Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits

James Kimotho; Zipporah N g’ang’a2; Edna Nyairo; Missiani Ochwoto; Nicholas Nzioka; Francis Ogolla; Michael Kiptoo

doi:doi:10.11648/j.ajim.20150301.13

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Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits

James Kimotho, Zipporah N g’ang’a2, Edna Nyairo, Missiani Ochwoto, Nicholas Nzioka, Francis Ogolla, Michael Kiptoo

Published in American Journal of Internal Medicine (Volume 3, Issue 1)

Received: 22 January 2015 Accepted: 2 February 2015 Published: 10 February 2015

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Abstract

Background: Human Immunodeficiency Virus (HIV) is characterized by high rates of genetic variability in vivo that could affect the performance of the HIV-1 Antibody-Based Detection Kits in use in Kenya. Objective: This study aimed at establishing the diversity of Envelope gp41 Epitopes and its effects on performance of the currently used HIV diagnostic kits in Kenya. Methods: Two hundred (200) HIV positives and 200 HIV negatives samples were collected from the Regional Blood Transfusion Centers (RBTCs) in Kenya. Viral RNA was extracted from 96 HIV Positive samples and sequenced on gp41-immunodominant region (IDR).The sequences obtained were analyzed using various applications in the Los Alamos HIV Database. The HIV gp41-IDR consensus sequence generated was used to synthesize gp41 IDR peptide. The Global HIV gp41-IDR Consensus nucleotide sequence was obtained from literature and used also to synthesis corresponding gp41 IDR peptide. The two peptides were used to prepare HIV Testing ELISA kits. The400 plasma samples that had been collected from this study from RBTCs were tested using five HIV testing kits approved for use in Kenya. The same samples were tested using the two ELISA system developed. Results: The HIV Consensus gp41-IDR peptide from Kenya displays a similarity of 93.0% against HXB2 sequence and 95.3% against Global HIV Consensus gp41-IDR amino acid sequence. There were 331 (7.8%) substitutions in the Consensus gp41-IDR peptides (Kenya) out of which 151substitutions were due to the substitution in positions A96→N (n = 79) and A101→S (n = 75). Both Consensus gp41-IDR peptides (Kenya) and Consensus gp41-IDR peptides (Global) showed common substitutions rate of 4.2% (n = 151). All the kits that were used showed 100% agreement in results. Conclusion: Although the HIV Consensus gp41-IDR peptides (Kenya) showed marked substitutions in respect to Consensus gp41-IDR peptide (Global) there was no difference in effects on the performance of the HIV-1 Antibody-Based Detection Kits in use in Kenya.

Published in	American Journal of Internal Medicine (Volume 3, Issue 1)
DOI	10.11648/j.ajim.20150301.13
Page(s)	15-22
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2015. Published by Science Publishing Group

Keywords

Diversity, HIV, Substitution, Consensus, Immunodominant Region, gp41

References

[1]	UNAIDS. (2013). AIDS epidemic update: December 2013.
[2]	National AIDS and STI Control Programme, Ministry of Health, Kenya. September 2013. Kenya AIDS
[3]	Hutchinson, J. A. (2009). The Biology and evolution of HIV. Annual Review of Anthropology, 30, 5-108.
[4]	Lihana, R. W; Khamadi, S.A.; Lwembe, R. M.; Ochieng, W.; Kinyua, J.G.; Kiptoo, M. K.; Muriuki, J. K.; Lagat, N.; Osman, S.; Mwangi, J. M.; Okoth, F. A. and Songok E.M. (2009). The changing trend of HIV type 1 subtypes in Nairobi. AIDS Research and Human Retroviruses, 25, 337-42
[5]	Temin H. (1993). Retrovirus variations and reverse transcription: Abnormal strand transfers results in retrovirus genetic variation. Proceedings of the National Academy of Sciences, 90, 6900-3.
[6]	Wain-Hobson, S. (1999). Multiple infected cells and rampant recombination 6th Annual International Discussion Meeting on HIV Dynamics and Evolution; Atlanta
[7]	Holland, D. E. (1994). Mutation rates and rapid evolution of RNA viruses. In: The evolutionary biology of viruses. Morse, S.S. (ed).New York, Raven Press, 161- 85
[8]	Wei, X.; Liu, X.; Dobbs, T.; Kuehl, D.; Nkengasong, J.; Hu, D.; and Bharat Parekh, B. (2010). Development of Two Avidity-Based Assays to Detect Recent HIV Type 1 Seroconversion Using a Multisubtype gp41 Recombinant Protein. AIDS Research and Human Retroviruses, 26(1), 61-71. http://online.liebertpub.com/doi/abs/10.1089/aid.2009.0133. Accessed on 31st Dec 2014.
[9]	Thorstensson, R.; Andersson, S.; Lindbaeck, S.; Dias, F.; Mhalu, F.; Gaines, H. and Biberfeld, G. (1998) Evaluation of 14 commercial HIV-1/HIV-2 antibody assays using serum panels of diﬀerent geographical origin and clinical stage including a unique sero-conversion panel. Journal of Virological Methods, 70, 139-151.
[10]	Masciotra, S.; Rudolph, D. L.; Der Groen, G. V.; Yang, C and Lal.R.B. (2000). Serological Detection of Infection with Diverse Human and Simian Immunodeﬁciency Viruses Using Consensus env Peptides. Clinical and Diagnostic Laboratory Immunology, 7(40), 706–709
[11]	Bártolo and Taveira. (2012). HIV-1 Diversity and Its Implications in Diagnosis, Transmission, Disease Progression, and Antiretroviral Therapy. www.intechopen.com/download/pdf/28892. Accessed on 2nd Dec 2014
[12]	Ho, D; Neumann, A; Perelson, A; Chen, W; Leonard, J.M. and Makowitz, M. (1995). Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature, 373, 123-6
[13]	Kenya National Bureau of Statistics. (2010). HIV/AIDS-Related Knowledge, Attitudes, And Behaviour, Kenya Demographic and Health Survey (KDHS) 2008-09, 173-207.
[14]	http://www.measuredhs.com/pubs/pdf/FR229/FR229.pdf. Accessed on 2nd Dec 2014
[15]	Horal, P.B.; Svennerholm, S.; Jeansson, L.; Rymo, W. W.; Hall,and A.Vahlne. (1991). Continuous epitopes of the human immunodeﬁciency virus type 1 (HIV-1) transmembrane glycoprotein and reactivity of human sera to synthetic peptides representing various HIV-1 isolates. J. Virol. 65:2718–2723.
[16]	Oldstone, M. B.; A. Tishon, H.; Lewicki, H. J.; Kyson, V. A.; Feher, N.; AssaMunt and P. Wright, E. (1991). Mapping the anatomy of the immunodominant domain of the human immunodeﬁciency virus gp41 transmembrane protein: peptide conformation analysis using monoclonal antibodies and proton nuclear magnetic resonance spectroscopy. J. Virol. 65:1727–1734.
[17]	Parekh BS, Hu DJ, Vanichseni S, Satten GA, Candal D. (2001) Evaluation of a sensitive/less-sensitive testing algorithm using the 3A11-LS assay for detecting recent HIV seroconversion among individuals with HIV-1 subtype B or E infection in Thailand. AIDS Res Hum Retroviruses 17: 453–458.
[18]	Young CL, Hu DJ, Byers R, Vanichseni S, Young NL. (2003) Evaluation of a sensitive/less sensitive testing algorithm using the bioMerieux Vironostika-LS assay for detecting recent HIV-1 subtype B’ or E infection in Thailand. AIDS Res Hum Retroviruses 19: 481–486.
[19]	Johnson, R. P., A. Trocha, T. M. Buchanan, and B. D. Walker. 1992. Identificationof overlapping class I-restricted cytotoxic T cell epitopes in a conserved region of the human immunodeficiency virus type 1 envelope glycoprotein: definition of minimum epitopes and analysis of the effects of sequence variation. J. Exp. Med. 175:961–971.

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James Kimotho, Zipporah N g’ang’a2, Edna Nyairo, Missiani Ochwoto, Nicholas Nzioka, et al. (2015). Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits. American Journal of Internal Medicine, 3(1), 15-22. https://doi.org/10.11648/j.ajim.20150301.13

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James Kimotho; Zipporah N g’ang’a2; Edna Nyairo; Missiani Ochwoto; Nicholas Nzioka, et al. Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits. Am. J. Intern. Med. 2015, 3(1), 15-22. doi: 10.11648/j.ajim.20150301.13

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AMA Style

James Kimotho, Zipporah N g’ang’a2, Edna Nyairo, Missiani Ochwoto, Nicholas Nzioka, et al. Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits. Am J Intern Med. 2015;3(1):15-22. doi: 10.11648/j.ajim.20150301.13

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@article{10.11648/j.ajim.20150301.13,
  author = {James Kimotho and Zipporah N g’ang’a2 and Edna Nyairo and Missiani Ochwoto and Nicholas Nzioka and Francis Ogolla and Michael Kiptoo},
  title = {Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits},
  journal = {American Journal of Internal Medicine},
  volume = {3},
  number = {1},
  pages = {15-22},
  doi = {10.11648/j.ajim.20150301.13},
  url = {https://doi.org/10.11648/j.ajim.20150301.13},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajim.20150301.13},
  abstract = {Background: Human Immunodeficiency Virus (HIV) is characterized by high rates of genetic variability in vivo that could affect the performance of the HIV-1 Antibody-Based Detection Kits in use in Kenya. Objective: This study aimed at establishing the diversity of Envelope gp41 Epitopes and its effects on performance of the currently used HIV diagnostic kits in Kenya. Methods: Two hundred (200) HIV positives and 200 HIV negatives samples were collected from the Regional Blood Transfusion Centers (RBTCs) in Kenya. Viral RNA was extracted from 96 HIV Positive samples and sequenced on gp41-immunodominant region (IDR).The sequences obtained were analyzed using various applications in the Los Alamos HIV Database. The HIV gp41-IDR consensus sequence generated was used to synthesize gp41 IDR peptide. The Global HIV gp41-IDR Consensus nucleotide sequence was obtained from literature and used also to synthesis corresponding gp41 IDR peptide. The two peptides were used to prepare HIV Testing ELISA kits. The400 plasma samples that had been collected from this study from RBTCs were tested using five HIV testing kits approved for use in Kenya. The same samples were tested using the two ELISA system developed. Results: The HIV Consensus gp41-IDR peptide from Kenya displays a similarity of 93.0% against HXB2 sequence and 95.3% against Global HIV Consensus gp41-IDR amino acid sequence. There were 331 (7.8%) substitutions in the Consensus gp41-IDR peptides (Kenya) out of which 151substitutions were due to the substitution in positions A96→N (n = 79) and A101→S (n = 75). Both Consensus gp41-IDR peptides (Kenya) and Consensus gp41-IDR peptides (Global) showed common substitutions rate of 4.2% (n = 151). All the kits that were used showed 100% agreement in results. Conclusion: Although the HIV Consensus gp41-IDR peptides (Kenya) showed marked substitutions in respect to Consensus gp41-IDR peptide (Global) there was no difference in effects on the performance of the HIV-1 Antibody-Based Detection Kits in use in Kenya.},
 year = {2015}
}

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TY - JOUR
T1 - Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits
AU - James Kimotho
AU - Zipporah N g’ang’a2
AU - Edna Nyairo
AU - Missiani Ochwoto
AU - Nicholas Nzioka
AU - Francis Ogolla
AU - Michael Kiptoo
Y1 - 2015/02/10
PY - 2015
N1 - https://doi.org/10.11648/j.ajim.20150301.13
DO - 10.11648/j.ajim.20150301.13
T2 - American Journal of Internal Medicine
JF - American Journal of Internal Medicine
JO - American Journal of Internal Medicine
SP - 15
EP - 22
PB - Science Publishing Group
SN - 2330-4324
UR - https://doi.org/10.11648/j.ajim.20150301.13
AB - Background: Human Immunodeficiency Virus (HIV) is characterized by high rates of genetic variability in vivo that could affect the performance of the HIV-1 Antibody-Based Detection Kits in use in Kenya. Objective: This study aimed at establishing the diversity of Envelope gp41 Epitopes and its effects on performance of the currently used HIV diagnostic kits in Kenya. Methods: Two hundred (200) HIV positives and 200 HIV negatives samples were collected from the Regional Blood Transfusion Centers (RBTCs) in Kenya. Viral RNA was extracted from 96 HIV Positive samples and sequenced on gp41-immunodominant region (IDR).The sequences obtained were analyzed using various applications in the Los Alamos HIV Database. The HIV gp41-IDR consensus sequence generated was used to synthesize gp41 IDR peptide. The Global HIV gp41-IDR Consensus nucleotide sequence was obtained from literature and used also to synthesis corresponding gp41 IDR peptide. The two peptides were used to prepare HIV Testing ELISA kits. The400 plasma samples that had been collected from this study from RBTCs were tested using five HIV testing kits approved for use in Kenya. The same samples were tested using the two ELISA system developed. Results: The HIV Consensus gp41-IDR peptide from Kenya displays a similarity of 93.0% against HXB2 sequence and 95.3% against Global HIV Consensus gp41-IDR amino acid sequence. There were 331 (7.8%) substitutions in the Consensus gp41-IDR peptides (Kenya) out of which 151substitutions were due to the substitution in positions A96→N (n = 79) and A101→S (n = 75). Both Consensus gp41-IDR peptides (Kenya) and Consensus gp41-IDR peptides (Global) showed common substitutions rate of 4.2% (n = 151). All the kits that were used showed 100% agreement in results. Conclusion: Although the HIV Consensus gp41-IDR peptides (Kenya) showed marked substitutions in respect to Consensus gp41-IDR peptide (Global) there was no difference in effects on the performance of the HIV-1 Antibody-Based Detection Kits in use in Kenya.
VL - 3
IS - 1
ER -

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Author Information

James Kimotho

Kenya Medical Research Institute, Nairobi, Kenya
Zipporah N g’ang’a2

South Eastern Kenya University, School of Pure and Applied Science, Kitui, Kenya
Edna Nyairo

Kenya Medical Research Institute, Nairobi, Kenya
Missiani Ochwoto

Kenya Medical Research Institute, Nairobi, Kenya
Nicholas Nzioka

Kenya Medical Research Institute, Nairobi, Kenya
Francis Ogolla

Kenya Medical Research Institute, Nairobi, Kenya
Michael Kiptoo

Kenya Medical Research Institute, Nairobi, Kenya

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Plain Text BibTeX RIS

APA Style

James Kimotho, Zipporah N g’ang’a2, Edna Nyairo, Missiani Ochwoto, Nicholas Nzioka, et al. (2015). Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits. American Journal of Internal Medicine, 3(1), 15-22. https://doi.org/10.11648/j.ajim.20150301.13

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James Kimotho; Zipporah N g’ang’a2; Edna Nyairo; Missiani Ochwoto; Nicholas Nzioka, et al. Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits. Am. J. Intern. Med. 2015, 3(1), 15-22. doi: 10.11648/j.ajim.20150301.13

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James Kimotho, Zipporah N g’ang’a2, Edna Nyairo, Missiani Ochwoto, Nicholas Nzioka, et al. Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits. Am J Intern Med. 2015;3(1):15-22. doi: 10.11648/j.ajim.20150301.13

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@article{10.11648/j.ajim.20150301.13,
  author = {James Kimotho and Zipporah N g’ang’a2 and Edna Nyairo and Missiani Ochwoto and Nicholas Nzioka and Francis Ogolla and Michael Kiptoo},
  title = {Diversity within the Immunodominant Epitopes of Envelope gp41 HIV-1 in Kenya and Its Effects on Performance of the HIV-1 Antibody-Based Detection Kits},
  journal = {American Journal of Internal Medicine},
  volume = {3},
  number = {1},
  pages = {15-22},
  doi = {10.11648/j.ajim.20150301.13},
  url = {https://doi.org/10.11648/j.ajim.20150301.13},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajim.20150301.13},
  abstract = {Background: Human Immunodeficiency Virus (HIV) is characterized by high rates of genetic variability in vivo that could affect the performance of the HIV-1 Antibody-Based Detection Kits in use in Kenya. Objective: This study aimed at establishing the diversity of Envelope gp41 Epitopes and its effects on performance of the currently used HIV diagnostic kits in Kenya. Methods: Two hundred (200) HIV positives and 200 HIV negatives samples were collected from the Regional Blood Transfusion Centers (RBTCs) in Kenya. Viral RNA was extracted from 96 HIV Positive samples and sequenced on gp41-immunodominant region (IDR).The sequences obtained were analyzed using various applications in the Los Alamos HIV Database. The HIV gp41-IDR consensus sequence generated was used to synthesize gp41 IDR peptide. The Global HIV gp41-IDR Consensus nucleotide sequence was obtained from literature and used also to synthesis corresponding gp41 IDR peptide. The two peptides were used to prepare HIV Testing ELISA kits. The400 plasma samples that had been collected from this study from RBTCs were tested using five HIV testing kits approved for use in Kenya. The same samples were tested using the two ELISA system developed. Results: The HIV Consensus gp41-IDR peptide from Kenya displays a similarity of 93.0% against HXB2 sequence and 95.3% against Global HIV Consensus gp41-IDR amino acid sequence. There were 331 (7.8%) substitutions in the Consensus gp41-IDR peptides (Kenya) out of which 151substitutions were due to the substitution in positions A96→N (n = 79) and A101→S (n = 75). Both Consensus gp41-IDR peptides (Kenya) and Consensus gp41-IDR peptides (Global) showed common substitutions rate of 4.2% (n = 151). All the kits that were used showed 100% agreement in results. Conclusion: Although the HIV Consensus gp41-IDR peptides (Kenya) showed marked substitutions in respect to Consensus gp41-IDR peptide (Global) there was no difference in effects on the performance of the HIV-1 Antibody-Based Detection Kits in use in Kenya.},
 year = {2015}
}

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