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Comparison of an in-house ‘home-brew’ and commercial ViroSeq integrase genotyping assays on HIV-1 subtype C samples


Autoři: Kaelo K. Seatla aff001;  Wonderful T. Choga aff003;  Mompati Mogwele aff001;  Thabo Diphoko aff001;  Dorcas Maruapula aff001;  Lucy Mupfumi aff001;  Rosemary M. Musonda aff001;  Christopher F. Rowley aff004;  Ava Avalos aff001;  Ishmael Kasvosve aff002;  Sikhulile Moyo aff001;  Simani Gaseitsiwe aff001
Působiště autorů: Botswana Harvard AIDS Institute Partnership Gaborone, Botswana aff001;  Department of Medical Laboratory Sciences, School of Allied Health Professionals, University of Botswana, Gaborone, Botswana aff002;  Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa aff003;  Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America aff004;  Careena Centre for Health, Gaborone, Botswana aff005;  Ministry of Health and Wellness, Gaborone, Botswana aff006
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0224292

Souhrn

Background

Roll-out of Integrase Strand Transfer Inhibitors (INSTIs) such as dolutegravir for HIV combination antiretroviral therapy (cART) in sub-Saharan Africa necessitates the development of affordable HIV drug resistance (HIVDR) assays targeting the Integrase gene. We optimised and evaluated an in-house integrase HIV-1 drug resistance assay (IH-Int) and compared it to a commercially available assay, ViroSeq Integrase Genotyping kit (VS-Int) amongst HIV-1 clade C infected individuals.

Methods

We used 54 plasma samples from treatment naïve participants and one plasma sample from a patient failing INSTI based cART. Specimens were genotyped using both the VS-Int and IH-Int assays. Stanford HIV drug resistance database were used for integrase resistance interpretation. We compared the major and minor resistance mutations, pairwise nucleotide and amino-acid identity, costs and assay time.

Results

Among 55 specimens tested with IH-Int, 53 (96.4%) successfully amplified compared to 45/55 (81.8%) for the VS-Int assay. The mean nucleotide and amino acid similarity from 33 paired sequences was 99.8% (SD ± 0.30) and 99.8% (SD ± 0.39) for the IH-Int and VS-Int assay respectively. The reagent cost/sample were 32 USD and 147 USD for IH-Int and VS-Int assay, respectively. All sequenced samples were confirmed as HIV-1 subtype C.

Conclusions

The IH-Int assay had a high amplification success rate and high concordance with the commercial assay. It is significantly cheaper compared to the commercial assay. Our assay has the needed specifications for routine monitoring of participants on Dolutegravir based regimens in Botswana.

Klíčová slova:

Antimicrobial resistance – Drug screening – Genotyping – HIV-1 – Nucleotide sequencing – Reverse transcriptase-polymerase chain reaction – Viral load


Zdroje

1. Burton AH, Mertens TE. Provisional country estimates of prevalent adult human immunodeficiency virus infections as of end 1994: a description of the methods. International journal of epidemiology. 1998;27(1):101–7. Epub 1998/05/01. doi: 10.1093/ije/27.1.101 9563702.

2. UNAIDS. Fact sheet—Latest global and regional statistics on the status of the AIDS epidemic. 18 JULY 2018 [9 November 2018]. http://www.unaids.org/sites/default/files/media_asset/UNAIDS_FactSheet_en.pdf.

3. Collaborators GH. Estimates of global, regional, and national incidence, prevalence, and mortality of HIV, 1980–2015: the Global Burden of Disease Study 2015. The lancet HIV. 2016;3(8):e361–e87. Epub 2016/07/30. doi: 10.1016/S2352-3018(16)30087-X 27470028.

4. Palella FJ Jr., Delaney KM, Moorman AC, Loveless MO, Fuhrer J, Satten GA, et al. Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators. The New England journal of medicine. 1998;338(13):853–60. Epub 1998/03/27. doi: 10.1056/NEJM199803263381301 9516219.

5. Farahani M, Price N, El-Halabi S, Mlaudzi N, Keapoletswe K, Lebelonyane R, et al. Trends and determinants of survival for over 200 000 patients on antiretroviral treatment in the Botswana National Program: 2002–2013. Aids. 2016;30(3):477–85. Epub 2015/12/05. doi: 10.1097/QAD.0000000000000921 26636931.

6. AIDSinfo. U.S. Department of Health and Human Services, FDA-Approved HIV Medicines [May 21, 2019]. https://aidsinfo.nih.gov/understanding-hiv-aids/fact-sheets/21/58/fda-approved-hiv-medicines.

7. UNAIDS C, the Bill & Melinda Gates Foundation, Unitaid, DFID, PEPFAR, USAID, the Global Fund to Fight AIDS, Tuberculosis and, Malaria MLLaAP. New high-quality antiretroviral therapy to be launched in South Africa, Kenya and over 90 low- and middle-income countries at reduced price 2017 [May 21, 2019]. https://www.unaids.org/en/resources/presscentre/pressreleaseandstatementarchive/2017/september/20170921_TLD.

8. WHO. Dolutegravir (DTG) and the fixed dose combination (FDC) of tenofovir/lamivudine/dolutegravir (TLD) 2018 [4 November 2018]. http://www.who.int/hiv/pub/arv/DTG-TLD-arv_briefing_2018.pdf.

9. Cahn P, Pozniak AL, Mingrone H, Shuldyakov A, Brites C, Andrade-Villanueva JF, et al. Dolutegravir versus raltegravir in antiretroviral-experienced, integrase-inhibitor-naive adults with HIV: week 48 results from the randomised, double-blind, non-inferiority SAILING study. Lancet (London, England). 2013;382(9893):700–8. Epub 2013/07/09. doi: 10.1016/S0140-6736(13)61221-0 23830355.

10. Raffi F, Rachlis A, Stellbrink HJ, Hardy WD, Torti C, Orkin C, et al. Once-daily dolutegravir versus raltegravir in antiretroviral-naive adults with HIV-1 infection: 48 week results from the randomised, double-blind, non-inferiority SPRING-2 study. Lancet (London, England). 2013;381(9868):735–43. Epub 2013/01/12. doi: 10.1016/S0140-6736(12)61853-4 23306000.

11. Gupta RK, Gregson J, Parkin N, Haile-Selassie H, Tanuri A, Andrade Forero L, et al. HIV-1 drug resistance before initiation or re-initiation of first-line antiretroviral therapy in low-income and middle-income countries: a systematic review and meta-regression analysis. The Lancet Infectious Diseases. 2018;18(3):346–55. doi: 10.1016/S1473-3099(17)30702-8 29198909

12. TenoRes Study G. Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study. Lancet Infect Dis. 2016;16(5):565–75. Epub 2016/02/03. doi: 10.1016/S1473-3099(15)00536-8 26831472.

13. Phillips AN, Stover J, Cambiano V, Nakagawa F, Jordan MR, Pillay D, et al. Impact of HIV Drug Resistance on HIV/AIDS-Associated Mortality, New Infections, and Antiretroviral Therapy Program Costs in Sub-Saharan Africa. The Journal of infectious diseases. 2017;215(9):1362–5. Epub 2017/02/17. doi: 10.1093/infdis/jix089 28329236.

14. Meireles MV, Pascom ARP, Duarte EC, McFarland W. Comparative effectiveness of first-line antiretroviral therapy: results from a large real-world cohort after the implementation of Dolutegravir. Aids. 2019. Epub 2019/05/15. doi: 10.1097/qad.0000000000002254 31082860.

15. Walmsley S, Baumgarten A, Berenguer J, Felizarta F, Florence E, Khuong-Josses MA, et al. Brief Report: Dolutegravir Plus Abacavir/Lamivudine for the Treatment of HIV-1 Infection in Antiretroviral Therapy-Naive Patients: Week 96 and Week 144 Results From the SINGLE Randomized Clinical Trial. J Acquir Immune Defic Syndr. 2015;70(5):515–9. Epub 2015/08/12. doi: 10.1097/QAI.0000000000000790 26262777.

16. Underwood MR, Johns BA, Sato A, Martin JN, Deeks SG, Fujiwara T. The activity of the integrase inhibitor dolutegravir against HIV-1 variants isolated from raltegravir-treated adults. Journal of acquired immune deficiency syndromes (1999). 2012;61(3):297–301. doi: 10.1097/QAI.0b013e31826bfd02 22878423.

17. Garrido C, Soriano V, Geretti AM, Zahonero N, Garcia S, Booth C, et al. Resistance associated mutations to dolutegravir (S/GSK1349572) in HIV-infected patients—impact of HIV subtypes and prior raltegravir experience. Antiviral research. 2011;90(3):164–7. Epub 2011/03/29. doi: 10.1016/j.antiviral.2011.03.178 21439330.

18. Seatla KK, Avalos A, Moyo S, Mine M, Diphoko T, Mosepele M, et al. Four-class drug-resistant HIV-1 subtype C in a treatment experienced individual on dolutegravir-based antiretroviral therapy in Botswana. Aids. 2018;32(13):1899–902. Epub 2018/06/13. doi: 10.1097/QAD.0000000000001920 29894383.

19. Achieng L, Riedel DJ. Dolutegravir Resistance and Failure in a Kenyan Patient. The Journal of infectious diseases. 2019;219(1):165–7. Epub 2018/08/31. doi: 10.1093/infdis/jiy436 30165703.

20. DHHS. Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the Use of Antiretroviral Agents in Adults and Adolescents Living with HIV. Department of Health and Human Services. [5th November 2018]. http://www.aidsinfo.nih.gov/ContentFiles/AdultandAdolescentGL.pdf.

21. EACS. European AIDS Clinical Society (EACS) Guidelines version 9.1 October 2018,English [5 November 2018]. http://www.eacsociety.org/files/2018_guidelines-9.1-english.pdf.

22. WHO. Global action plan on HIV drug resistance 2017–2021. Geneva: World Health Organization; 2017.Licence: CC BY-NC-SA 3.0 IGO 2017 [May 21, 2019]. https://www.who.int/hiv/pub/drugresistance/hivdr-action-plan-2017-2021/en/.

23. Cochrane S, Daniel J, Forsyth S, Smit E. First reported case of integrase (R263K, G163R) and reverse transcriptase (M184V)-transmitted drug resistance from a drug-naive patient failing Triumeq. Aids. 2018;32(13):1905–7. Epub 2018/07/26. doi: 10.1097/QAD.0000000000001919 30045059.

24. Boyd SD, Maldarelli F, Sereti I, Ouedraogo GL, Rehm CA, Boltz V, et al. Transmitted raltegravir resistance in an HIV-1 CRF_AG-infected patient. Antiviral therapy. 2011;16(2):257–61. Epub 2011/03/31. doi: 10.3851/IMP1749 21447876.

25. Young B, Fransen S, Greenberg KS, Thomas A, Martens S, St Clair M, et al. Transmission of integrase strand-transfer inhibitor multidrug-resistant HIV-1: case report and response to raltegravir-containing antiretroviral therapy. Antiviral therapy. 2011;16(2):253–6. Epub 2011/03/31. doi: 10.3851/IMP1748 21447875.

26. Achieng L, Riedel DJ. Dolutegravir Resistance and Failure in a Kenyan Patient. The Journal of infectious diseases. 2018. Epub 2018/08/31. doi: 10.1093/infdis/jiy436 30165703.

27. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America. 1977;74(12):5463–7. doi: 10.1073/pnas.74.12.5463 271968.

28. Bessong PO, Nwobegahay J. Genetic Analysis of HIV-1 Integrase Sequences from Treatment Naive Individuals in Northeastern South Africa. Int J Mol Sci. 2013;14(3):5013–24. Epub 2013/03/05. doi: 10.3390/ijms14035013 23455469.

29. Hearps AC, Greengrass V, Hoy J, Crowe SM. An HIV-1 integrase genotype assay for the detection of drug resistance mutations. Sexual health. 2009;6(4):305–9. Epub 2009/11/18. doi: 10.1071/SH09041 19917199.

30. To SW, Chen JH, Wong KH, Chan KC, Ng HM, Wu H, et al. Performance comparison of an in-house integrase genotyping assay versus the ViroSeq Integra48, and study of HIV-1 integrase polymorphisms in Hong Kong. Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology. 2013;58(1):299–302. Epub 2013/07/28. doi: 10.1016/j.jcv.2013.06.040 23886504.

31. Van Laethem K, Schrooten Y, Covens K, Dekeersmaeker N, De Munter P, Van Wijngaerden E, et al. A genotypic assay for the amplification and sequencing of integrase from diverse HIV-1 group M subtypes. Journal of virological methods. 2008;153(2):176–81. Epub 2008/08/19. doi: 10.1016/j.jviromet.2008.07.008 18706932.

32. CMS. Center for Medicare and Medicaid Services, Clinical Laboratory Fee Schedule, Code 87906 (Genotype dna/rna hiv) and Code 87901 (Genotype dna hiv reverse t) 2019 [May 21, 2019]. https://www.cms.gov/apps/ama/license.asp?file=/Medicare/Medicare-Fee-for-Service-Payment/ClinicalLabFeeSched/Downloads/19CLABQ1.zip.

33. Inzaule SC, Hamers RL, Paredes R, Yang C, Schuurman R, Rinke de Wit TF. The Evolving Landscape of HIV Drug Resistance Diagnostics for Expanding Testing in Resource-Limited Settings. AIDS reviews. 2017;19(4):219–30. Epub 2017/02/10. 28182618.

34. Inzaule S, Yang C, Kasembeli A, Nafisa L, Okonji J, Oyaro B, et al. Field evaluation of a broadly sensitive HIV-1 in-house genotyping assay for use with both plasma and dried blood spot specimens in a resource-limited country. Journal of clinical microbiology. 2013;51(2):529–39. Epub 2012/12/12. doi: 10.1128/JCM.02347-12 23224100.

35. Rowley CF, MacLeod IJ, Maruapula D, Lekoko B, Gaseitsiwe S, Mine M, et al. Sharp increase in rates of HIV transmitted drug resistance at antenatal clinics in Botswana demonstrates the need for routine surveillance. The Journal of antimicrobial chemotherapy. 2016;71(5):1361–6. Epub 2016/03/02. doi: 10.1093/jac/dkv500 26929269.

36. Wallis CL, Papathanasopoulos MA, Lakhi S, Karita E, Kamali A, Kaleebu P, et al. Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1. J Virol Methods. 2010;163(2):505–8. Epub 2009/11/18. doi: 10.1016/j.jviromet.2009.11.011 19917318.

37. Codes G. Sequencher® version 5.4.6 DNA sequence analysis software, Gene Codes Corporation, Ann Arbor, MI USA [May 21, 2019]. http://www.genecodes.com/.

38. Hall TA, editor BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic acids symposium series; 1999: [London]: Information Retrieval Ltd., c1979-c2000.

39. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research. 1994;22(22):4673–80. Epub 1994/11/11. doi: 10.1093/nar/22.22.4673 7984417.

40. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular biology and evolution. 2016;33(7):1870–4. Epub 2016/03/24. doi: 10.1093/molbev/msw054 27004904.

41. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular biology and evolution. 1993;10(3):512–26. doi: 10.1093/oxfordjournals.molbev.a040023 8336541

42. Liu TF, Shafer RW(2006). Web Resources for HIV type 1 Genotypic-Resistance Test Interpretation. Clin Infect Dis 42(11):1608–18. Epub 2006 Apr 28 doi: 10.1086/503914 16652319

43. Pineda-Pena AC, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, et al. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases. 2013;19:337–48. Epub 2013/05/11. doi: 10.1016/j.meegid.2013.04.032 23660484.

44. MoHW. HANDBOOK OF THE BOTSWANA 2016 INTEGRATED HIV CLINICAL CARE GUIDELINES [May 22, 2019]. https://www.moh.gov.bw/guidelines.html.

45. Beddows S, Galpin S, Kazmi SH, Ashraf A, Johargy A, Frater AJ, et al. Performance of two commercially available sequence-based HIV-1 genotyping systems for the detection of drug resistance against HIV type 1 group M subtypes. Journal of medical virology. 2003;70(3):337–42. Epub 2003/05/27. doi: 10.1002/jmv.10401 12766994.

46. Aghokeng AF, Mpoudi-Ngole E, Chia JE, Edoul EM, Delaporte E, Peeters M. High failure rate of the ViroSeq HIV-1 genotyping system for drug resistance testing in Cameroon, a country with broad HIV-1 genetic diversity. Journal of clinical microbiology. 2011;49(4):1635–41. Epub 2011/01/29. doi: 10.1128/JCM.01478-10 21270223.

47. Zhou Z, Wagar N, DeVos JR, Rottinghaus E, Diallo K, Nguyen DB, et al. Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings. PLoS One. 2011;6(11):e28184. Epub 2011/12/02. doi: 10.1371/journal.pone.0028184 22132237.

48. Ammaranond P, Sanguansittianant S, Raju PA, Cunningham P, Horthongkham N. Development of a cost-effective assay for genotyping of HIV-1 non-B subtype for drug resistance. Journal of virological methods. 2014;199:102–7. Epub 2014/01/28. doi: 10.1016/j.jviromet.2014.01.007 24462843.


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