Bioinformatics Analysis Of Coding-region Of Classical Swine Fever Virus Genome

Classical Swine Fever Virus (CSFV), one of the main pathogens damaging pig industry in the world. Bio informatics research is conducive to the further molecular biology research of CSFV through the total scan of coding-region of CSFV genome, without the prior knowledge of virulence, replication mechanism and pathogenesis of CSFV.Firstly, we detected the selection pressure and recombination of all50strainsCSFVavailable complete coding region, to provide the first complete overview of the evolution of CSFV. The results showed the overall ω (nonsynonymous/synonymous) of12proteins under one-radio model were all lower than1,indicating that the selection pressure of CSFV was subject to strong purifying selection. Among the12proteins, NS3, NS4A and NS4B proteins underwent the stronger purifying selection; meanwhile Npro, Erns, E1, E2and NS5A proteins were detected the positively selection sites, underwent the stonger positive selection, indicating that the adaptive evolution of CSFV were related to the host immune response. Furthermore,4putative recombination virus strains, and HCLV/99, ALD and SWH were new found, were detected in50sample sequences by recombination analysis. The proteins related to the genome recombination were involved in the immunity and virulence of CSFV, and the recombination changed the phylogenetic tree branch of recombination strain. However the recombination loci were detected in most proteins except NS3, NS4A and NS4B proteins which processed the shorter genetic distance. Our research suggested that the mutation and recombination under the selection pressure of the host immune system promoted the evolution of coding region in CSFV. Subsequently, We introduced a novel variable into our original algorithm based on the maximum entropy, with an accompanying RSST program, which was used to analyze these sequences. Results showed that12proteins the coding regions, Npro, C, Erns, E1, E2, p7, NS2, NS3, NS4A, NS4B, NS5A,NS5B, contained29,9,37,25,41,8,65,115,6,50, 59, and103positions with maximum information content, respectively. Following the entropy theory, we assumed that the corresponding amino acids at the above-mentioned positions might play an important role in the function of these proteins. The importance of the amino acids at a large quantity ofpositions has been experimentally demonstrated, suggesting that our method is effective on prediction of important sites in viral coding-regions. Furthermore, a large number of important amino acidsthat we predicted were absented in previous experimental studies because of poor experimental conditionsand little known information about some proteins.Finally, based on the main antigen protein Erns and E2of CSFV, we compared the structure of avirulent strain with highly virulent strain. The results of analysis of amino acid composition and physicochemical properties showed that only Alfort(J04358) is special, and belong to genotype Ⅱ, suggesting that there is a big difference in amino acid composition and physicochemical properties of Erns between different genotypes of CSFV. The result of second structure comparison showed that only164th of Erns in the swine fever Lapinised strains-specific amino acid sites influence the formation of the second strture, suggesting that it may be associated with the transfer function at the end of Erns protein.The result of tertiary structure comparison showed that only346th of E2in the swine fever Lapinised strains-specific amino acid sitesinfluence the formation of tertiary structure, and it located in the membrane area of E2, suggesting that the loci may be related to the membrane function of E2proteins, and affect the intensity of host innate immune response.Our studies would provide the foundation for vaccine targets and the more and more complex situation of CSFV epidemiological research.