To Profile Nucleoside Reverse Transcriptase Inhibitor Drug-Resistance and Susceptibility Patterns of Naive HIV Positive Patients from Machakos Level 5 Hospital

  • Mr. Stanley Kiprop PG Student, Biomedical Science, University of Eastern Africa Baraton, P.O.BOX. 2500-30100 Eldoret, Kenya
  • Dr. Gracelyn P. Francis Lecturer, Department of Biological Sciences and Agriculture, University of Eastern Africa, Baraton, P.O.BOX 2500 – 30100 Eldoret, Kenya
  • Dr. Mutemi Muthangya Lecturer, Department of Biological and Physical Sciences, South Eastern Kenya University, P.O.BOX 170-90200 Kitui, Kenya
Keywords: Anti retroviral therapy, Nucleoside Reverse Transcriptase Inhibitor

Abstract

This study focused on Nucleoside Reverse Transcriptase drug-resistance profiling and the susceptibility patterns for the plasma samples obtained from HIV-positive naïve patients enrolled at Machakos Level 5 Hospital. The research's specific objectives were to profile resistance to Nucleoside Reverse Transcriptase Inhibitor drugs and then identify the markers for resistance to Nucleoside Reverse Transcriptase Inhibitor. This study used an experimental research design; DNA was extracted from the plasma samples, and PCR was amplified using polymerase-gene specific primers and later Gel electrophoresis. Then finally, cycle sequencing of the polymerase (pol) gen. The amplified products were sequenced, and drug-resistant mutations were determined using Los Alamos HIV DR database. All amplified samples from the PCR had the gel cut/excised and cleaned using the QIA quick gel extraction kit protocol. Sequences with high relatedness were fetched in a FASTA format and aligned using the Mega Evolutionary Genetic Analysis (MEGA) software version 10 using the Neighbor Joining (NJ) algorithm and the 1000 Bootstrap resampling algorithm. The main HIV strain detected in this study was the HIV A1 subtype, the major sub-subtype in Kenya. No other subtypes were noted in the study. Regarding NRTIs, the major mutation noted was D67E which indicated inadequate level, zidovudine resistance, and drug susceptibility to abacavir, emtricitabine, lamivudine, and tenofovir noted with no resistance to NNRTIs. However, there were minor mutations noted. Drug resistance mutations were found in high numbers associated with viral load and treatment time. Importantly, patients with triple and dual-class drug resistance should immediately alter ART regimens to alter the possibility of transmitting multi-drug-resistant HIV-1 strains.

References

. Adhiambo, M., Makwaga, O., Adungo, F., Kimani, H., Mulama, D.H., Korir, J.C. and Mwau, M., (2021). Human immunodeficiency virus (HIV) type 1 genetic diversity in HIV positive individuals on antiretroviral therapy in a cross-sectional study conducted in Teso, Western Kenya. The Pan African Medical Journal, 38.

. Adungo, F.O., Gicheru, M.M., Adungo, N.I., Matilu, M.M., Lihana, R.W. and Khamadi, S.A., (2014). Diversity of human immunodeficiency virus type-1 subtypes in Western Kenya.

. Akhome, P. (2021). HIV subtypes. Available online at https://www.aidsmap.com/about-hiv/hiv-1-subtypes accessed 30th October 2021.

. Bbosa, N., Kaleebu, P. and Ssemwanga, D., (2019). HIV subtype diversity worldwide. Current Opinion in HIV and AIDS, 14(3), pp.153-160.

. Beyrer, C., & Pozniak, A. (2017). HIV drug resistance—an emerging threat to epidemic control. New England Journal of Medicine, 377(17), 1605-1607.

. Gounder, K., Oyaro, M., Padayachi, N., Zulu, T.M., de Oliveira, T., Wylie, J. and Ndung'u, T., (2017). Complex Subtype Diversity of HIV-1 Among Drug Users in Major Kenyan Cities. AIDS research and human retroviruses, 33(5), pp.500-510.

. Gupta, R. K., Jordan, M. R., Sultan, B. J., Hill, A., Davis, D. H., Gregson, J., ... & Bertagnolio, S. (2012). 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. The Lancet, 380(9849), 1250-1258.

. Hassan, A.S., Esbjörnsson, J., Wahome, E., Thiong'o, A., Makau, G.N., Price, M.A. and Sanders, E.J., (2018) HIV-1 subtype diversity, transmission networks, and transmitted drug resistance amongst acute and early infected MSM populations from Coastal Kenya. PloS one, 13(12), p.e0206177.

. Immunopedia. (2021). ARV Mode of Action – NRTI. Available online at https://www.immunopaedia.org.za/treatment-diagnostics/hiv-infection-treatment/arv-mode-of-action/ accessed 5th November 2021.

. Kageha, S., Lihana, R.W., Okoth, V., Mwau, M., Okoth, F.A., Songok, E.M., Ngaira, J.M. and Khamadi, S.A., (2012). HIV type 1 subtype surveillance in central Kenya. AIDS research and human retroviruses, 28(2), pp.228-231.

. Khamadi, S.A., Lihana, R.W., Osman, S., Mwangi, J., Muriuki, J., Lagat, N., Kinyua, J., Mwau, M., Kageha, S., Okoth, V. and Ochieng, W., (2009). Genetic diversity of HIV type 1 along the coastal strip of Kenya. AIDS research and human retroviruses, 25(9), pp.919-923.

. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of molecular evolution, 16(2), 111-120.

. Kinyua, J.G., Lihana, R.W., Kiptoo, M., Muasya, T., Odera, I., Muiruri, P. and Songok, E.M., (2018). Antiretroviral resistance among HIV-1 patients on first-line therapy attending a comprehensive care clinic in Kenyatta National Hospital, Kenya: a retrospective analysis. Pan African Medical Journal, 29(1), pp.1-6.

. Kitawi, R.C., Nzomo, T., Mwatelah, R.S., Aman, R., Kimulwo, M.J., Masankwa, G., Lwembe, R.M., Okendo, J., Ogutu, B. and Ochieng, W., (2015). HIV-1 subtype diversity based on envelope C2V3 sequences from Kenyan patients on highly active antiretroviral therapy. AIDS research and human retroviruses, 31(4), pp.452-455.

. Koigi, P., Ngayo, M. O., Khamadi, S., Ngugi, C., & Nyamache, A. K. (2014). HIV type 1 drug resistance patterns among patients failing first- and second-line antiretroviral therapy in Nairobi, Kenya. BMC research notes, 7(1), 1-6.

. Lihana, R.W., Khamadi, S.A., Lubano, K., Lwembe, R., Kiptoo, M.K., Lagat, N., Kinyua, J.G., Okoth, F.A., Songok, E.M., Makokha, E.P. and Ichimura, H., (2009). HIV type 1 subtype diversity and drug resistance among HIV type 1-infected Kenyan patients initiating antiretroviral therapy. AIDS research and human retroviruses, 25(12), pp.1211-1217.

. Liu, T. F., & Shafer, R. W. (2006). Web resources for HIV type 1 genotypic-resistance test interpretation. Clinical infectious diseases, 42(11), 1608-1618.

. Luvai, E., Waihenya, R., Munyao, J., Sanguli, L., Mwachari, C. and Khamadi, S., (2015). HIV-1 Drug Resistance Mutations in Patients Failing 1st Line Therapy in a Comprehensive Care Center in Nairobi, Kenya.

. Mabeya, S.N., (2021). HIV-1 Genetic Diversity, Tropism and Drug Resistance Mutations among HIV Infected Patients Attending Comprehensive Care Clinic in Kisii Teaching and Referral Hospital, Kenya (Doctoral dissertation, JKUAT-COHES).

. Magdeldin, S. (Ed.). (2012). Gel electrophoresis: Principles and basics. BoD–Books on Demand.

. NASCOP, (2018), Guidelines on Use of Antiretroviral Drugs for Treating and Preventing HIV Infection in Kenya, (2018) Edition. Available online at: https://www.nascop.or.ke/new-guidelines/ Accessed 30th November 2021.

. Ndembi, N., Takehisa, J., Zekeng, L., Kobayashi, E., Ngansop, C., Songok, E. M., ... & Ichimura, H. (2004). Genetic diversity of HIV type 1 in rural eastern Cameroon. JAIDS Journal of Acquired Immune Deficiency Syndromes, 37(5), 1641-1650.

. Nishimaki, T., & Sato, K. (2019). An extension of the Kimura two-parameter model to the natural evolutionary process. Journal of molecular evolution, 87(1), 60-67.

. Onywera, H., Maman, D., Inzaule, S., Auma, E., Were, K., Fredrick, H., ... & Zeh, C. (2017). Surveillance of HIV-1 pol transmitted drug resistance in acutely and recently infected antiretroviral drug-naive persons in rural western Kenya. PloS one, 12(2), e0171124.

. Rhee, S.Y., Gonzales, M.J., Kantor, R., Betts, B.J., Ravela, J. and Shafer, R.W., (2003). Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic acids research, 31(1), pp.298-303.

. Rhee, S.Y., Kantor, R., Katzenstein, D.A., Camacho, R., Morris, L., Sirivichayakul, S., Jorgensen, L., Brigido, L.F., Schapiro, J.M., Shafer, R.W. and International Non-Subtype B HIV-1 Working Group, (2006). HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. AIDS (London, England), 20(5), p.643.

. Saida, S. J., Manikandan, A., Kaliyaperumal, M., Rumalla, C. S., Khan, A. A., Jayaraman, V. B., ... & Rao, S. V. (2019). Identification, isolation and characterization of dolutegravir forced degradation products and their cytotoxicity potential. Journal of pharmaceutical and biomedical analysis, 174, 588-594.

. Saitou, N., & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution, 4(4), 406-425.

. Shafer, R.W., Jung, D.R. and Betts, B.J., (2000). Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries. Nature medicine, 6(11), pp.1290-1292.

. Songok, E. M., Lwembe, R. M., Kibaya, R., Kobayashi, K., Ndembi, N., Kita, K., ... & Ichimura, H. (2004). Active generation and selection for HIV intersubtype A/D recombinant forms in a coinfected patient in Kenya. AIDS research and human retroviruses, 20(2), 255-258.

. UNAIDS. Data Book 2017 - Joint United Nations Programme on HIV/AIDS. Geneva: UNAIDS; 2017.

. United Nations (UN). Sustainable Development Goals - Goal 3: Ensure healthy lives and promote wellbeing for all at all ages. New York: UN; 2015.

. Yang, O. O., Lin, H., Dagarag, M., Ng, H. L., Effros, R. B., & Uittenbogaart, C. H. (2005). Decreased perforin and granzyme B expression in senescent HIV-1-specific cytotoxic T lymphocytes. Virology, 332(1), 16-19.

Published
2022-06-11
How to Cite
Mr. Stanley Kiprop, Dr. Gracelyn P. Francis, & Dr. Mutemi Muthangya. (2022). To Profile Nucleoside Reverse Transcriptase Inhibitor Drug-Resistance and Susceptibility Patterns of Naive HIV Positive Patients from Machakos Level 5 Hospital. International Journal of Sciences: Basic and Applied Research (IJSBAR), 62(2), 366-379. Retrieved from https://gssrr.org/index.php/JournalOfBasicAndApplied/article/view/14156
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Articles