Concordance between allele-specific PCR and ultra-deep pyrosequencing for the detection of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations

Journal of Virological Methods

Volumn 207, Issue , 2014, Pages 182-187

  Hunt, Gillian M ^a,b   Morris, Lynn ^a,b   Moorthy, Anitha ^c   Coovadia, Ashraf ^d   Abrams, Elaine J ^e   Strehlau, Renate ^d   Kuhn, Louise ^f   Persaud, Deborah ^c  

^a NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES   (South Africa)

^b UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^e Department of Medicine   (United States)

^f Vagelos College of Physicians and Surgeons   (United States)

Author keywords

Allele specific PCR; HIV 1 drug resistance; Low frequency NNRTI variants; Ultra deep sequencing

Indexed keywords

ALLELE SPECIFIC POLYMERASE CHAIN REACTION; ARTICLE; CHILD; CONTROLLED STUDY; GENOTYPING TECHNIQUE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; INFANT; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; MUTATIONAL ANALYSIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; ULTRA DEEP PYROSEQUENCING; VIRUS MUTATION; VIRUS RESISTANCE; WILD TYPE; ALLELE; ANTIVIRAL RESISTANCE; CLASSIFICATION; CLINICAL TRIAL; COMPARATIVE STUDY; DNA SEQUENCE; DRUG EFFECTS; FEMALE; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MALE; MICROBIAL SENSITIVITY TEST; MISSENSE MUTATION; NEWBORN; PROCEDURES; RANDOMIZED CONTROLLED TRIAL; VIROLOGY;

REVERSE TRANSCRIPTASE, HUMAN IMMUNODEFICIENCY VIRUS 1; RNA DIRECTED DNA POLYMERASE;

ALLELES; DRUG RESISTANCE, VIRAL; FEMALE; GENOTYPING TECHNIQUES; HIV INFECTIONS; HIV REVERSE TRANSCRIPTASE; HIV-1; HUMANS; INFANT; INFANT, NEWBORN; MALE; MICROBIAL SENSITIVITY TESTS; MUTATION, MISSENSE; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84904863155     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2014.07.010     Document Type: Article

References (25)

1. Newton C.R., Graham A., Heptinstall L.E., Powell S.J., Summers C., Kalsheker N., Smith J.C., Markham A.F. Analysis of any point mutation in DNA The amplification refractory mutation system (ARMS). Nucleic Acids Res. 1989, 17:2503-2516.
2. Eshleman S.H., Jackson J.B. Nevirapine resistance after single dose prophylaxis. AIDS Rev. 2002, 4:59-63.
3. Clavel F., Hance A.J. HIV drug resistance. N. Engl. J. Med. 2004, 350:1023-1035.
4. Eshleman S.H., Guay L.A., Mwatha A., Cunningham S.P., Brown E.R., Musoke P., Mmiro F., Jackson J.B. Comparison of nevirapine (NVP) resistance in Ugandan women 7 days vs 6-8 weeks after single-dose nvp prophylaxis: HIVNET 012. AIDS Res. Hum. Retroviruses 2004, 20:595-599.
5. Loubser S., Balfe P., Sherman G., Hammer S., Kuhn L., Morris L. Decay of K103N mutants in cellular DNA and plasma RNA after single-dose nevirapine to reduce mother-to-child HIV transmission. AIDS 2006, 20:995-1002.
6. Palmer S., Boltz V., Martinson N., Maldarelli F., Gray G., McIntyre J., Mellors J., Morris L., Coffin J. Persistence of nevirapine-resistant HIV-1 in women after single-dose nevirapine therapy for prevention of maternal-to-fetal HIV-1 transmission. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:7094-7099.
7. Johnson J.A., Li J.F., Wei X., Lipscomb J., Bennett D., Brant A., Cong M.E., Spira T., Shafer R.W., Heneine W. Simple PCR assays improve the sensitivity of HIV-1 subtype B drug resistance testing and allow linking of resistance mutations. PloS One 2007, 2:e638.
8. Martinson N.A., Morris L., Gray G., Moodley D., Pillay V., Cohen S., Dhlamini P., Puren A., Bhayroo S., Steyn J., McIntyre J.A. Selection and persistence of viral resistance in HIV-infected children after exposure to single-dose nevirapine. J. Acquired Immune Defic. Synd. 2007, 44:148-153.
9. Pillay V., Ledwaba J., Hunt G., Rakgotho M., Singh B., Makubalo L., Bennett D.E., Puren A., Morris L. Antiretroviral drug resistance surveillance among drug-naive HIV-1-infected individuals in Gauteng Province South Africa in 2002 and 2004. Antivir. Ther. 2008, 13(Suppl. 2):101-107.
10. Boltz V.F., Maldarelli F., Martinson N., Morris L., McIntyre J.A., Gray G., Hopley M.J., Kimura T., Mayers D.L., Robinson P., Mellors J.W., Coffin J.M., Palmer S.E. Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design. J. Virol. Methods 2009, 164:122-126.
11. Simen B.B., Simons J.F., Hullsiek K.H., Novak R.M., Macarthur R.D., Baxter J.D., Huang C., Lubeski C., Turenchalk G.S., Braverman M.S., Desany B., Rothberg J.M., Egholm M., Kozal M.J. 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.
12. Coovadia A., Abrams E.J., Stehlau R., Meyers T., Martens L., Sherman G., Hunt G., Hu C.C., Tsai W.Y., Morris L., Kuhn L. Reuse of nevirapine in exposed HIV-infected children after protease inhibitor-based viral suppression: a randomized controlled trial. JAMA 2010, 304:1082-1090.
13. Ji H., Masse N., Tyler S., Liang B., Li Y., Merks H., Graham M., Sandstrom P., Brooks J. HIV drug resistance surveillance using pooled pyrosequencing. PloS One 2010, 5:e9263.
14. Lataillade M., Chiarella J., Yang R., Schnittman S., Wirtz V., Uy J., Seekins D., Krystal M., Mancini M., McGrath D., Simen B., Egholm M., Kozal M. 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. MacLeod I.J., Rowley C.F., Thior I., Wester C., Makhema J., Essex M., Lockman S. Minor resistant variants in nevirapine-exposed infants may predict virologic failure on nevirapine-containing ART. J. Clin. Virol. 2010, 48:162-167.
16. Rowley C.F., Boutwell C.L., Lee E.J., MacLeod I.J., Ribaudo H.J., Essex M., Lockman S. Ultrasensitive detection of minor drug-resistant variants for HIV after nevirapine exposure using allele-specific PCR: clinical significance. AIDS Res. Hum. Retroviruses 2010, 26:293-300.
17. Delobel P., Saliou A., Nicot F., Dubois M., Trancart S., Tangre P., Aboulker J.P., Taburet A.M., Molina J.M., Massip P., Marchou B., Izopet J. Minor HIV-1 variants with the K103N resistance mutation during intermittent efavirenz-containing antiretroviral therapy and virological failure. PloS One 2011, 6:e21655.
18. Gilles A., Meglecz E., Pech N., Ferreira S., Malausa T., Martin J.F. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genom. 2011, 12:245.
19. Hunt G.M., Coovadia A., Abrams E.J., Sherman G., Meyers T., Morris L., Kuhn L. HIV-1 drug resistance at antiretroviral treatment initiation in children previously exposed to single-dose nevirapine. Aids 2011, 25:1461-1469.
20. Johnson V.A., Calvez V., Gunthard H.F., Paredes R., Pillay D., Shafer R., Wensing A.M., Richman D.D. 2011 update of the drug resistance mutations in HIV-1. Top. Antivir. Med. 2011, 19:156-164.
21. Moorthy A., Kuhn L., Coovadia A., Meyers T., Strehlau R., Sherman G., Tsai W.Y., Chen Y.H., Abrams E.J., Persaud D. Induction therapy with protease-inhibitors modifies the effect of nevirapine resistance on virologic response to nevirapine-based HAART in children. Clin. Infect. Dis. 2011, 52:514-521.
22. Taylor B.S., Hunt G., Abrams E.J., Coovadia A., Meyers T., Sherman G., Strehlau R., Morris L., Kuhn L. Rapid development of antiretroviral drug resistance mutations in HIV-infected children less than two years of age initiating protease inhibitor-based therapy in South Africa. AIDS Res. Hum. Retroviruses 2011, 27:945-956.
23. Balzer S., Malde K., Jonassen I. Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics 2011, 27:i304-i309.
24. Kuhn L., Coovadia A., Strehlau R., Martens L., Hu C.C., Meyers T., Sherman G., Hunt G., Persaud D., Morris L., Tsai W.Y., Abrams E.J. Switching children previously exposed to nevirapine to nevirapine-based treatment after initial suppression with a protease-inhibitor-based regimen: long-term follow-up of a randomised, open-label trial. Lancet Infect. Dis. 2012, 12:521-530.
25. Lehman D.A., Wamalwa D.C., McCoy C.O., Matsen F.A., Langat A., Chohan B.H., Benki-Nugent S., Custers-Allen R., Bushman F.D., John-Stewart G.C., Overbaugh J. Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment. J. Acquired Immune Defic. Synd. 2012, 60:225-233.