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Correlation between genotypic (V3 population sequencing) and phenotypic (Trofile ES) methods of characterizing co-receptor usage of HIV-1 from 200 treatment-naïve HIV patients screened for Study A4001078.

Portsmouth S, Valluri SR, Däumer M, Thiele B, Valdez H, Lewis M, Craig C, Thielen A, James I, Demarest J, Heera J.

Antiviral Res. 2013 Jan;97(1):60-5. doi: 10.1016/j.antiviral.2012.11.002. Epub 2012 Nov 16.


Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients.

Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Jensen MA, Thielen A, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR.

J Infect Dis. 2011 Jan 15;203(2):237-45. doi: 10.1093/infdis/jiq030.


Performance of genotypic algorithms for predicting HIV-1 tropism measured against the enhanced-sensitivity Trofile coreceptor tropism assay.

Sánchez V, Masiá M, Robledano C, Padilla S, Ramos JM, Gutiérrez F.

J Clin Microbiol. 2010 Nov;48(11):4135-9. doi: 10.1128/JCM.01204-10. Epub 2010 Sep 22.


Comparison of genotypic and phenotypic HIV type 1 tropism assay: results from the screening samples of Cenicriviroc Study 202, a randomized phase II trial in treatment-naive subjects.

Kagan RM, Johnson EP, Siaw MF, Van Baelen B, Ogden R, Platt JL, Pesano RL, Lefebvre E.

AIDS Res Hum Retroviruses. 2014 Feb;30(2):151-9. doi: 10.1089/AID.2013.0123. Epub 2013 Aug 14.


Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies.

McGovern RA, Thielen A, Mo T, Dong W, Woods CK, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR.

AIDS. 2010 Oct 23;24(16):2517-25. doi: 10.1097/QAD.0b013e32833e6cfb.


Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism.

Weber J, Vazquez AC, Winner D, Gibson RM, Rhea AM, Rose JD, Wylie D, Henry K, Wright A, King K, Archer J, Poveda E, Soriano V, Robertson DL, Olivo PD, Arts EJ, Quiñones-Mateu ME.

J Clin Microbiol. 2013 May;51(5):1517-27. doi: 10.1128/JCM.00092-13. Epub 2013 Mar 13.


Population-based sequencing of the V3-loop can predict the virological response to maraviroc in treatment-naive patients of the MERIT trial.

McGovern RA, Thielen A, Portsmouth S, Mo T, Dong W, Woods CK, Zhong X, Brumme CJ, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR.

J Acquir Immune Defic Syndr. 2012 Nov 1;61(3):279-86. doi: 10.1097/QAI.0b013e31826249cf.


Maraviroc treatment in non-R5-HIV-1-infected patients results in the selection of extreme CXCR4-using variants with limited effect on the total viral setpoint.

McGovern RA, Symons J, Poon AF, Harrigan PR, van Lelyveld SF, Hoepelman AI, van Ham PM, Dong W, Wensing AM, Nijhuis M.

J Antimicrob Chemother. 2013 Sep;68(9):2007-14. doi: 10.1093/jac/dkt153. Epub 2013 May 14.


Genotypic analysis of the V3 region of HIV from virologic nonresponders to maraviroc-containing regimens reveals distinct patterns of failure.

Swenson LC, Chui CK, Brumme CJ, Chan D, Woods CK, Mo T, Dong W, Chapman D, Lewis M, Demarest JF, James I, Portsmouth S, Goodrich J, Heera J, Valdez H, Harrigan PR.

Antimicrob Agents Chemother. 2013 Dec;57(12):6122-30. doi: 10.1128/AAC.01534-13. Epub 2013 Sep 30.


A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients.

Kagan RM, Johnson EP, Siaw M, Biswas P, Chapman DS, Su Z, Platt JL, Pesano RL.

PLoS One. 2012;7(9):e46334. doi: 10.1371/journal.pone.0046334. Epub 2012 Sep 27.


Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping.

Prosperi MC, Bracciale L, Fabbiani M, Di Giambenedetto S, Razzolini F, Meini G, Colafigli M, Marzocchetti A, Cauda R, Zazzi M, De Luca A.

Retrovirology. 2010 Jun 30;7:56. doi: 10.1186/1742-4690-7-56.


Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc.

Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Thielen A, Jensen MA, Knapp DJ, Chapman D, Portsmouth S, Lewis M, James I, Heera J, Valdez H, Harrigan PR.

Clin Infect Dis. 2011 Oct;53(7):732-42. doi: 10.1093/cid/cir493.


Evolution of proviral DNA HIV-1 tropism under selective pressure of maraviroc-based therapy.

Baroncelli S, Galluzzo CM, Weimer LE, Pirillo MF, Volpe A, Mercuri A, Cavalli A, Fragola V, Monno L, Degli Antoni A, Ladisa N, Francisci D, Bucciardini R, Floridia M.

J Antimicrob Chemother. 2012 Jun;67(6):1479-85. doi: 10.1093/jac/dks055. Epub 2012 Feb 23.


Evaluation of the genotypic prediction of HIV-1 coreceptor use versus a phenotypic assay and correlation with the virological response to maraviroc: the ANRS GenoTropism study.

Recordon-Pinson P, Soulié C, Flandre P, Descamps D, Lazrek M, Charpentier C, Montes B, Trabaud MA, Cottalorda J, Schneider V, Morand-Joubert L, Tamalet C, Desbois D, Macé M, Ferré V, Vabret A, Ruffault A, Pallier C, Raymond S, Izopet J, Reynes J, Marcelin AG, Masquelier B; ANRS AC11 Resistance Study Group.

Antimicrob Agents Chemother. 2010 Aug;54(8):3335-40. doi: 10.1128/AAC.00148-10. Epub 2010 Jun 7.


HIV-1 tropism determination using a phenotypic Env recombinant viral assay highlights overestimation of CXCR4-usage by genotypic prediction algorithms for CRF01_AE and CRF02_AG [corrected].

Mulinge M, Lemaire M, Servais JY, Rybicki A, Struck D, da Silva ES, Verhofstede C, Lie Y, Seguin-Devaux C, Schmit JC, Bercoff DP.

PLoS One. 2013 May 8;8(5):e60566. doi: 10.1371/journal.pone.0060566. Print 2013. Erratum in: PLoS One. 2013;8(7). doi:10.1371/annotation/7c0b830d-e75d-4128-ab54-7d5ecfd99d19.


Co-receptor usage and prediction of V3 genotyping algorithms in HIV-1 subtype B' from paid blood donors experienced anti-retroviral therapy in Chinese central province.

Qu S, Ma L, Yuan L, Xu W, Hong K, Xing H, Huang Y, Yu X, Shao Y.

Virol J. 2010 Oct 22;7:280. doi: 10.1186/1743-422X-7-280.


High concordance of genotypic coreceptor prediction in plasma-viral RNA and proviral DNA of HIV-1 subtype C: implications for use of whole blood DNA in resource-limited settings.

Gupta S, Neogi U, Srinivasa H, Shet A.

J Antimicrob Chemother. 2013 Sep;68(9):2003-6. doi: 10.1093/jac/dkt138. Epub 2013 Apr 30.


Evaluation of genotypic tropism prediction tests compared with in vitro co-receptor usage in HIV-1 primary isolates of diverse subtypes.

Delgado E, Fernández-García A, Vega Y, Cuevas T, Pinilla M, García V, Sánchez M, González M, Sánchez AM, Thomson MM, Pérez-Álvarez L.

J Antimicrob Chemother. 2012 Jan;67(1):25-31. doi: 10.1093/jac/dkr438. Epub 2011 Oct 18.


Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism.

Gibson RM, Meyer AM, Winner D, Archer J, Feyertag F, Ruiz-Mateos E, Leal M, Robertson DL, Schmotzer CL, Quiñones-Mateu ME.

Antimicrob Agents Chemother. 2014;58(4):2167-85. doi: 10.1128/AAC.02710-13. Epub 2014 Jan 27.


Discordance in HIV-1 co-receptor use prediction by different genotypic algorithms and phenotype assay: intermediate profile in relation to concordant predictions.

Trabaud MA, Icard V, Scholtes C, Perpoint T, Koffi J, Cotte L, Makhloufi D, Tardy JC, André P.

J Med Virol. 2012 Mar;84(3):402-13. doi: 10.1002/jmv.23209.

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