Minority resistant HIV-1 variants and the response to first-line NNRTI therapy

Journal of Clinical Virology

Volumn 62, Issue , 2015, Pages 20-24

  Nicot, F ^a   Saune K ^a,b,c   Raymond, S ^a,b,c   Jeanne, N ^a   Carcenac, R ^a   Lefebvre, C ^a   Cuzin, L ^a   Marchou, B ^a,c   Delobel, P ^a,b,c   Izopet, J ^a,b,c  

^a TOULOUSE UNIVERSITY HOSPITAL   (France)

^b France   (France)

^c UNIVERSITÉ PAUL SABATIER   (France)

Author keywords

Deep sequencing; Human immunodeficiency virus; Minority variants

Indexed keywords

ABACAVIR; DIDANOSINE; EFAVIRENZ; EMTRICITABINE; LAMIVUDINE; NEVIRAPINE; NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR; TENOFOVIR; VIRUS RNA; ZIDOVUDINE; RNA DIRECTED DNA POLYMERASE INHIBITOR;

ADULT; ANTIVIRAL RESISTANCE; ARTICLE; CD4 LYMPHOCYTE COUNT; DRUG RESISTANCE MUTATION; DRUG RESPONSE; FEMALE; GENOTYPE; GENOTYPIC SUSCEPTIBILITY SCORE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 SUBTYPE B; MAJOR CLINICAL STUDY; MALE; PYROSEQUENCING; SCORING SYSTEM; ULTRADEEP PYROSEQUENCING; DNA SEQUENCE; DRUG EFFECTS; FOLLOW UP; GENETIC VARIABILITY; GENETICS; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HIV INFECTIONS; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNOLOGY; MIDDLE AGED; MUTATION; VIROLOGY; VIRUS LOAD;

ADULT; ANTIRETROVIRAL THERAPY, HIGHLY ACTIVE; CD4 LYMPHOCYTE COUNT; DRUG RESISTANCE, VIRAL; FEMALE; FOLLOW-UP STUDIES; GENETIC VARIATION; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; MALE; MIDDLE AGED; MUTATION; REVERSE TRANSCRIPTASE INHIBITORS; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; VIRAL LOAD;

EID: 84920396797     PISSN: 13866532     EISSN: 18735967     Source Type: Journal    
DOI: 10.1016/j.jcv.2014.10.020     Document Type: Article

References (30)

1. Dunn D.T., Coughlin K., Cane P.A. Genotypic resistance testing in routine clinical care. Curr Opin HIV AIDS 2011, 6:251-257.
2. Halvas E.K., Aldrovandi G.M., Balfe P., Beck I.A., Boltz V.F., Coffin J.M., et al. Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency. J Clin Microbiol 2006, 44:2612-2614.
3. Hirsch M.S., Gunthard H.F., Schapiro J.M., Brun-Vezinet F., Clotet B., Hammer S.M., et al. Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis 2008, 47:266-285.
4. Metzner K.J., Bonhoeffer S., Fischer M., Karanicolas R., Allers K., Joos B., et al. Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions. J Infect Dis 2003, 188:1433-1443.
5. Paredes R., Marconi V.C., Campbell T.B., Kuritzkes D.R. Systematic evaluation of allele-specific real-time PCR for the detection of minor HIV-1 variants with pol and env resistance mutations. J Virol Methods 2007, 146:136-146.
6. Simen B.B., Simons J.F., Hullsiek K.H., Novak R.M., Macarthur R.D., Baxter J.D., et al. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 2009, 199:693-701.
7. St John E.P., Simen B., Turenchalk G.S., Braverman M.S., Abbate I., Aerssens J., et al. A follow-up multicenter collaborative study on HIV-1 drug resistance and tropism testing using 454 massively parallel pyrosequencing. Antivir Ther 2011, 16:A102.
8. Wang C., Mitsuya Y., Gharizadeh B., Ronaghi M., Shafer R.W. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 2007, 17:1195-1201.
9. Li J.Z., Paredes R., Ribaudo H.J., Svarovskaia E.S., Metzner K.J., Kozal M.J., 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, 305:1327-1335.
10. Li J.Z., Kuritzkes D.R. Clinical implications of HIV-1 minority variants. Clin Infect Dis 2013, 56:1667-1674.
11. Swenson L.C., Mo T., Dong W.W.Y., Zhong X., Woods C.K., Jensen M.A., 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.
12. Nicot F., Saliou A., Raymond S., Sauné K., Dubois M., Massip P., et al. Minority variants associated with resistance to HIV-1 nonnucleoside reverse transcriptase inhibitors during primary infection. J Clin Virol 2012, 55:107-113.
13. Gianella S., Delport W., Pacold M.E., Young J.A., Choi J.Y., Little S.J., et al. Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants. J Virol 2011, 85:8359-8367.
14. Lataillade M., Chiarella J., Yang R., Schnittman S., Wirtz V., Uy J., 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:e10952.
15. Messiaen P., Verhofstede C., Vandenbroucke I., Dinakis S., Van Eygen V., Thys K., et al. Ultra-deep sequencing of HIV-1 reverse transcriptase before start of an NNRTI-based regimen in treatment-naive patients. Virology 2012, 426:7-11.
16. Macalalad A.R., Zody M.C., Charlebois P., Lennon N.J., Newman R.M., Malboeuf C.M., et al. Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Comput Biol 2012, 8:e1002417.
17. Riddler S.A., Haubrich R., DiRienzo A.G., Peeples L., Powderly W.G., Klingman K.L., et al. Class-sparing regimens for initial treatment of HIV-1 infection. N Engl J Med 2008, 358:2095-2106.
18. Zhang Z., Hamatake R., Hong Z. Clinical utility of current NNRTIs and perspectives of new agents in this class under development. Antivir Chem Chemother 2004, 15:121-134.
19. Johnson V.A., Calvez V., Gunthard H.F., Paredes R., Pillay D., Shafer R.W., et al. Update of the drug resistance mutations in HIV-1: March 2013. Top Antivir Med 2013, 21:6-14.
20. Gilles A., Meglécz E., Pech N., Ferreira S., Malausa T., Martin J.-F. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 2011, 12:245.
21. Vercauteren J., Wensing A.M., van de Vijver D.A., Albert J., Balotta C., Hamouda O., et al. Transmission of drug-resistant HIV-1 is stabilizing in Europe. J Infect Dis 2009, 200:1503-1508.
22. Chaix M.L., Descamps D., Wirden M., Bocket L., Delaugerre C., Tamalet C., et al. Stable frequency of HIV-1 transmitted drug resistance in patients at the time of primary infection over 1996-2006 in France. AIDS (London, England) 2009, 23:717-724.
23. Lambert-Niclot S., Charpentier C., Storto A., Fofana D., Soulie C., Fourati S., et al. Rilpivirine, emtricitabine and tenofovir resistance in HIV-1-infected rilpivirine-naive patients failing antiretroviral therapy. J Antimicrob Chemother 2013, 68:1237-1242.
24. Descamps D., Assoumou L., Chaix M-L., Chaillon A., Pakianather S., de Rougemont A., et al. National sentinel surveillance of transmitted drug resistance in antiretroviral-naive chronically HIV-infected patients in France over a decade: 2001-2011. J Antimicrob Chemother 2013, 68:2626-2631.
25. Descamps D., Chaix M.L., Montes B., Pakianather S., Charpentier C., Storto A., et al. Increasing prevalence of transmitted drug resistance mutations and non-B subtype circulation in antiretroviral-naive chronically HIV-infected patients from 2001 to 2006/2007 in France. J Antimicrob Chemother 2010, 65:2620-2627.
26. Wheeler W.H., Ziebell R.A., Zabina H., Pieniazek D., Prejean J., Bodnar U.R., et al. Prevalence of transmitted drug resistance associated mutations and HIV-1 subtypes in new HIV-1 diagnoses, U.S.-2006. AIDS 2010, 24:1203-1212.
27. Tambuyzer L., Azijn H., Rimsky L.T., Vingerhoets J., Lecocq P., Kraus G., et al. Compilation and prevalence of mutations associated with resistance to non-nucleoside reverse transcriptase inhibitors. Antivir Ther 2009, 14:103-109.
28. Goodman D.D., Zhou Y., Margot N.A., McColl D.J., Zhong L., Borroto-Esoda K., 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 (London, England) 2011, 25:325-333.
29. Delobel P., Saliou A., Nicot F., Dubois M., Trancart S., Tangre P., et al. Minor HIV-1 variants with the K103N resistance mutation during intermittent efavirenz-containing antiretroviral therapy and virological failure. PLoS ONE 2011, 6:e21655.
30. Heera J., Harrigan P.R., Lewis M., Chapman D., Biswas P., Swenson L.C., et al. Predicting maraviroc responses according to number or percentage of X4-using virus among treatment-experienced patients 2011, Boston, MA, USA.