A genotypic assay for the amplification and sequencing of integrase from diverse HIV-1 group M subtypes

Journal of Virological Methods

Volumn 153, Issue 2, 2008, Pages 176-181

  Van Laethem, Kristel ^a,b   Schrooten, Yoeri ^a,b   Covens, Kris ^a   Dekeersmaeker, Nathalie ^a   De Munter, Paul ^b   Van Wijngaerden, Eric ^b   Van Ranst, Marc ^a,b   Vandamme, Anne Mieke ^a  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^b UNIVERSITY HOSPITALS LEUVEN   (Belgium)

Author keywords

HIV 1 subtypes; PCR; Resistance; Sequencing

Indexed keywords

INTEGRASE; VIRUS RNA;

ARTICLE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; VIRUS LOAD;

DNA, COMPLEMENTARY; DRUG RESISTANCE, VIRAL; GENOTYPE; HIV INTEGRASE; HIV INTEGRASE INHIBITORS; HIV-1; HUMANS; MICROBIAL SENSITIVITY TESTS; POLYMERASE CHAIN REACTION; PYRROLIDINONES; RNA, VIRAL; SEQUENCE ANALYSIS, DNA;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 53049097137     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2008.07.008     Document Type: Article

References (17)

1. Abecasis A., Deforche K., Snoeck J., Bachelor L.T., McKenna P., Carvalho A.P., Gomes P., Camacho R., and Vandamme A.-M. Protease mutation M89I/V is linked to therapy failure in patients infected with the HIV-1 non-B subtypes C, F or G. AIDS 19 (2005) 1799-1806
2. Abecasis A.B., Deforche K., Bachelor L.T., McKenna P., Carvalho A.P., Gomes P., Vandamme A.-M., and Camacho R.J. Investigation of baseline susceptibility to protease inhibitors in HIV-1 subtypes C, F G and CRF02_AG. Antivir. Ther. 11 (2006) 581-589
3. Cooper, D., Gatell, J., Rocktroh, J., Katlama, C., Yeni, P., Lazzarin, A., Chen, J., Isaaces, R., Teppler, H., Nguyen, B., and for the BENCHMRK-1 Study Group, 2007. Results of BENCHMRK-1, a phase III study evaluating the efficacy and safety of MK-0518, a novel HIV-1 integrase inhibitor, in patients with triple-class resistant virus. In: Proceedings of the 15th Conference on Retroviruses and Opportunistic Infections, Abstract 105aLB, Boston, US.
4. Deforche K., Silander T., Camacho R., Grossman Z., Soares M.A., Van Laethem K., Kantor R., Moreau Y., and Vandamme A.-M. Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance. Bioinformatics 22 (2006) 2975-2979
5. Deforche K., Camacho R., Grossman Z., Silander T., Soares M.A., Moreau Y., Shafer R.W., Van Laethem K., Carvalho A.P., Wynhoven B., Cane P., Snoeck J., Clarke J., Sirivichayakul S., Ariyoshi K., Holguin A., Rudich H., Rodrigues R., Bouzas M.B., Cahn P., Brigido L.F., Soriano V., Sugiura W., Phanuphak P., Morris L., Weber J., Pillay D., Tanuri A., Harrigan P.R., Shapiro J.M., Katzenstein D.A., Kantor R., and Vandamme A.-M. Bayesian network analysis of resistance pathways against HIV-1 protease inhibitors. Infect. Genet. Evol. 7 (2007) 382-390
6. de Oliveira T., Deforche K., Cassol S., Salminen M., Paraskevis D., Seebregts C., Snoeck J., van Rensburg E.J., Wensing A.M.J., van de Vijver D.A., Boucher C.A., Camacho R., and Vandamme A.-M. An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 21 (2005) 3797-3800. http://jose.med.kuleuven.be/subtypetool/html/index.html
7. DHHS panel on antiretroviral guidelines for adults and adolescents-a working group of the office of AIDS research advisory council (OARAC), 2007. Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents (01.12.07, http://AIDSinfo.nih.gov).
8. Grinsztejn B., Nguyen B.-Y., Katlama C., Gatell J.M., Lazzarin A., Vittecoq D., Gonzalez C.J., Chen J., Harvey C.M., Isaacs R.D., and for the Protocol 005 Team. Safety and efficacy of the HIV-1 integrase inhibitor raltegravir (MK-0518) in treatment-experienced patients with multidrug-resistant virus: a phase II randomised controlled trial. Lancet 369 (2007) 1261-1269
9. Hazuda D.J., Miller M.D., Nguyen B.Y., Zhao J., and for the P005 Study Team. Resistance to the HIV-integrase inhibitor raltegravir: analysis of protocol 005, a phase II study in patients with triple-class resistant HIV-1 infection. Antivir. Ther. 12 (2007) S10
10. In: Leitner T., Foley B., Hahn B., Marx P., McCutchan F., Mellors J., Wolinsky S., and Korber B. (Eds). HIV Sequence Compendium (2005), Published by Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM LA-UR 06-0680
11. Malet I., Delelis O., Valantin M.-A., Montes B., Soulie C., Wirden M., Tchertanov L., Peytavin G., Reynes J., Mouscadet J.-F., Katlama C., Calvez V., and Marcelin A.-G. Mutations associated with failure to raltegravir treatment affect integrase sensitivity to the inhibitor in vitro. Antimicrob. Agents Chemother. 52 (2008) 1351-1358
12. McColl D.J., Fransen S., Gupta S., Parkin N., Margot N., Chuck S., Cheng S., and Miller M.D. Resistance and cross-resistance to first generation integrase inhibitors: insights from a phase II study of elvitegravir (GS-9137). Antivir. Ther. 12 (2007) S11
13. Perno C.F., Cozzi-Lepri A., Balotta C., Forbici F., Violin M., Bertoli A., Facchi G., Pezzotti P., Cadeo G., Tositti G., Pasquinucci S., Pauluzzi S., Scalzini A., Salassa B., Vincenti A., Phillips A.N., Dianzani F., Appice A., Angarano G., Monno L., Ippolito G., Moroni M., d'Arminio Monforte A., and the Italian Cohort Naive Antiretroviral (I.C.O.N.A.) Study Group. Secondary mutations in the protease region of human immunodeficiency virus and virologic failure in drug-naive patients treated with protease inhibitor-based therapy. J. Infect. Dis. 184 (2001) 983-991
14. Shimura K., Kodama E., Sakagami Y., Matsuzaki Y., Watanabe W., Yamataka K., Watanabe Y., Ohata Y., Doi S., Sato M., Kano M., Ikeda S., and Matsuoka M. Broad antiretroviral activity and resistance profile of the novel human immunodeficiency virus integrase inhibitor elvitegravir (JTK-303/GS-9137). J. Virol. 82 (2008) 764-774
15. Snoeck J., Van Laethem K., Hermans P., Van Wijngaerden E., Derdelinckx I., Schrooten Y., van de Vijver D.A., De Wit S., Clumeck N., and Vandamme A.-M. Rising prevalence of HIV-1 non-B subtypes in Belgium: 1983-2001. J. Acquir. Immune Defic. Syndr. 35 (2004) 279-285
16. Steigbigel, R., Kumar, P., Eron, J., Schechter, M., Markowitz, M., Loufty, M., Zhao, J., Isaacs, R., Nguyen, B., Teppler, H., and for the BENCHMRK-2 Study Group, 2007. Results of BENCHMRK-2, a phase III study evaluating the efficacy and safety of MK-0518, a novel HIV-1 integrase inhibitor, in patients with triple-class resistant virus. In: Proceedings of the 15th Conference on Retroviruses and Opportunistic Infections, Abstract 105bLB, Boston, US.
17. Vercauteren J., Derdelinckx I., Sasse A., Bogaert M., Ceunen H., De Roo A., De Wit S., Deforche K., Echahidi F., Fransen K., Goffard J.C., Goubau P., Goudeseune E., Yombi J.C., Lacor P., Liesnard C., Moutschen M., Pierard D., Rens R., Schrooten Y., Vaira D., van den Heuvel A., van der Gucht B., Van Ranst M., Van Wijngaerden E., Vandercam B., Vekemans M., Verhofstede C., Clumeck N., Vandamme A.-M., and Van Laethem K. Prevalence and epidemiology of HIV type 1 drug resistance among newly diagnosed therapy-naive patients in Belgium from 2003 to 2006. AIDS Res. Hum. Retroviruses 24 (2008) 355-362