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

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.