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Regarding T cell, FSFGVTQEY epitope was highly recommended as therapeutic peptide vaccine to interact with MHC class I along with eight other epitopes that showed good population coverage against the whole world population.
Four epitopes showed high affinity to interact with MHC class II alleles (FNLTLLEPV, FAAIPFAQS, SFAAIPFAQ and FYVYKLQPL) with excellent population coverage throughout the world and Saudi Arabia.
Middle East Respiratory Syndrome (MERS) is a new viral emergent human disease caused by a novel strain of Coronavirus.
The use of peptides as therapeutics is experiencing renewed enthusiasm owing to advances in delivery, stability and design.Thus, the classical propensity scale methods and hidden Markov model programmed softwares from IEDB analysis resource ( were used for the following aspects: was used as linear B-cell epitope prediction from the conserved region with a default threshold value of 0.350.Prediction of surface accessibility: by using Emini surface accessibility prediction tool of the immune epitope database (IEDB) , the surface accessible epitopes were predicted from the conserved regions holding the default threshold value 1.000 or higher.Although the mortality of the infection is alarming (30-50%), as is its uncanny resemblance-at least in its clinical features to severe acute respiratory syndrome (SARS), there are no clinically approved vaccines or antiviral drugs available for either of these infections; thus, the development of effective therapeutic and preventive strategies that can be readily applied to new emergent strains is a research priority to save human lives and address the pandemic concerns .Although these methods are useful for vaccine development and successful in many cases, but they are time-consuming and fail when the pathogens cannot be cultivated in vitro, or when the most abundant antigens are variable in sequence.
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Retrieved strains, their accession numbers and date of collection are listed in supplementary table (S1). Determination of Conserved Regions The retrieved sequences were used as a platform to obtain conserved regions using multiple sequence alignment (MSA).