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. The 400 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.