In order to understand genetic feature of atypical porcine pestivirus(APPV)strains prevalent in Guangxi,a total of 23 samples including brain,liver,spleen and kidney were collected from newborn piglets with congenial tremors(CT)symptoms from three regions of Guangxi.The APPV was detected by fluorescence quantitation PCR(RT-qPCR)and the whole genome sequence of APPV positive samples was segmentally amplified by RT-PCR.The results showed 18 positive samples were detected(positive rate 78.26%)and 4 whole genome sequences of APPV were obtained after sequencing and splicing.A total of 9 APPV whole genome sequences of endemic strains in Guangxi including 4 strains that identified in this study were further analyzed.The similarity of these APPV epidemic strains was analyzed by BLAST and BioEdit,the linear antigen epitopes and N-glycosylation sites of Erns and E2 glycoprotein were predicted by Bepipred 2.0 software and NetNGlyc 1.0 online software;phylogenetic and recombination analysis with Mega 7.0 and RDP5 and SimPlot software was conducted.The results showed that the highest similarity of APPV Guangxi strains and GenBank strains was 89.9%-99.8%,which identified from Hebei,Hubei,Hunan,Sichuan,Guangxi and Guangdong provinces.Also,the Guangxi strains inter-and reference strains shared genome similarity with 79.4%-99.6%and 77.1%-98.3%respectively,suggested that genome evolution of the APPV was diversity and the differences among the APPV strains in Guangxi are relatively large.Phylogenetic analysis based on nucleotide sequences of ORF showed that there were three genotype clusters in the trees,the GX01-2019 strain and GX02-2018 strain belonged to I-2,and I-3 sub genotype,respectively.The GX02-2019 strain belonged to Ⅱ genotype,and the others belonged to I-1 sub genotype.Besides,the genetic trend of Npro,Erns and E2 was similar with ORF suggesting that APPV of Guangxi strains were mainly genotype I and without association to spatiotemporal dynamics,and genetic was diversity.Epitope prediction of Erns and E2 protein showed that Erns containing 7 antigen epitopes,including aa7-aa14,aa24-aa36,aa39-aa66,and E2 protein mainly containing 5 antigen epitopes,including aa5-aa9,aa16-aa25,aa35-aa111.In addition,the N-glycosylation sites prediction of Erns and E2 protein was 12NSTG15,43NETI46,64NYTC67,and 51NG(DorE)S(T)L54,64NTSS(I)67,respectively.A recombination signal was detected on genome of APPV_China/GX-WZ/2017.The major parent strain was GX01-2018,with similarity was 99.7%,and the minor parent strain was KU16-2 from South Korea,with similarity was 100%.This study provides basic data for molecular epidemiology research and genetic evolution analysis of APPV in Guangxi.
NETL
NSTL
万方数据
