Low-abundance resistant mutations in HIV-1 subtype c antiretroviral therapy-naïve individuals as revealed by pyrosequencing

Current HIV Research

Volumn 11, Issue 1, 2013, Pages 43-49

  Gonzalez, Sandra ^a   Tully, Damien C ^a,c   Gondwe, Clement ^a,b   Wood, Charles ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^b UNIVERSITY TEACHING HOSPITAL   (Zambia)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Antiretroviral therapy; Drug na ve; HIV 1; Low abundance variants; Subtype C; Ultra deep pyrosequencing; Zambia

Indexed keywords

NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR; PROTEINASE INHIBITOR; RNA DIRECTED DNA POLYMERASE INHIBITOR;

ANTIVIRAL RESISTANCE; ANTIVIRAL SUSCEPTIBILITY; ARTICLE; CLINICAL ARTICLE; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; INTERMETHOD COMPARISON; PERIPHERAL BLOOD MONONUCLEAR CELL; PREVALENCE; PYROSEQUENCING; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; STRUCTURAL GENE; ULTRA DEEP PYROSEQUENCING; VIRUS LOAD; VIRUS MUTATION;

EID: 84876726649     PISSN: 1570162X     EISSN: 18734251     Source Type: Journal    
DOI: 10.2174/157016213804999285     Document Type: Article

References (40)

1. Buckton AJ. New methods for the surveillance of HIV drug resistance in the resource poor world. Curr Opin Infect Dis 2008; 21: 653-658.
2. Novak RM, Chen L, MacArthur RD, et al. Prevalence of antiretroviral drug resistance mutations in chronically HIV infected, treatment-naive patients: implications for routine resistance screening before initiation of antiretroviral therapy. Clin Infect Dis 2005; 40: 468-474.
3. Little SJ, Holte S, Routy JP, et al. Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med 2002; 347: 385-394.
4. Simen BB, Simons JF, Hullsiek KH, et al. Low-abundance drugresistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 2009; 199: 693-701.
5. Lataillade M, Chiarella J, Yang R, 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.
6. Le T, Chiarella J, Simen BB, et al. Low-abundance HIV drugresistant viral variants in treatment-experienced persons correlate with historical antiretroviral use. PLoS One 2009; 4: e6079.
7. Hedskog C, Mild M, Jernberg J, et al. Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing. PLoS One 2010; 5: e11345.
8. Hemelaar J, Gouws E, Ghys PD, Osmanov S. Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS 2006; 20(16): W13-W23.
9. Gupta RK, Ford D, Mulenga V, et al. Drug resistance in human immunodeficiency virus type-1 infected Zambian children using adult fixed dose combination stavudine, lamivudine, and nevirapine. Pediatr Infect Dis J 2010; 29: e57-e62.
10. Hamers RL, Siwale M, Wallis CL, et al. HIV-1 drug resistance mutations are present in six percent of persons initiating antiretroviral therapy in Lusaka, Zambia. J Acquir Immune Defic Syndr 2010; 55: 95-101.
11. Gonzalez S, Gondwe C, Tully DC, et al. Short communication: antiretroviral therapy resistance mutations present in the HIV type 1 subtype C pol and env regions from therapy-naive patients in Zambia. AIDS Res Hum Retroviruses 2010; 26: 795-803.
12. Handema R, Terunuma H, Kasolo F, et al. Prevalence of drugresistance-associated mutations in antiretroviral drug-naïve Zambians infected with subtype C HIV-1. AIDS Res Hum Retroviruses 2003; 19: 151-160
13. Stringer JS, Zulu I, Levy J, et al. Rapid scale-up of antiretroviral therapy at primary care sites in Zambia: feasibility and early outcomes. JAMA 2006; 296: 782-793.
14. Yun Z, Fredriksson E, Sonnerborg A. Quantification of human immunodeficiency virus type 1 proviral DNA by the TaqMan realtime PCR assay. J Clin Microbiol 2002; 40: 3883-3884.
15. Zhang H, Zhou Y, Alcock C, et al. Novel single-cell-level phenotypic assay for residual drug susceptibility and reduced replication capacity of drug-resistant human immunodeficiency virus type 1. J Virol 2004; 78: 1718-1729.
16. Hoffmann C, Minkah N, Leipzig J, et al. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 2007; 35: e91.
17. Gifford RJ, Rhee SY, Eriksson N, et al. Sequence editing by Apolipoprotein B RNA-editing catalytic component-B and epidemiological surveillance of transmitted HIV-1 drug resistance. AIDS 2008; 22: 717-725.
18. Metzner KJ, Giulieri SG, Knoepfel SA, et al. Minority quasispecies of drug-resistant HIV-1 that lead to early therapy failure in treatment-naive and -adherent patients. Clin Infect Dis 2009; 48: 239-247.
19. Johnson JA, Li JF, Wei X, et al. Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naive populations and associate with reduced treatment efficacy. PLoS Med 2008; 5: e158.
20. Peuchant O, Thiebaut R, Capdepont S, et al. Transmission of HIV- 1 minority-resistant variants and response to first-line antiretroviral therapy. AIDS 2008; 22: 1417-1423.
21. Messiaen P, Verhofstede C, Vandenbroucke I, 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.
22. Jakobsen MR, Tolstrup M, Sogaard OS, et al. Transmission of HIV-1 drug-resistant variants: prevalence and effect on treatment outcome. Clin Infect Dis 2010; 50: 566-573.
23. Chi BH, Mwango A, Giganti M, et al. Early clinical and programmatic outcomes with tenofovir-based antiretroviral therapy in Zambia. J Acquir Immune Defic Syndr 2010; 54: 63-70.
24. Wolf K, Walter H, Beerenwinkel N, et al. Tenofovir resistance and resensitization. Antimicrob Agents Chemother 2003; 47: 3478-3484.
25. Naeger LK, Margot NA, Miller MD. Increased drug susceptibility of HIV-1 reverse transcriptase mutants containing M184V and zidovudine-associated mutations: analysis of enzyme processivity, chain-terminator removal and viral replication. Antivir Ther 2001; 6: 115-126.
26. Whitcomb JM, Parkin NT, Chappey C, Hellmann NS, Petropoulos CJ. Broad nucleoside reverse-transcriptase inhibitor crossresistance in human immunodeficiency virus type 1 clinical isolates. J Infect Dis 2003; 188: 992-1000.
27. Doualla-Bell F, Avalos A, Brenner B, et al. High prevalence of the K65R mutation in human immunodeficiency virus type 1 subtype C isolates from infected patients in Botswana treated with didanosine-based regimens. Antimicrob Agents Chemother 2006; 50: 4182-4185.
28. Toni TA, Brenner BG, Asahchop EL, Ntemgwa M, Moisi D, Wainberg MA. Development of an allele-specific PCR for detection of the K65R resistance mutation in patients infected with subtype C human immunodeficiency virus type 1. Antimicrob Agents Chemother 2010; 54: 907-911.
29. Orrell C, Walensky RP, Losina E, Pitt J, Freedberg KA, Wood R. HIV type-1 clade C resistance genotypes in treatment-naïve patients and after first virological failure in a large community antiretroviral therapy programme. Antivir Ther 2009; 14: 523-531.
30. Coutsinos D, Invernizzi CF, Moisi D, et al. A template-dependent dislocation mechanism potentiates K65R reverse transcriptase mutation development in subtype C variants of HIV-1. PLoS One 2011; 6: e20208.
31. Coutsinos D, Invernizzi CF, Xu H, Brenner BG, Wainberg MA. Factors affecting template usage in the development of K65R resistance in subtype C variants of HIV type-1. Antivir Chem Chemother 2010; 20: 117-131.
32. Coutsinos D, Invernizzi CF, Xu H, et al. Template usage is responsible for the preferential acquisition of the K65R reverse transcriptase mutation in subtype C variants of human immunodeficiency virus type 1. J Virol 2009; 83: 2029-2033.
33. Varghese V, Wang E, Babrzadeh F, et al. Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation. PLoS One 2010; 5: e10992.
34. Recordon-Pinson P, Papuchon J, Reigadas S, Deshpande A, Fleury H. K65R in Subtype C HIV-1 Isolates from Patients Failing on a First-Line Regimen Including d4T or AZT: Comparison of Sanger and UDP Sequencing Data. PLoS One 2012; 7: e36549.
35. Jayaweera DT, Espinoza L, Castro J. Etravirine: the renaissance of non-nucleoside reverse transcriptase inhibitors. Expert Opin Pharmacother 2008; 9: 3083-3094.
36. Stevens WS, Wallis CL, Sanne I, Venter F. Will etravirine work in patients failing nonnucleoside reverse transcriptase inhibitor-based treatment in southern Africa? J Acquir Immune Defic Syndr 2009; 52: 655-656.
37. Varghese V, Shahriar R, Rhee SY, et al. Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors. J Acquir Immune Defic Syndr 2009; 52: 309-315.
38. Rozera G, Abbate I, Bruselles A, et al. Archived HIV-1 minority variants detected by ultra-deep pyrosequencing in provirus may be fully replication competent. AIDS 2009; 23: 2541-2543.
39. Rozera G, Abbate I, Bruselles A, et al. Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations. Retrovirology 2009; 6: 15.
40. Soto-Ramirez LE, Rodriguez-Diaz R, Duran AS, et al. Antiretroviral resistance among HIV type 1-infected women first exposed to antiretrovirals during pregnancy: plasma versus PBMCs. AIDS Res Hum Retroviruses 2008; 24: 797-804.