scopus 로고
    • Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 Recommendations of an International AIDS Society-USA Panel
    • Hirsch MS, Gunthard HF, Schapiro JM, et al.: Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 Recommendations of an International AIDS Society-USA Panel. Clin Infect Dis 2008;47(2):266-285.
    • (2008) Clin Infect Dis , vol.47 , Issue.2 , pp. 266-285
    • Hirsch, M.S.1    Gunthard, H.F.2    Schapiro, J.M.3
  • 6
    • 33947375214 scopus 로고    scopus 로고
    • High rates of forward transmission events after acute/early HIV-1 infection
    • Brenner BG, Roger M, Routy JP, et al.: High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis 2007;195(7):951-959.
    • (2007) J Infect Dis , vol.195 , Issue.7 , pp. 951-959
    • Brenner, B.G.1    Roger, M.2    Routy, J.P.3
  • 7
    • 68449091365 scopus 로고    scopus 로고
    • The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection
    • Yerly S, Junier T, Gayet-Ageron A, et al.: The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection. AIDS 2009;23(11):1415-1423.
    • (2009) AIDS , vol.23 , Issue.11 , pp. 1415-1423
    • Yerly, S.1    Junier, T.2    Gayet-Ageron, A.3
  • 8
    • 77950229329 scopus 로고    scopus 로고
    • Impact of transmitted drug-resistance on treatment selection and outcome of firstline highly active antiretroviral therapy (HAART)
    • Bansi L, Geretti AM, Dunn D, et al.: Impact of transmitted drug-resistance on treatment selection and outcome of firstline highly active antiretroviral therapy (HAART). J Acquir Immune Defic Syndr 2010;53(5):633-639.
    • (2010) J Acquir Immune Defic Syndr , vol.53 , Issue.5 , pp. 633-639
    • Bansi, L.1    Geretti, A.M.2    Dunn, D.3
  • 9
    • 35448943576 scopus 로고    scopus 로고
    • Impact of transmission of drug-resistant HIV on the course of infection and the treatment success
    • Poggensee G, Kucherer C, Werning J, et al.: Impact of transmission of drug-resistant HIV on the course of infection and the treatment success. Data from the German HIV-1 Seroconverter Study. HIV Med 2007;8(8):511-519.
    • (2007) Data from the German HIV-1 Seroconverter Study. HIV Med , vol.8 , Issue.8 , pp. 511-519
    • Poggensee, G.1    Kucherer, C.2    Werning, J.3
  • 10
    • 79955477986 scopus 로고    scopus 로고
    • Effect of transmitted drug resistance on virological and immunological response to initial combination antiretroviral therapy for HIV (EuroCoord-CHAIN joint project): A European multicohort study
    • Wittkop L, Gunthard HF, de Wolf F, et al.: Effect of transmitted drug resistance on virological and immunological response to initial combination antiretroviral therapy for HIV (EuroCoord-CHAIN joint project): A European multicohort study. Lancet Infect Dis 2011;11(5):363-371.
    • (2011) Lancet Infect Dis , vol.11 , Issue.5 , pp. 363-371
    • Wittkop, L.1    Gunthard, H.F.2    De Wolf, F.3
  • 12
    • 19944428265 scopus 로고    scopus 로고
    • Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis
    • 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 Microbiol 2005;43(1): 406-413.
    • (2005) J Clin Microbiol , vol.43 , Issue.1 , pp. 406-413
    • Palmer, S.1    Kearney, M.2    Maldarelli, F.3
  • 13
    • 79551612715 scopus 로고    scopus 로고
    • Low level of the K103N HIV-1 above a threshold is associated with virological failure in treatment-naive individuals undergoing efavirenz-containing therapy
    • Goodman DD, Zhou Y, Margot NA, et al.: Low level of the K103N HIV-1 above a threshold is associated with virological failure in treatment-naive individuals undergoing efavirenz-containing therapy. AIDS 2011;25(3): 325-333.
    • (2011) AIDS , vol.25 , Issue.3 , pp. 325-333
    • Goodman, D.D.1    Zhou, Y.2    Margot, N.A.3
  • 14
    • 75749155415 scopus 로고    scopus 로고
    • Transmission of HIV-1 drug-resistant variants: Prevalence and effect on treatment outcome
    • Jakobsen MR, Tolstrup M, Sogaard OS, et al.: Transmission of HIV-1 drug-resistant variants: Prevalence and effect on treatment outcome. Clin Infect Dis 2010;50(4): 566-573.
    • (2010) Clin Infect Dis , vol.50 , Issue.4 , pp. 566-573
    • Jakobsen, M.R.1    Tolstrup, M.2    Sogaard, O.S.3
  • 15
    • 33750470308 scopus 로고    scopus 로고
    • Baseline detection of lowfrequency drug resistance-associated mutations is strongly associated with virological failure in previously antiretroviral-naive HIV-1-infected persons
    • Johnson JA, Li JF, Wei X, et al.: Baseline detection of lowfrequency drug resistance-associated mutations is strongly associated with virological failure in previously antiretroviral-naive HIV-1-infected persons. Antivir Ther 2006; 11(5):S79.
    • (2006) Antivir Ther , vol.11 , Issue.5 , pp. S79
    • Johnson, J.A.1    Li, J.F.2    Wei, X.3
  • 16
    • 77955199812 scopus 로고    scopus 로고
    • Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naive subjects in the CASTLE study
    • Lataillade M, Chiarella J, Yang R, et al.: Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naive subjects in the CASTLE study. PLoS One 2010;5(6):e10952.
    • (2010) PLoS One , vol.5 , Issue.6 , pp. e10952
    • Lataillade, M.1    Chiarella, J.2    Yang, R.3
  • 17
    • 61849172898 scopus 로고    scopus 로고
    • Lowabundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes
    • Simen BB, Simons JF, Hullsiek KH, et al.: Lowabundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 2009; 199(5):693-701.
    • (2009) J Infect Dis , vol.199 , Issue.5 , pp. 693-701
    • Simen, B.B.1    Simons, J.F.2    Hullsiek, K.H.3
  • 18
    • 78951491603 scopus 로고    scopus 로고
    • Prevalence of key resistance mutations K65R, K103N, and M184V as minority HIV-1 variants in chronically HIV-1 infected, treatment-naive patients
    • Metzner KJ, Rauch P, Braun P, et al.: 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 2011;50(2):156-161.
    • (2011) J Clin Virol , vol.50 , Issue.2 , pp. 156-161
    • Metzner, K.J.1    Rauch, P.2    Braun, P.3
  • 19
    • 27544452984 scopus 로고    scopus 로고
    • Detection of minor populations of drug-resistant HIV-1 in acute seroconverters
    • Metzner KJ, Rauch P, Walter H, et al.: Detection of minor populations of drug-resistant HIV-1 in acute seroconverters. AIDS 2005;19(16):1819-1825.
    • (2005) AIDS , vol.19 , Issue.16 , pp. 1819-1825
    • Metzner, K.J.1    Rauch, P.2    Walter, H.3
  • 20
    • 34547829263 scopus 로고    scopus 로고
    • DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations
    • Hoffmann C, Minkah N, Leipzig J, et al.: DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 2007;35(13):e91.
    • (2007) Nucleic Acids Res , vol.35 , Issue.13 , pp. e91
    • Hoffmann, C.1    Minkah, N.2    Leipzig, J.3
  • 21
    • 79956044149 scopus 로고    scopus 로고
    • Accuracy and quality assessment of 454 GS-FLX titanium pyrosequencing
    • Gilles A, Meglecz E, Pech N, et al.: Accuracy and quality assessment of 454 GS-FLX titanium pyrosequencing. BMC Genom 2011;12:245.
    • (2011) BMC Genom , vol.12 , pp. 245
    • Gilles, A.1    Meglecz, E.2    Pech, N.3
  • 22
    • 34547643929 scopus 로고    scopus 로고
    • Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance
    • Wang C, Mitsuya Y, Gharizadeh B, et al.: Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance. Genome Res 2007; 17(8):1195-1201.
    • (2007) Genome Res , vol.17 , Issue.8 , pp. 1195-1201
    • Wang, C.1    Mitsuya, Y.2    Gharizadeh, B.3
  • 23
    • 0344629203 scopus 로고    scopus 로고
    • Bias and artifacts in multitemplate polymerase chain reactions (PCR)
    • Kanagawa T: Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng 2003;96(4): 317-323.
    • (2003) J Biosci Bioeng , vol.96 , Issue.4 , pp. 317-323
    • Kanagawa, T.1
  • 24
    • 0029817259 scopus 로고    scopus 로고
    • HIV quasispecies and resampling
    • Liu SL, Rodrigo AG, Shankarappa R, et al.: HIV quasispecies and resampling. Science 1996;273(5274):415-416.
    • (1996) Science , vol.273 , Issue.5274 , pp. 415-416
    • Liu, S.L.1    Rodrigo, A.G.2    Shankarappa, R.3
  • 25
    • 84055200527 scopus 로고    scopus 로고
    • Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID
    • Jabara CB, Jones CD, Roach J, et al.: Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci USA 2011;108(50):20166-20171.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.50 , pp. 20166-20171
    • Jabara, C.B.1    Jones, C.D.2    Roach, J.3
  • 26
    • 33748664202 scopus 로고    scopus 로고
    • Factors associated with fewer visits for HIV primary care at a tertiary care center in the Southeastern US
    • Napravnik S, Eron JJ Jr, McKaig RG, et al.: Factors associated with fewer visits for HIV primary care at a tertiary care center in the Southeastern U.S. AIDS Care 2006; 18(Suppl 1):S45-50.
    • (2006) AIDS Care , vol.18 , pp. S45-50
    • Napravnik, S.1    Eron, J.J.2    McKaig, R.G.3
  • 27
    • 0042121237 scopus 로고    scopus 로고
    • Multiple sequence alignment with the Clustal series of programs
    • Chenna R, Sugawara H, Koike T, et al.: Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003;31(13):3497-3500.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3497-3500
    • Chenna, R.1    Sugawara, H.2    Koike, T.3
  • 28
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, Peterson D, Peterson N, et al.: MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28(10):2731-2739.
    • (2011) Mol Biol Evol , vol.28 , Issue.10 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3
  • 29
    • 62749200513 scopus 로고    scopus 로고
    • Drug resistance mutations for surveillance of transmitted HIV-1 drugresistance: 2009 update
    • Bennett DE, Camacho RJ, Otelea D, et al.: Drug resistance mutations for surveillance of transmitted HIV-1 drugresistance: 2009 update. PLoS One 2009;4(3):e4724.
    • (2009) PLoS One , vol.4 , Issue.3 , pp. e4724
    • Bennett, D.E.1    Camacho, R.J.2    Otelea, D.3
  • 30
    • 77956204474 scopus 로고    scopus 로고
    • Nucleic acid template and the risk of a PCR-induced HIV-1 drug resistance mutation
    • Varghese V, Wang E, Babrzadeh F, et al.: Nucleic acid template and the risk of a PCR-induced HIV-1 drug resistance mutation. PLoS One 2010;5(6):e10992.
    • (2010) PLoS One , vol.5 , Issue.6 , pp. e10992
    • Varghese, V.1    Wang, E.2    Babrzadeh, F.3
  • 31
    • 0033918632 scopus 로고    scopus 로고
    • A note on robust variance estimation for cluster-correlated data
    • Williams RL: A note on robust variance estimation for cluster-correlated data. Biometrics 2000;56(2):645-646.
    • (2000) Biometrics , vol.56 , Issue.2 , pp. 645-646
    • Williams, R.L.1
  • 32
    • 40949107410 scopus 로고    scopus 로고
    • Preexisting resistance to nonnucleoside reverse-transcriptase inhibitors predicts virologic failure of an efavirenz-based regimen in treatment-naive HIV-1-infected subjects
    • Kuritzkes DR, Lalama CM, Ribaudo HJ, et al.: Preexisting resistance to nonnucleoside reverse-transcriptase inhibitors predicts virologic failure of an efavirenz-based regimen in treatment-naive HIV-1-infected subjects. J Infect Dis 2008;197(6):867-870.
    • (2008) J Infect Dis , vol.197 , Issue.6 , pp. 867-870
    • Kuritzkes, D.R.1    Lalama, C.M.2    Ribaudo, H.J.3
  • 33
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley DR, Balasubramanian S, Swerdlow HP, et al.: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008;456(7218):53-59.
    • (2008) Nature , vol.456 , Issue.7218 , pp. 53-59
    • Bentley, D.R.1    Balasubramanian, S.2    Swerdlow, H.P.3
  • 34
    • 79551545281 scopus 로고    scopus 로고
    • Large scale loss of data in low-diversity illumina sequencing libraries can be recovered by deferred cluster calling
    • Krueger F, Andrews SR, and Osborne CS: Large scale loss of data in low-diversity illumina sequencing libraries can be recovered by deferred cluster calling. PLoS One 2011;6(1):e16607.
    • (2011) PLoS One , vol.6 , Issue.1 , pp. e16607
    • Krueger, F.1    Andrews, S.R.2    Osborne, C.S.3
  • 35
    • 77956042549 scopus 로고    scopus 로고
    • Reduced fitness in cell culture of HIV-1 with nonnucleoside reverse transcriptase inhibitor-resistant mutations correlates with relative levels of reverse transcriptase content and RNase H activity in virions
    • Wang J, Bambara RA, Demeter LM, and Dykes C: Reduced fitness in cell culture of HIV-1 with nonnucleoside reverse transcriptase inhibitor-resistant mutations correlates with relative levels of reverse transcriptase content and RNase H activity in virions. J Virol 2010;84(18):9377-9389.
    • (2010) J Virol , vol.84 , Issue.18 , pp. 9377-9389
    • Wang, J.1    Bambara, R.A.2    Demeter, L.M.3    Dykes, C.4
  • 36
    • 84879149218 scopus 로고    scopus 로고
    • L74V increases the reverse transcriptase content of HIV-1 virions with nonnucleoside reverse transcriptase drug-resistant mutations L100I + K103N and K101E + G190S, which results in increased fitness
    • Wang J, Li D, Bambara RA, et al.: L74V increases the reverse transcriptase content of HIV-1 virions with nonnucleoside reverse transcriptase drug-resistant mutations L100I + K103N and K101E + G190S, which results in increased fitness. J Gen Virol 2013;94(Pt 7):1597-1607.
    • (2013) J Gen Virol , vol.94 , pp. 1597-1607
    • Wang, J.1    Li, D.2    Bambara, R.A.3
  • 37
    • 79953745195 scopus 로고    scopus 로고
    • Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: A systematic review and pooled analysis
    • Li JZ, Paredes R, Ribaudo HJ, et al.: Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: A systematic review and pooled analysis. JAMA 2011;305(13):1327-1335.
    • (2011) JAMA , vol.305 , Issue.13 , pp. 1327-1335
    • Li, J.Z.1    Paredes, R.2    Ribaudo, H.J.3


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