Implementing HIV-1 genotypic resistance testing in antiretroviral therapy programs in africa: Needs, opportunities, and challenges

AIDS Reviews

Volumn 15, Issue 4, 2013, Pages 221-229

  Lessells, Richard J ^a,b   Avalos, Ava ^c   De Oliveira, Tulio ^a,d  

^a UNIVERSITY OF KWAZULU NATAL   (South Africa)

^b LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^c Department of HIV AIDS Prevention and Care   (Botswana)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Antiretroviral therapy; Drug resistance; HIV 1; Treatment failure

Indexed keywords

NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR; PROTEINASE INHIBITOR; STAVUDINE; TENOFOVIR DISOPROXIL; THYMIDINE DERIVATIVE; TUBERCULOSTATIC AGENT; ZIDOVUDINE;

AFRICA; ANTIBIOTIC RESISTANCE; BOTSWANA; COST EFFECTIVENESS ANALYSIS; GENOTYPE; HEALTH CARE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INCOME; REVIEW; SOUTH AFRICA; TREATMENT FAILURE; WORLD HEALTH ORGANIZATION;

AFRICA; ANTI-HIV AGENTS; COST-BENEFIT ANALYSIS; DRUG RESISTANCE, VIRAL; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; WORLD HEALTH ORGANIZATION;

EID: 84890362740     PISSN: 11396121     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (76)

1. Joint United Nations Programme on HIV/AIDS (UNAIDS). Global report: UNAIDS report on the global AIDS epidemic 2013. 2013. Available at: http://www.unaids.org/en/media/unaids/contentassets/documents/epidemiology/2013/ gr2013/UNAIDS-Global-Report-2013-en.pdf. [Accessed 7 October 2013].
2. Hamers R, Kityo C, Lange J, Wit T, Mugyenyi P. Global threat from drug resistant HIV in sub-Saharan Africa. BMJ. 2012;344:e4159.
3. Cambiano V, Bertagnolio S, Jordan M, Lundgren J, Phillips A. Transmission of drug resistant HIV and its potential impact on mortality and treatment outcomes in resource-limited settings. J Infect Dis. 2013;207(Suppl 2):S57-62.
4. Bennett D, Bertagnolio S, Sutherland D, Gilks C. The World Health Organization's global strategy for prevention and assessment of HIV drug resistance. Antivir Ther. 2008;13(Suppl 2):1-13.
5. Jordan M, Bennett D, Wainberg M, et al. Update on World Health Organization HIV Drug Resistance Prevention and Assessment Strategy: 2004-2011. Clin Infect Dis. 2012;54(Suppl 4):S245-9.
6. World Health Organization. World Health Organization global strategy for the surveillance and monitoring of HIV drug resistance: an update. 2012. Available at: http://apps.who.int/iris/bitstream/10665/77349/1/9789241504768- eng.pdf. [Accessed 7 October 2013].
7. Atun R, Bataringaya J. Building a durable response to HIV/AIDS: implications for health systems. J Acquir Immune Defic Syndr. 2011;57(Suppl 2):S91-5.
8. Katzenstein DA. HIV RNA and Genotype in resource limited settings. Can we do better? Clin Infect Dis. 2013. [Epub ahead of print].
9. World Health Organization. The HIV drug resistance report 2012. Available at: http://apps.who.int/iris/bitstream/10665/75183/1/ 9789241503938-eng.pdf. [Accessed 7 October 2013].
10. Gupta R, Jordan M, Sultan B, et al. Global trends in antiretroviral resistance in treatment-naive individuals with HIV after rollout of antiretroviral treatment in resource-limited settings: a global collaborative study and meta-regression analysis. Lancet. 2012;380:1250-8.
11. Manasa J, Katzenstein D, Cassol S, Newell M, de Oliveira T. Primary drug resistance in South Africa: data from 10 years of surveys. AIDS Res Hum Retroviruses. 2012;28:558-65.
12. Hunt G, Ledwaba J, Basson A, et al. Surveillance of transmitted HIV-1 drug resistance in Gauteng and KwaZulu-Natal Provinces, South Africa, 2005-2009. Clin Infect Dis. 2012;54(Suppl 4):S334-8.
13. McMahon J, Elliott J, Bertagnolio S, Kubiak R, Jordan M. Viral suppression after 12 months of antiretroviral therapy in low- and middle-income countries: a systematic review. Bull World Health Organ. 2013;91:377-85E.
14. Aghokeng A, Monleau M, Eymard-Duvernay S, et al. Extraordinary heterogeneity of virological outcomes in Patients Receiving HAART and Monitored with the World Health Organization (WHO) Public Health Approach in sub-Saharan Africa and south-east Asia. Clin Infect Dis. 2013, Oct 23. [Epub ahead of print].
15. Hamers R, Sigaloff K, Wensing A, et al. Patterns of HIV-1 drug resistance after first-line antiretroviral therapy (ART) failure in 6 sub-Saharan African countries: implications for second-line ART strategies. Clin Infect Dis. 2012;54:1660-9.
16. Manasa J, Lessells R, Skingsley A, et al. High-levels of acquired drug resistance in adult patients failing first-line antiretroviral therapy in a rural HIV treatment programme in KwaZulu-Natal, South Africa. PLoS One. 2013;8:e72152.
17. Sunpath H, Wu B, Gordon M, et al. High rate of K65R for antiretroviral therapy-naive patients with subtype C HIV infection failing a tenofovircontaining first-line regimen. AIDS. 2012;26:1679-84.
18. Hoffmann C, Ledwaba J, Li J, et al. Resistance to tenofovir-based regimens during treatment failure of subtype C HIV-1 in South Africa. Antivir Ther. 2013. Jun 10. [Epub ahead of print].
19. Coutsinos D, Invernizzi C, Xu H, Brenner B, Wainberg M. Factors affecting template usage in the development of K65R resistance in subtype C variants of HIV type-1. Antivir Chem Chemother. 2010;20:117-31.
20. Sigaloff K, Calis J, Geelen S, van Vugt M, de Wit T. HIV-1-resistance- associated mutations after failure of first-line antiretroviral treatment among children in resource-poor regions: a systematic review. Lancet Infect Dis. 2011;11:769-79.
21. van Zyl G, van der Merwe L, Claassen M, et al. Protease inhibitor resistance in South African children with virologic failure. Pediatr Infect Dis J. 2009;28:1125-7.
22. Asboe D, Aitken C, Boffito M, et al. British HIV Association guidelines for the routine investigation and monitoring of adult HIV-1-infected individuals 2011. HIV Med. 2012;13:1-44.
23. Vandamme A, Camacho R, Ceccherini-Silberstein F, et al. European recommendations for the clinical use of HIV drug resistance testing: 2011 update. AIDS Rev. 2011;13:77-108.
24. Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. Available at: http://aidsinfo.nih.gov/contentfiles/lvguidelines/ AdultandAdolescentGL.pdf. [Accessed 7 October 2013].
25. Dunn D, Coughlin K, Cane P. Genotypic resistance testing in routine clinical care. Curr Opin HIV AIDS. 2011;6:251-7.
26. Elliott J, Lynen L, Calmy A, et al. Rational use of antiretroviral therapy in low-income and middle-income countries: optimizing regimen sequencing and switching. AIDS. 2008;22:2053-67.
27. De Luca A, Hamers R, Schapiro J. Antiretroviral treatment sequencing strategies to overcome HIV type 1 drug resistance in adolescents and adults in low-middle-income countries. J Infect Dis. 2013;207(Suppl 2):S63-9.
28. Pillay D, Albert J, Bertagnolio S, et al. Implications of HIV drug resistance on first- and second-line therapies in resource-limited settings: report from a workshop organized by the Collaborative HIV and Anti-HIV Drug Resistance Network. Antivir Ther. 2013. Jun 5. [Epub ahead of print].
29. Singh B. Absence of drug resistance in patients with treatment failure in rural KwaZulu-Natal, South Africa. MSc thesis. London School of Hygiene and Tropical Medicine; 2013.
30. Johnston V, Cohen K, Wiesner L, et al. Viral suppression following switch to second-line antiretroviral therapy: associations with nucleoside reverse transcriptase inhibitor resistance and subtherapeutic drug concentrations prior to switch. J Infect Dis. 2013. Sep 11 [Epub ahead of print].
31. Murphy R, Sunpath H, Lu Z, et al. Outcomes after virologic failure of first-line ART in South Africa. AIDS. 2010;24:1007-12.
32. Levison J, Orrell C, Gallien S, et al. Virologic failure of protease inhibitor-based second-line antiretroviral therapy without resistance in a large HIV treatment program in South Africa. PLoS One. 2012;7:e32144.
33. Sigaloff K, Hamers R, Wallis C, et al. Second-line antiretroviral treatment successfully re-suppresses drug-resistant HIV-1 after first-line failure: prospective cohort in Sub-Saharan Africa. J Infect Dis. 2012;205:1739-44.
34. Wallis C, Mellors J, Venter W, Sanne I, Stevens W. Protease inhibitor resistance is uncommon in HIV-1 subtype C infected patients on failing second-line lopinavir/r-containing antiretroviral therapy in South Africa. AIDS Res Treat. 2011;2011:769627.
35. van Zyl G, van Mens T, McIlleron H, et al. Low lopinavir plasma or hair concentrations explain second-line protease inhibitor failures in a re-source- limited setting. J Acquir Immune Defic Syndr. 2011;56:333-9.
36. Harries A, Zachariah R, van Oosterhout J, et al. Diagnosis and management of antiretroviral-therapy failure in resource-limited settings in sub-Saharan Africa: challenges and perspectives. Lancet Infect Dis. 2010;10:60-5.
37. Berg K, Arnsten J. Practical and conceptual challenges in measuring antiretroviral adherence. J Acquir Immune Defic Syndr. 2006;43(Suppl 1):S79-87.
38. Barnighausen T, Chaiyachati K, Chimbindi N, Peoples A, Haberer J, Newell M. Interventions to increase antiretroviral adherence in sub-Saharan Africa: a systematic review of evaluation studies. Lancet Infect Dis. 2011;11:942-51.
39. Baxter J, Mayers D, Wentworth D, et al. A randomized study of antiretroviral management based on plasma genotypic antiretroviral resistance testing in patients failing therapy. CPCRA 046 Study Team for the Terry Beirn Community Programs for Clinical Research on AIDS. AIDS. 2000;14:F83-93.
40. Durant J, Clevenbergh P, Halfon P, et al. Drug-resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet. 1999;353:2195-9.
41. Tural C, Ruiz L, Holtzer C, et al. Clinical utility of HIV-1 genotyping and expert advice: the Havana trial. AIDS. 2002;16:209-18.
42. University of Washington. OLA Resistance Study. Available at: http://clinicaltrials.gov/ct2/show/NCT01898754 [Accessed 1 October 2013].
43. Levison J, Wood R, Scott C, et al. The clinical and economic impact of genotype testing at first-line antiretroviral therapy failure for HIV-infected patients in South Africa. Clin Infect Dis. 2013;56:587-97.
44. Lorenzana S, Hughes M, Grinsztejn B, et al. Genotype assays and third-line ART in resource-limited settings: a simulation and cost-effectiveness analysis of a planned clinical trial. AIDS. 2012;26:1083-93.
45. Sohn A, Nuttall J, Zhang F. Sequencing of antiretroviral therapy in children in low- and middle-income countries. Curr Opin HIV AIDS. 2010;5:54-60.
46. Calmy A, Ford N, Hirschel B, et al. HIV viral load monitoring in resource-limited regions: optional or necessary? Clin Infect Dis. 2007;44:128-34.
47. Clinton Health Access Initiative. HIV viral load testing. Market analysis. Available at: http://mat1.gtimg.com/gongyi/2012/enzhenduandahui/ 6ZachKatz.pdf [Accessed online]. [Accessed 7 October 2013].
48. Stevens W, Marshall T. Challenges in implementing HIV load testing in South Africa. J Infect Dis. 2010;201(Suppl 1):S78-84.
49. Scott L. South Africa's experiences and future plans for CD4 and viral load implementation. In: 7th IAS Conference on HIV Pathogenesis, Treatment and Prevention. Kuala Lumpur, Malaysia; 2013.
50. Stevens W. South Africa's "Reality Check": >1 million Xpert tests. In: 5th Annual Global Laboratory Initiative Partners' Meeting Veyrie-du-Lac, France; 2013.
51. Department of Health RoSA. The South African Antiretroviral Treatment Guidelines. 2013. Available at: http://www.doh.gov.za/docs/policy/2013/ART- Treatment-Guidelines-Final-25March2013.pdf. [Accessed 7 October 2013].
52. Ministry of Health GoB. Botswana National HIV & AIDS Treatment Guidelines. 2012. Available at: http://www.hiv.gov.bw/sites/default/files/ documents/Bots%20Nat%20HIV-AIDS%20Treat%20Guide%2009-07-2012-0.pdf. [Accessed 7 October 2013].
53. Kircher M, Kelso J. High-throughput DNA sequencing - concepts and limitations. Bioessays. 2010;32:524-36.
54. PRNewswire. Life Technologies and SATuRN Collaborate to Increase Access to HIV Testing in Africa. Available at: http://www.prnewswire.com/news-releases/ life-technologies-and-saturn-collaborate-to-increase-access- to-hiv-testing-in-africa-163526506.html [Accessed online]. [Accessed 7 October 2013].
55. Wallis C, Papathanasopoulos M, Lakhi S, et al. Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1. J Virol Methods. 2010;163:505-8.
56. Aitken S, Kliphuis A, Wallis C, et al. Development and evaluation of an assay for HIV-1 protease and reverse transcriptase drug resistance genotyping of all major group-M subtypes. J Clin Virol. 2012;54:21-5.
57. Aitken S, Bronze M, Wallis C, et al. A pragmatic approach to HIV-1 drug resistance determination in resource-limited settings by use of a novel genotyping assay targeting the reverse transcriptase-encoding region only. J Clin Microbiol. 2013;51:1757-61.
58. Manasa J, Danaviah S, Pillay S, et al. Affordable HIV-1 Drug resistance monitoring system for resource limited settings. J Vis Exp. 2013. [In press].
59. de Oliveira T, Shafer R, Seebregts C. Public database for HIV drug resistance in southern Africa. Nature. 2010;464:673.
60. Paredes R. Importance of minor variants and their detection (ultra-deep sequencing) in the management of HIV infection. J Int AIDS Soc. 2012;15:18309.
61. Bertagnolio S, Parkin N, Jordan M, Brooks J, Garcia-Lerma J. Dried blood spots for HIV-1 drug resistance and viral load testing: A review of current knowledge and WHO efforts for global HIV drug resistance surveillance. AIDS Rev. 2010;12:195-208.
62. Buckton A. New methods for the surveillance of HIV drug resistance in the resource poor world. Curr Opin Infect Dis. 2008;21:653-8.
63. Parkin N, de Mendoza C, Schuurman R, et al. Evaluation of in-house genotyping assay performance using dried blood spot specimens in the Global World Health Organization laboratory network. Clin Infect Dis. 2012;54(Suppl 4):S273-9.
64. Hamers R, Straatsma E, Kityo C, et al. Building capacity for the assessment of HIV drug resistance: experiences from the PharmAccess African Studies to Evaluate Resistance network. Clin Infect Dis. 2012;54(Suppl 4):S261-5.
65. Land S, Zhou J, Cunningham P, et al. Capacity building and predictors of success for HIV-1 drug resistance testing in the Asia-Pacific region and Africa. J Int AIDS Soc. 2013;16:18580.
66. Department of Health RoSA. Multi-drug resistant tuberculosis. A policy framework on decentralised and deinstitutionalised management for South Africa. Pretoria, South Africa: Department of Health; 2011.
67. Libin P, Beheydt G, Deforche K, et al. RegaDB: community-driven data management and analysis for infectious diseases. Bioinformatics. 2013;29:1477-80.
68. Roberts T, Bygrave H, Fajardo E, Ford N. Challenges and opportunities for the implementation of virological testing in resource-limited settings. J Int AIDS Soc. 2012;15:17324.
69. Pai N, Pai M. Point-of-care diagnostics for HIV and tuberculosis: landscape, pipeline, and unmet needs. Discov Med. 2012;13:35-45.
70. Wang S, Xu F, Demirci U. Advances in developing HIV-1 viral load assays for resource-limited settings. Biotechnol Adv. 2010;28:770-81.
71. Tang M, Liu T, Shafer R. The HIVdb system for HIV-1 genotypic resistance interpretation. Intervirology. 2012;55:98-101.
72. Van Laethem K, De Luca A, Antinori A, Cingolani A, Perna C, Vandamme A. A genotypic drug resistance interpretation algorithm that significantly predicts therapy response in HIV-1-infected patients. Antivir Ther. 2002;7:123-9.
73. Meynard J, Vray M, Morand-Joubert L, et al. Phenotypic or genotypic resistance testing for choosing antiretroviral therapy after treatment failure: a randomized trial. AIDS. 2002;16:727-36.
74. Snoeck J, Kantor R, Shafer R, et al. Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependent. Antimicrob Agents Chemother. 2006;50:694-701.
75. Frentz D, Boucher C, Assel M, et al. Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time. PLoS One. 2010;5:e11505.
76. Ahonkhai A, Bassett I, Ferris T, Freedberg K. Improving HIV outcomes in resource-limited countries: the importance of quality indicators. BMC Health Serv Res. 2012;12:427.