Abstract:

【Objective】 The 3′-UTR of CSFV was sequenced and analyzed, for the understanding of the influence of 3′-UTR on replication, multiplication, and virulence of virus. 【Method】 The 3′-UTR of CSFV Thiverval, HCLV and Shimen strains were amplified and sequenced using RT-PCR method. The alignment was carried out using DNAstar and Sequencher software. The RNA secondary structures of different 3′-UTR were predicted using RNAstructure software. 【Result】 The longest 3′-UTR of Thiverval strain was 259 base pairs (bp) with a 32 nt insertion. The shortest 3′-UTR had only 233 bp with a 6 nt insertion. The longest 3′-UTR of HCLV strain was 244 bp with a 17 nt insertion and the shortest 3′-UTR was 235 bp with a 8 nt insertion. At the same time, to maintain the similar 3′-UTR structure, the free energy of vaccine strain is higher than that of virulent strain, and the free energy in 3′-UTR of vaccine strain is rising with length of insert. 【Conclusion】 The 3′-UTR of CSFV vaccine strains have two variable regions. The insertion of attenuated Thiverval and HCLV strains 3′-UTR represent distinct heterogeneity in different clones of the same sample. The insertion of vaccine strains 3′-UTR could affect the stability of the secondary structure, which might be a reason for the attenuated virulence.

Key words: classical swine fever virus, 3′-UTR, heterogeneity, RNA secondary structure