Genomic comparison of foot-and-mouth disease virus R strain and its chick-passaged attenuated strain

The present study examined the genomic differences between foot-and-mouth disease virus (FMDV) R strain and its attenuated, chick-passaged (R304) strain. Eleven pairs of primers were used to amplify the complete genome of FMDV R and R304 by RT-PCR. Each fragment was cloned into pMD18-T vector and sequenced. Nucleotide analyses showed that the genome encoding regions of R and R304 strains open reading frame (ORF) were both 6966 nucleotides (nt) in length, encoding 2322 amino acids. One hundred and ten nucleotides or 32 amino acids were found to be mutated most frequently were in the 3A gene. The next highest rates of mutation were observed in the LP and 1D genes. No mutations were found in either the 2A or 2C genes. The length of 5′IRES region and 3′UTR were 450 nt and 94 nt, respectively. The 5′IRES region and 3′UTR had only 4 nt and 3 nt mutation, respectively after attenuation. The R304 poly(A) tail length of 18 nt, while that of the R strain was 30 nt. This result demonstrated the primary genomic changes of a FMDV and its attenuated strain, which has important implications in understanding the molecular epidemiology and functional genomics of FMDV.