Genotypic prediction of HIV-1 CRF01-AE tropism

Journal of Clinical Microbiology

Volumn 51, Issue 2, 2013, Pages 564-570

  Raymond, Stéphanie ^a,b,c   Delobel, Pierre ^a,b,c   Rogez, Sylvie ^d   Encinas, Stéphanie ^a,c   Bruel, Patrick ^a,c   Pasquier, Christophe ^a,b,c   Sandres Sauné, Karine ^a,b,c   Marchou, Bruno ^c   Massip, Patrice ^c   Izopet, Jacques ^a,b,c  

^a INSERM   (France)

^b UNIVERSITÉ PAUL SABATIER   (France)

^c CHU PURPAN   (France)

^d LIMOGES UNIVERSITY HOSPITAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE RECEPTOR CXCR4;

ADULT; ALGORITHM; ARTICLE; CLINICAL ARTICLE; FEMALE; GENE SEQUENCE; GENOTYPE; GENOTYPING TECHNIQUE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; VIRAL TROPISM;

ADULT; ALGORITHMS; AMINO ACID SEQUENCE; FEMALE; GENETIC ASSOCIATION STUDIES; GENOTYPE; HIV ENVELOPE PROTEIN GP120; HIV-1; HUMANS; MALE; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PHENOTYPE; RECEPTORS, CCR5; RECEPTORS, CXCR4; ROC CURVE; SEQUENCE ALIGNMENT; VIRAL TROPISM;

EID: 84873036323     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.02328-12     Document Type: Article

References (32)

1. Berger EA, Murphy PM, Farber JM. 1999. Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. Annu. Rev. Immunol. 17:657-700.
2. Dorr P, Westby M, Dobbs S, Griffin P, Irvine B, Macartney M, Mori J, Rickett G, Smith-Burchnell C, Napier C, Webster R, Armour D, Price D, Stammen B, Wood A, Perros M. 2005. Maraviroc (UK-427, 857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity. Antimicrob. Agents Chemother. 49:4721- 4732.
3. Raymond S, Delobel P, Mavigner M, Cazabat M, Souyris C, Sandres- Saune K, Cuzin L, Marchou B, Massip P, Izopet J. 2008. Correlation between genotypic predictions based on V3 sequences and phenotypic determination of HIV-1 tropism. AIDS 22:F11-F16.
4. Skrabal K, Low AJ, Dong W, Sing T, Cheung PK, Mammano F, Harrigan PR. 2007. Determining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic model. J. Clin. Microbiol. 45:279 -284.
5. Taylor BS, Sobieszczyk ME, McCutchan FE, Hammer SM. 2008. The challenge of HIV-1 subtype diversity. N. Engl. J. Med. 358:1590 -1602.
6. Delgado E, Fernández-GarcíA A, Vega Y, Cuevas T, Pinilla M, GarcíA V, Sánchez M, González M, Sánchez AM, Thomson MM, Pérez-Álvarez L. 2012. Evaluation of genotypic tropism prediction tests compared with in vitro co-receptor usage in HIV-1 primary isolates of diverse subtypes. J. Antimicrob. Chemother. 67:25-31.
7. Garrido C, Roulet V, Chueca N, Poveda E, Aguilera A, Skrabal K, Zahonero N, Carlos S, Garcia F, Faudon JL, Soriano V, de Mendoza C. 2008. Evaluation of eight different bioinformatics tools to predict viral tropism in different human immunodeficiency virus type 1 subtypes. J. Clin. Microbiol. 46:887- 891.
8. Raymond S, Delobel P, Chaix ML, Cazabat M, Encinas S, Bruel P, Sandres-Saune K, Marchou B, Massip P, Izopet J. 2011. Genotypic prediction of HIV-1 subtype D tropism. Retrovirology 8:56. doi:10.1186/1742-4690-8-56.
9. Raymond S, Delobel P, Mavigner M, Cazabat M, Souyris C, Encinas S, Sandres-Saune K, Pasquier C, Marchou B, Massip P, Izopet J. 2009. Genotypic prediction of human immunodeficiency virus type 1 CRF02-AG tropism. J. Clin. Microbiol. 47:2292-2294.
10. Raymond S, Delobel P, Mavigner M, Ferradini L, Cazabat M, Souyris C, Sandres-Saune K, Pasquier C, Marchou B, Massip P, Izopet J. 2010. Prediction of HIV type 1 subtype C tropism by genotypic algorithms built from subtype B viruses. J. Acquir. Immune Defic. Syndr. 53:167-175.
11. Seclén E, Garrido C, Gonzalez MD, Gonzalez-Lahoz J, de Mendoza C, Soriano V, Poveda E. 2010. High sensitivity of specific genotypic tools for detection of X4 variants in antiretroviral-experienced patients suitable to be treated with CCR5 antagonists. J. Antimicrob. Chemother. 65:1486- 1492.
12. Hemelaar J, Gouws E, Ghys PD, Osmanov S. 2006. Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS 20:W13-W23.
13. Abecasis A. 2008. Demographic determinants of HIV-1 subtype distribution in Europe. Sixth Eur. HIV Drug Resist. Workshop, Budapest, Hungary. http://www.hivpresentation.com/assets/0E533013-423A-F6F7-C45CBE252EB509AD.PDF.
14. de Silva UC, Warachit J, Sattagowit N, Jirapongwattana C, Panthong S, Utachee P, Yasunaga T, Ikuta K, Kameoka M, Boonsathorn N. 2010. Genotypic characterization of HIV type 1 env gp160 sequences from three regions in Thailand. AIDS Res. Hum. Retroviruses 26:223-227.
15. Luu QP, Dean J, Do TTD, Carr MJ, Dunford L, Coughlan S, Connell J, Nguyen HT, Hall WW, Nguyen Thi LA. 2012. HIV type 1 coreceptor tropism, CCR5 genotype, and integrase inhibitor resistance profiles in Vietnam: implications for the introduction of new antiretroviral regimens. AIDS Res. Hum. Retroviruses 28:1344 -1348.
16. Utachee P, Jinnopat P, Isarangkura-Na-Ayuthaya P, de Silva UC, Nakamura S, Siripanyaphinyo U, Wichukchinda N, Tokunaga K, Yasunaga T, Sawanpanyalert P, Ikuta K, Auwanit W, Kameoka M. 2009. Genotypic characterization of CRF01-AE env genes derived from human immunodeficiency virus type 1-infected patients residing in central Thailand. AIDS Res. Hum. Retroviruses 25:229 -236.
17. Zhang C, Xu S, Wei J, Guo H. 2009. Predicted co-receptor tropism and sequence characteristics of China HIV-1 V3 loops: implications for the future usage of CCR5 antagonists and AIDS vaccine development. Int. J. Infect. Dis. 13:e212- e216.
18. Nie J, Zhang C, Liu W, Wu X, Li F, Wang S, Liang F, Song A, Wang Y. 2010. Genotypic and phenotypic characterization of HIV-1 CRF01-AE env molecular clones from infections in China. J. Acquir. Immune Defic. Syndr. 53:440-450.
19. Raymond S, Delobel P, Mavigner M, Cazabat M, Souyris C, Encinas S, Bruel P, Sandres-Saune K, Marchou B, Massip P, Izopet J. 2010. Development and performance of a new recombinant virus phenotypic entry assay to determine HIV-1 coreceptor usage. J. Clin. Virol. 47:126- 130.
20. González N, Pérez-Olmeda M, Mateos E, Cascajero A, Alvarez A, Spijkers S, GarcíA-Pérez J, Sánchez-Palomino S, Ruiz-Mateos E, Leal M, Alcami J. 2010. A sensitive phenotypic assay for the determination of human immunodeficiency virus type 1 tropism. J. Antimicrob. Chemother. 65:2493-2501.
21. Whitcomb JM, Huang W, Fransen S, Limoli K, Toma J, Wrin T, Chappey C, Kiss LD, Paxinos EE, Petropoulos CJ. 2007. Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism. Antimicrob. Agents Chemother. 51:566 -575.
22. Poveda E, Paredes R, Moreno S, Alcamí J, Córdoba J, Delgado R, Gutiérrez F, Llibre JM, García Deltoro M, Hernández- Quero J, Pulido F, Iribarren JA, García F. 2012. Update on clinical and methodological recommendations for genotypic determination of HIV tropism to guide the usage of CCR5 antagonists. AIDS Rev. 14:208 -217.
23. Thielen A, Sichtig N, Braun P, Daümer P, Walter H, Noah C, Wolf E, Müller H, Stürmer M, Lengauer T, Kaiser R, Obermeier H. 2009. Performance of genotypic coreceptor measurement using geno2pheno[coreceptor] in B- and non-B HIV subtypes in a large cohort of therapy-experienced patients in Germany, p 99-100. In Reviews in antiviral therapy, vol 1. Virology Education, Stockholm, Sweden.
24. Li Y, Rey-Cuille MA, Hu SL. 2001. N-linked glycosylation in the V3 region of HIV type 1 surface antigen modulates coreceptor usage in viral infection. AIDS Res. Hum. Retroviruses 17:1473-1479.
25. Ogert RA, Lee MK, Ross W, Buckler-White A, Martin MA, Cho MW. 2001. N-linked glycosylation sites adjacent to and within the V1/V2 and the V3 loops of dualtropic human immunodeficiency virus type 1 isolate DH12 gp120 affect coreceptor usage and cellular tropism. J. Virol. 75: 5998-6006.
26. Polzer S, Dittmar MT, Schmitz H, Schreiber M. 2002. The N-linked glycan g15 within the V3 loop of the HIV-1 external glycoprotein gp120 affects coreceptor usage, cellular tropism, and neutralization. Virology 304:70-80.
27. Poveda E, Seclen E, Gonzalez Mdel M, Garcia F, Chueca N, Aguilera A, Rodriguez JJ, Gonzalez-Lahoz J, Soriano V. 2009. Design and validation of new genotypic tools for easy and reliable estimation of HIV tropism before using CCR5 antagonists. J. Antimicrob. Chemother. 63:1006-1010.
28. Recordon-Pinson P, Soulie C, Flandre P, Descamps D, Lazrek M, Charpentier C, Montes B, Trabaud MA, Cottalorda J, Schneider V, Morand-Joubert L, Tamalet C, Desbois D, Mace M, Ferre V, Vabret A, Ruffault A, Pallier C, Raymond S, Izopet J, Reynes J, Marcelin AG, Masquelier B. 2010. 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. 54:3335-3340.
29. Vandekerckhove LPR, Wensing AMJ, Kaiser R, Brun-Vézinet F, Clotet B, De Luca A, Dressler S, Garcia F, Geretti AM, Klimkait T, Korn K, Masquelier B, Perno CF, Schapiro JM, Soriano V, Sönnerborg A, Vandamme A-M, Verhofstede C, Walter H, Zazzi M, Boucher CAB. 2011. European guidelines on the clinical management of HIV-1 tropism testing. Lancet Infect. Dis. 11:394-407.
30. Pfeifer N, Lengauer T. 2012. Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data. Bioinformatics 28:i589 -i595.
31. McGovern R, Wdong Zhong X, Knapp D, Thielen A, Chapman D, Lewis M, James I, Valdez H, Harrigan PR. 2010. 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, abstr P-92. Seventeenth Conference on Retroviruses and Opportunistic Infections, San Francisco, CA. http://www.retroconference.org/2010/Abstracts/39053.htm.
32. Delobel P, Nugeyre MT, Cazabat M, Pasquier C, Marchou B, Massip P, Barre-Sinoussi F, Israel N, Izopet J. 2007. Population-based sequencing of the V3 region of env for predicting the coreceptor usage of human immunodeficiency virus type 1 quasispecies. J. Clin. Microbiol. 45:1572- 1580.