Parameters influencing baseline HIV-1 genotypic tropism testing related to clinical outcome in patients on maraviroc

PLoS ONE

Volumn 10, Issue 5, 2015, Pages

  Sierra, Saleta ^a   Dybowski, J Nikolai ^b   Pironti, Alejandro ^c   Heider, Dominik ^b,e   Güney, Lisa ^a   Thielen, Alex ^c,f   Reuter, Stefan ^d,g   Esser, Stefan ^b   Fätkenheuer, Gerd ^a   Lengauer, Thomas ^c   Hoffmann, Daniel ^b   Pfister, Herbert ^a   Jensen, Björn ^d   Kaiser, Rolf ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

^b UNIVERSITY OF DUISBURG ESSEN   (Germany)

^c MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^d UNIVERSITY HOSPITAL DÜSSELDORF   (Germany)

^e TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^f Technische University   (Germany)

^g KLINIKUM LEVERKUSEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MARAVIROC; CYCLOHEXANE DERIVATIVE; HUMAN IMMUNODEFICIENCY VIRUS FUSION INHIBITOR; TRIAZOLE DERIVATIVE;

ADULT; AGED; ARTICLE; CD4 LYMPHOCYTE COUNT; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA DETERMINATION; DNA SEQUENCE; ENHANCED TROFILE ASSAY; FEMALE; GENE AMPLIFICATION; GENOTYPIC SUSCEPTIBILITY SCORE; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; MAJOR CLINICAL STUDY; MALE; MEDICATION COMPLIANCE; MUTATION; NEXT GENERATION SEQUENCING; PREDICTION; RNA ANALYSIS; RNA SEQUENCE; SCORING SYSTEM; SEQUENCE ANALYSIS; T CUP ANALYSIS; TREATMENT RESPONSE; VIRAL TROPISM; VIRUS DETECTION; VIRUS LOAD; ADOLESCENT; DRUG EFFECTS; GENETIC ASSOCIATION STUDY; GENETICS; GENOTYPE; HIV INFECTIONS; MIDDLE AGED; TREATMENT OUTCOME; VERY ELDERLY; VIROLOGY; VIRUS GENE; YOUNG ADULT;

HUMAN IMMUNODEFICIENCY VIRUS 1;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; CYCLOHEXANES; FEMALE; GENES, VIRAL; GENETIC ASSOCIATION STUDIES; GENOTYPE; HIV FUSION INHIBITORS; HIV INFECTIONS; HIV-1; HUMANS; MALE; MIDDLE AGED; TREATMENT OUTCOME; TRIAZOLES; VIRAL TROPISM; YOUNG ADULT;

EID: 84929376775     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0125502     Document Type: Article

References (51)

1. Cooper DA, Heera J, Goodrich J, Tawadrous M, Saag M, Dejesus E, et al. Maraviroc versus efavirenz, both in combination with zidovudine-lamivudine, for the treatment of antiretroviral-naive subjects with CCR5-tropic HIV-1 infection. J Infect Dis. 2010; 201: 803-813. doi: 10.1086/650697 PMID: 20151839
2. Gulick RM, Lalezari J, Goodrich J, Clumeck N, DeJesus E, Horban A, et al. Maraviroc for previously treated patients with R5 HIV-1 infection. N Engl J Med. 2008; 359: 1429-1441. doi: 10.1056/NEJMoa0803152 PMID: 18832244
3. Fatkenheuer G, Nelson M, Lazzarin A, Konourina I, Hoepelman AI, Lampiris H, et al. Subgroup analyses of maraviroc in previously treated R5 HIV-1 infection. N Engl J Med. 2008; 359: 1442-1455. doi: 10.1056/NEJMoa0803154 PMID: 18832245
4. Braun P, Wiesmann F. Phenotypic assays for the determination of coreceptor tropism in HIV-1 infected individuals. Eur J Med Res. 2007; 12: 463-472. PMID: 17933728
5. Svicher V, D'Arrigo R, Alteri C, Andreoni M, Angarano G, Antinori A, et al. Performance of genotypic tropism testing in clinical practice using the enhanced sensitivity version of Trofile as reference assay: results from the OSCAR Study Group. New Microbiol. 2010; 33: 195-206. PMID: 20954437
6. Recordon-Pinson P, Soulie C, Flandre P, Descamps D, Lazrek M, Charpentier C, et al. Evaluation of the genotypic prediction of HIV-1 coreceptor use versus a phenotypic assay and correlation with the virological response to maraviroc: the ANRS GenoTropism study. Antimicrob Agents Chemother. 2010; 54: 3335-3340. doi: 10.1128/AAC.00148-10 PMID: 20530226
7. Reuter S, Braken P, Jensen B, Sierra-Aragon S, Oette M, Balduin M, et al. Maraviroc in treatment-experienced patients with HIV-1 infection - experience from routine clinical practice. Eur J Med Res. 2010; 15: 231-237. PMID: 20696631
8. Swenson LC, Daumer M, Paredes R. Next-generation sequencing to assess HIV tropism. Curr Opin HIV AIDS. 2012; 7: 478-485. doi: 10.1097/COH.0b013e328356e9da PMID: 22832710
9. Pou C, Codoñer F, Thielen A, Bellido R, Cabrera C, Dalmau J, et al. High Resolution Tropism Kinetics by Quantitative Deep Sequencing in HIV-1-infected Subjects Initiating Suppressive First-line ART; 2010 February, 16-19; San Francisco, CA, USA. pp. Abstract 544.
10. Portsmouth S, Valluri s, Daeumer M, Thiele B, Valdez H, Lewis M, et al. Population and ultra-deep sequencing for tropism determination are correlated with Trofile ES: genotypic re-analysis of the A4001078 maraviroc study; 2010; Glasgow, UK. Journal of the International AIDS Society 13: Suppl. 4, P128. pp. Abstract 128.
11. Brumme CJ, Wilkin T, Su Z, Schapiro J, Kagan R, Chapman D, et al. Relative Performance of ESTA, Trofile, 454 Deep Sequencing, and "Reflex" Testing for HIV Tropism in the MOTIVATE Screening Population of Therapy-experienced Patients; 2011 Feb 27-March 2; Boston, USA. pp. Abstract 666.
12. Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Jensen MA, et al. Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis. 2011; 203: 237-245. doi: 10.1093/infdis/jiq030 PMID: 21288824
13. Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Thielen A, et al. Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc. Clin Infect Dis. 2011; 53: 732-742. doi: 10.1093/cid/cir493 PMID: 21890778
14. Vandekerckhove LP, Wensing AM, Kaiser R, Brun-Vezinet F, Clotet B, De Luca A, et al. European guidelines on the clinical management of HIV-1 tropism testing. Lancet Infect Dis. 2011; 11: 394-407.doi: 10.1016/S1473-3099(10)70319-4 PMID: 21429803
15. Eberle J, Noah C, Wolf E, Stürmer M, Braun P, Korn K, et al. (2014) Empfehlungen zur Bestimmung des HIV-1-Korezeptor-Gebrauchs (DAIG recommendations for the HIV-1 tropism testing).
16. Sander O, Sing T, Sommer I, Low AJ, Cheung PK, Harrigan P, et al. Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Computational Biology. 2007; 3: e58. PMID: 17397254
17. Dybowski JN, Heider D, Hoffmann D. Prediction of co-receptor usage of HIV-1 from genotype. PLoS Comput Biol. 2010; 6: e1000743. doi: 10.1371/journal.pcbi.1000743 PMID: 20419152
18. Sierra S, Kaiser R, Thielen A, Schuelter E, Heger E, Luebke N, et al. Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach. J Vis Exp. 2011; 58: 3624.
19. Thielen A, Martini N, Thiele B, Däumer M-. Validation of HIV-1 drug resistance testing by deep sequencing: insights from comparative Sanger sequencing. Antiviral Ther. 2014; 19: A78.
20. Price RW, Brew B, Sidtis J, Rosenblum M, Scheck AC, Cleary P. The brain in AIDS: central nervous system HIV-1 infection and AIDS dementia complex. Science. 1988; 239: 586-592. PMID: 3277272
21. Saracino A, Monno L, Brindicci G, Trillo G, Altamura M, Punzi G, et al. Are the proposed env mutations actually associated with resistance to maraviroc? J Acquir Immune Defic Syndr. 2010; 53: 550-552.doi: 10.1097/QAI.0b013e3181ba46a6 PMID: 20220379
22. Menendez-Arias L. Molecular basis of human immunodeficiency virus type 1 drug resistance: Overview and recent developments. Antiviral Res. 2013.
23. McGovern R, Dong W, Zhong X, Knapp D, Thielen A, Chapman D, et al. Population-based Sequencing of the V3-loop Is Comparable to the Enhanced Sensitivity Trofile Assay in Predicting Virologic Response to Maraviroc of Treatment-naïve Patients in the MERIT Trial; 2010 February, 16-19; San Francisco, CA, USA. pp. Abstract 92.
24. Cabral GB, Ferreira JL, Coelho LP, Fonsi M, Estevam DL, Cavalcanti JS, et al. Concordance of HIV Type 1 Tropism Phenotype to Predictions Using Web-Based Analysis of V3 Sequences: Composite Algorithms May Be Needed to Properly Assess Viral Tropism. AIDS Res Hum Retroviruses. 2012; 28:734-738. doi: 10.1089/AID.2011.0251 PMID: 21919801
25. Obermeier M, Symons J, Wensing AM. HIV population genotypic tropism testing and its clinical significance. Curr Opin HIV AIDS. 2012; 7: 470-477. doi: 10.1097/COH.0b013e328356eaa7 PMID: 22832711
26. Verhofstede C, Brudney D, Reynaerts J, Vaira D, Fransen K, De Bel A, et al. Concordance between HIV-1 genotypic coreceptor tropism predictions based on plasma RNA and proviral DNA. HIV Med. 2011; 12: 544-552. doi: 10.1111/j.1468-1293.2011.00922.x PMID: 21518222
27. Prosperi MC, Bracciale L, Fabbiani M, Di Giambenedetto S, Razzolini F, Meini G, et al. Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping. Retrovirology. 2010; 7: 56. doi: 10.1186/1742-4690-7-56 PMID: 20591141
28. Obermeier M, Carganico A, Bieniek B, Schleehauf D, Dupke S, Fischer K, et al. Tropism testing from proviral DNA - analysis of a subgroup from the Berlin Maraviroc cohort. Reviews in Antiviral. 2010; 1:23.
29. Soulie C, Calvez V, Marcelin AG. Coreceptor usage in different reservoirs. Curr Opin HIV AIDS. 2012; 7: 450-455. doi: 10.1097/COH.0b013e328356e9c2 PMID: 22832709
30. Swenson LC, Dong WW, Mo T, Demarest J, Chapman D, Ellery S, et al. Use of Cellular HIV DNA to Predict Virologic Response to Maraviroc: Performance of Population-Based and Deep Sequencing. Clin Infect Dis. 2013.
31. Klimkait T. The XTrack System: Application and Advantage. Intervirology. 2012; 55: 118-122. doi: 10.1159/000332003 PMID: 22286880
32. Harrigan PR, Zhong X, Lewis M, Dong W, Knapp D, Swenson L, et al. The influence of PCR amplification variation on the ability of population-based PCR to detect non-R5 HIV; 2010 March, 17-19; Sorrento, Italy. pp. Abstract 38.
33. Knapp DJ, McGovern RA, Dong W, Poon AF, Swenson LC, Zhong X, et al. Factors influencing the sensitivity and specificity of conventional sequencing in human immunodeficiency virus type 1 tropism testing. J Clin Microbiol. 2013; 51: 444-451. doi: 10.1128/JCM.00739-12 PMID: 23175258
34. Poveda E, Alcami J, Paredes R, Cordoba J, Gutierrez F, Llibre JM, et al. Genotypic determination of HIV tropism - clinical and methodological recommendations to guide the therapeutic use of CCR5 antagonists. AIDS Rev. 2010; 12: 135-148. PMID: 20842202
35. Portsmouth S, Valluri SR, Daumer M, Thiele B, Valdez H, Lewis M, et al. Correlation between genotypic (V3 population sequencing) and phenotypic (Trofile ES) methods of characterizing co-receptor usage of HIV-1 from 200 treatment-naive HIV patients screened for Study A4001078. Antiviral Res. 2013; 97:60-65. doi: 10.1016/j.antiviral.2012.11.002 PMID: 23165088
36. McGovern RA, Thielen A, Portsmouth S, Mo T, Dong W, Woods CK, et al. Population-based sequencing of the V3-loop can predict the virological response to maraviroc in treatment-naive patients of the MERIT trial. J Acquir Immune Defic Syndr. 2012; 61: 279-286. doi: 10.1097/QAI.0b013e31826249cf PMID: 23095934
37. Swenson LC, Knapp D, Harrigan PR. Calibration and accuracy of the geno2pheno co-receptor algorithm for predicting HIV tropism for single and triplicate measurements of V3 genotype; 2010; Glasgow, UK. Journal of the International AIDS Society. pp. Abstract O123.
38. Symons J, Vandekerckhove L, Paredes R, Verhofstede C, Bellido R, Demecheleer E, et al. Impact of triplicate testing on genotypic HIV-1 tropism prediction in routine clinical practice. Clin Microbiol Infect. 2011.
39. Westby M, Lewis M, Whitcomb J, Youle M, Pozniak AL, James IT, et al. Emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants in a minority of HIV-1-infected patients following treatment with the CCR5 antagonist maraviroc is from a pretreatment CXCR4-using virus reservoir. J Virol. 2006; 80: 4909-4920. PMID: 16641282
40. Baroncelli S, Galluzzo CM, Weimer LE, Pirillo MF, Volpe A, Mercuri A, et al. Evolution of proviral DNA HIV-1 tropism under selective pressure of maraviroc-based therapy. J Antimicrob Chemother. 2012; 67: 1479-1485. doi: 10.1093/jac/dks055 PMID: 22361986
41. Jiao Y, Wang P, Zhang H, Zhang T, Zhang Y, Zhu H, et al. HIV-1 co-receptor usage based on V3 loop sequence analysis: preferential suppression of CXCR4 virus post HAART? Immunol Invest. 2011; 40: 597-613. doi: 10.3109/08820139.2011.569673 PMID: 21513481
42. Mortier V, Dauwe K, Vancoillie L, Staelens D, Van Wanzeele F, Vogelaers D, et al. Frequency and predictors of HIV-1 co-receptor switch in treatment naive patients. PLoS One. 2013; 8: e80259. doi: 10.1371/journal.pone.0080259 PMID: 24244665
43. Edo-Matas D, Rachinger A, Setiawan LC, Boeser-Nunnink BD, van't Wout AB, Lemey P, et al. The evolution of human immunodeficiency virus type-1 (HIV-1) envelope molecular properties and coreceptor use at all stages of infection in an HIV-1 donor-recipient pair. Virology. 2012; 422: 70-80. doi: 10.1016/j.virol.2011.10.005 PMID: 22047989
44. Brieu N, Portales P, Carles MJ, Corbeau P. Interleukin-7 induces HIV type 1 R5-to-X4 switch. Blood. 2011; 117: 2073-2074. doi: 10.1182/blood-2010-10-311860 PMID: 21310936
45. Nakayama EE, Hoshino Y, Xin X, Liu H, Goto M, Watanabe N, et al. Polymorphism in the interleukin-4 promoter affects acquisition of human immunodeficiency virus type 1 syncytium-inducing phenotype. J Virol. 2000; 74: 5452-5459. PMID: 10823849
46. Klein MR, Keet IP, D'Amaro J, Bende RJ, Hekman A, Mesman B, et al. Associations between HLA frequencies and pathogenic features of human immunodeficiency virus type 1 infection in seroconverters from the Amsterdam cohort of homosexual men. J Infect Dis. 1994; 169: 1244-1249. PMID: 8195600
47. D'Aquila RT, Sutton L, Savara A, Hughes MD, Johnson VA. CCR5/delta(ccr5) heterozygosity: a selective pressure for the syncytium-inducing human immunodeficiency virus type 1 phenotype. NIAID AIDS Clinical Trials Group Protocol 241 Virology Team. J Infect Dis. 1998; 177: 1549-1553. PMID: 9607832
48. Schapiro JM, Boucher CA, Kuritzkes DR, van de Vijver DA, Llibre JM, Lewis M, et al. Baseline CD4(+)T-cell counts and weighted background susceptibility scores strongly predict response to maraviroc regimens in treatment-experienced patients. Antivir Ther. 2011; 16: 395-404. doi: 10.3851/IMP1759 PMID: 21555822
49. Brumme CJ, Dong W, Chan D, Mo T, Swenson l, Woods C, et al. Short-term variation of HIV tropism readouts in the absence of CCR5 antagonists; 2010 November, 7-11; Glasgow, UK. Journal of the International AIDS Society. pp. Abstract O123. doi: 10.1186/1758-2652-13-7 PMID: 20196856
50. Battaglioli-DeNero AM. Strategies for improving patient adherence to therapy and long-term patient outcomes. J Assoc Nurses AIDS Care. 2007; 18: S17-22. PMID: 17275718
51. Wirden M, Soulie C, Fourati S, Valantin MA, Simon A, Ktorza N, et al. Pitfalls of HIV genotypic tropism testing after treatment interruption. J Antimicrob Chemother. 2013; 68: 188-189. doi: 10.1093/jac/dks362 PMID: 22954492