Sabry M. El-Bahr1,2, Mahmoud Kandeel1,3, I.F. Albokhadaim1, M. Al-Nazawi1 and Hafiz Ahmed4
1Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University,
Al-Ahsa 31982, P.O. 400, Saudi Arabia
2Department of Biochemistry, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21523, Egypt
3Department of Pharmacology, Faculty of Veterinary Medicine, Kafr Elsheikh University, Egypt
4GlycoMentra Inc., 1450 South Rolling Road, Baltimore, MD 21227, USA
In this study, we provide a comprehensive reverse diagnostic workflow, in which, the in-silico amino acid composition was employed retrogradely to shortlist the viral spike antigenic epitopes to infer diagnostics efficiency. This study was aimed to explore the analytical estimates of changes in epitope composition among MERS-CoV lineages. This can be used as a predictor of the effectiveness of rapid diagnostic testing. Therefore, MERS-CoV lineage-specific spike protein sequences were extracted, aligned and compared. In addition, the degree of sequence similarity, as well as pairwise comparison, phylogenetic relations and antigenic epitopes analysis, have been conducted. The current findings indicated that no differences were observed in length and range of epitopes for each virus among all studied lineages. Most of epitopes sequences were conserved. However, few sequences showed few single amino acid mutations. About 20% of epitopes were located at the receptor-binding domain (RBD) and 80% of these were located in the other Spike`s domains. These mutations were related to lineage 2 and 3 and not for lineage 1, 4 and 5. The number of difference among viruses accession no (ALA49781, ALA49594, ALA49440, ALA50001, ALA49935, ALA49847, ALA49825, ALA49561, ALA49374, ALA49803, ALA49660, ALA49352, ALA49671, ALA49341, AHX00711, AHY22565, AJG44124, AJG44091, ALA49429, ALA49418, ALA49902, AHY22525, AHX71946, AHE78108.1, AHI48672.1, AHI48550) was maximum of 8. No gaps were observed in the epitopes alignment. The identity of spike protein among the lineages ranged from 99.5 -100%. The study concluded that any of studied epitopes are suitable for production of rapid tests of MERS CoV in dromedary camels, particularly that produced from lineages 1, 4 and 5.
Key words: MERS CoV, camels, epitopes, viral lineage, rapid test