Translation Elongation Rate Measurement of Epstein-Barr Virus Strain GD1

BACKGROUND: Epstein-Barr Virus (EBV) has a great co relationship with human malignancies such as gastric carcinoma. Synonymous codon investigations in viruses could help designing vaccine, to generate immunity. Codon Adaptation Index (CAI) has measured translation elongation rate, among the highly expressed genes. The aim of this study was: usage of “CAI” to measure translation efficiency to know how fast EBV-GD1 could produce its proteins. METHODS: The complete genomic sequences of human herpes virus 4 strain GD1 have retrieved from <http://www.ncbi.nlm.nih.gov/sites/gquery> (GenBank accession no. AY961628) to extract all protein-coding genes. The sequences have analyzed with DAMBE software. RESULTS: The results have shown that CAI values for the EBV-GD1 genes were 0.76356 ± 0.02957. The highest and lowest CAI values were 0.82233 and 0.68321 respectively. The results have shown that highly expressed genes mostly had more codon usage bias than low expressed genes. CONCLUSION: The results provide and introduce not only a system, but also the principles in order to understand the pathogenesis and evolution of EBV-GD1, to open a window, in order to make a better product or vaccine to challenge with the virus.