ANALYSIS OF THE GENETIC DIVERSITY AND PHYLOGENETIC RELATIONSHIP OF HIV (GP-41) SEQUENCES FROM DIFFERENT REGIONS OF PAKISTAN

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Muhammad Zahid Ali
Rabeea Zia
Danish Daniyal
Sumbal Nosheen
Syed Sohail Ahmad
Mazhar
Sana Sardar
Anis Shahzad Khan
Sumaira Salahuddin Lodhi
Azhar Abbas
Shah Zeb
Ayesha Kousar
Muhammad Naveed

Keywords

Human Immunodeficiency Virus, HIV associated biomarkers, polymorphism, envelop gene GP41

Abstract

Background: The Human Immunodeficiency Virus (HIV) is a highly morphic, retrovirus that rapidly evolves through mutation as well as recombination. However, no significant data of sequenced glycoprotein (GP41) of HIV exist in Pakistan due to its fast mutation rate. The purpose of this study is to analyze the polymorphism rate in HIV envelop gene (GP41).


Methodology: The current study was conducted at The University of Haripur, Department of Microbiology. Initially, RNA extraction and reverse transcription were carried out under Punjab AIDS Control Program, the molecular analyses was carried out at the microbiology lab of The University of Haripur. Molecular sequencing was done by the Center for Applied Microbiology (CAMB), Lahore and the blood parameters were analyzed at the Yahya Welfare Complex Haripur, KP, Pakistan.


Results: Out of 57, thirty seven (37) were identified as HIV positive by CMIA method and confirmed by PCR. Out of 37 isolated, 4 (10.8%) isolates carry GP41 gene. GP41 of HIV1 was divided into 2 fragments of 494 bp and 552 bp for PCR amplification, after sequencing process, the resultant sequences were merged to obtain a complete GP41 sequence. Bioinformatic analysis of sequenced data detected substitutions in 11 codon positions. Alanine substitution with threonine, arginine with cysteine, serine with proline, serine with leucine, valine with leucine, serine with alanine were detected. Some of these substitutions were related to enfuvirtide resistance.


Conclusion: This study serves as a platform for healthcare providers to monitor HIV-related clinical biomarkers, preventing early toxicity, improving patient quality of life, and reducing mortality rates. The study's polymorphism analysis reveals substitution points for refined drug design against the frequently mutating envelope gene, enhancing therapeutic resistance coverage.

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References

1. Finlayson, T., et al., Changes in HIV preexposure prophylaxis awareness and use among men who have sex with men—20 urban areas, 2014 and 2017. Morbidity and Mortality Weekly Report, 2019. 68(27): p. 597.
2. Melhuish, A. and P. Lewthwaite, Natural history of HIV and AIDS. Medicine, 2018. 46(6): p. 356-361.
3. HIV/AIDS, J.U.N.P.o., Confronting Discrimination Overcoming HIV-Related Stigma in Health Care Settings and Beyond. 2017, Joint United Nations Programme on HIV/AIDS.
4. Sullivan, P.S., et al., Epidemiology of HIV in the USA: epidemic burden, inequities, contexts, and responses. The Lancet, 2021. 397(10279): p. 1095-1106.
5. Rabold, E.M., et al., Systematic review of reported HIV outbreaks, Pakistan, 2000–2019. Emerging infectious diseases, 2021. 27(4): p. 1039.
6. Hasham, K., N. Ahmed, and B. Zeshan, Circulating microRNAs in oncogenic viral infections: Potential diagnostic biomarkers. SN Applied Sciences, 2020. 2(3): p. 1-13.
7. Ahmad, A., et al., Narrative on Hydrogen Therapy and its Clinical Applications: Safety and Efficacy. Current Pharmaceutical Design, 2022. 28(31): p. 2519-2537.
8. Al-Mhanna, S.B., et al., Effectiveness of physical activity on immunity markers and quality of life in cancer patient: a systematic review. PeerJ, 2022. 10: p. e13664.
9. Al-Hatamleh, M.A., et al., Applications of alginate-based nanomaterials in enhancing the therapeutic effects of bee products. Frontiers in Molecular Biosciences, 2022. 9: p. 350.
10. Perrier, M., et al., HIV-1 protease, Gag and gp41 baseline substitutions associated with virological response to a PI-based regimen. Journal of Antimicrobial Chemotherapy, 2019. 74(6): p. 1679-1692.
11. Auld, A.F., et al., Lower levels of antiretroviral therapy enrollment among men with HIV compared with women—12 countries, 2002–2013. Morbidity and Mortality Weekly Report, 2015. 64(46): p. 1281-1286.
12. Mussa, A., et al., High-dose vitamin C for cancer therapy. Pharmaceuticals, 2022. 15(6): p. 711.
13. Mohd Salim, N.H., et al., The Immunosuppressive Effect of TNFR2 Expression in the Colorectal Cancer Microenvironment. Biomedicines, 2023. 11(1): p. 173.
14. Wondimeneh, Y., et al., HBV and HCV seroprevalence and their correlation with CD4 cells and liver enzymes among HIV positive individuals at University of Gondar Teaching Hospital, Northwest Ethiopia. Virology journal, 2013. 10: p. 1-8.
15. Worobey, M., et al., Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature, 2008. 455(7213): p. 661-664.
16. Zou, S., et al., Prevalence, incidence, and residual risk of human immunodeficiency virus and hepatitis C virus infections among United States blood donors since the introduction of nucleic acid testing. Transfusion, 2010. 50(7): p. 1495-1504.
17. Waheed, U., et al., Epidemiology of HIV/AIDS and Syphilis among high risk groups in Pakistan. Pakistan Journal of Zoology, 2017. 49(5).
18. Van Griensven, F., et al., Evidence of a previously undocumented epidemic of HIV infection among men who have sex with men in Bangkok, Thailand. Aids, 2005. 19(5): p. 521-526.
19. Sheikh, A., 519P Seroprevalence of blood borne viruses among blood donors attended during an earthquake campaign at Gwadar Port, a south-west coastal area of Pakistan. Annals of Oncology, 2015. 26: p. ix156.
20. Siraprapasiri, T., et al., The impact of Thailand's public health response to the HIV epidemic 1984–2015: understanding the ingredients of success. Journal of virus eradication, 2016. 2: p. 7-14.
21. Swanepoel, C.R., et al., Kidney disease in the setting of HIV infection: conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference. Kidney international, 2018. 93(3): p. 545-559.

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