Complete Genome Sequencing and Molecular Structure Prediction of C81 Attenuated Strain of CSFV

Seven pair of primers covering the whole genome of Classical swine fever virus(CSFV) attenuated strain were devised according to the published sequences . 7 cDNA fragments were amplified by RT-PCR from PK-15 cell infected by CSFV attenuated strain. The amplifid fragments were further sequenced after cloned into the pMD18-T vector. The whole genome sequence of C81-strain was assembled by DNASIS (GenBank: AY663656). The genome is 12310 nucleotides in length and contains one large open reading frame encoding a polyprotein of 3898 amino acids. Sequence comparison with other CSFV strains revealed major differences in the open reading frame,84.4%～99.6% identities at the nucleotide level and 91.6%～99.4% identities at the amino acid level.26 ORF phylogenetic trees of CSFV strain were also protracted. The nucleotide sequence and secondary structure of CSFV 5′-untranslated region (5′-UTR) were compared and deduced, and found the major difference exists among diverse virus strains. Furthermore, functional domains and 3-D structure of CSFV/ C81 polyprotein were predicted.