IN SILICO EPITOPE PREDICTION OF COAT PROTEIN GENE OF SUGARCANE MOSAIC VIRUS
Abstract
Sugarcane mosaic virus (ScMV) cause economic losses in the production of sugarcane, maize, sorghum, and some other graminaceous species. Detection of ScMV isolates using a very specific and efficient tool is needed for virus diagnosis and management. In this study, sequence analysis of ScMV partial coat protein (CP) was used to determine conserved sequences-potential epitope regions. PCR amplification of ScMV partial CP gene of an Egyptian isolate of ScMV (ScMV-Egy) resulted in 360 bp. Using multiple sequence analysis, 3 major substitutions were detected, (C8822→T, G8831→T, and T8846→C) and resulted in one amino acid substitution (K2894→N). None of the 3 substitutions affected the predicted RNA structure. Analysis of antigenicity, hydrophobicity, solvent accessibility, and exposed surface area resulted in 5 highly scored epitopes: TRATREEFDRW2878, DDTQMTVVMSGL2899, EEFDRWYEAI2883 TRATREE2878 and TVVMSGLMVWCI2904. The highly score-epitopes should be useful for producing sero-diagnostic ScMV antiserum. Further in vivo experiments to validate the predicted epitopes are needed.
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