Sequence Analysis Of S And N Gene Of Porcine Epidemic Diarrhea Virus In Guangxi

Porcine epidemic diarrhea, caused by porcine epidemic diarrhea virus (PEDV), is an intestinal infectious disease, characterizing by watery diarrhea, vomiting and dehydration. In order to understand the prevalence of PEDV and the characteristics of the current genetic evolution in Guangxi, our study provides scientific basis for better prevention and control. In this study,184cases were detected from506samples by RT-PCR in Guangxi region from2012to2013, and then partial N gene of86strains and S gene of41strains were cloned and sequenced.Sequence analyses of the N genes were performed,the results showed that86strains had nucleotide identities of94.2%-100%and94.1%-100%with reference strains. Phylogenetic analysis of N gene indicated that Guangxi strain could be divided into two groups. Cluster2consisted of the Korean strains DR13, Japanese strain83P-5and six strains from our study (GP35-8, LC037-22, LC107-5, LC107-5, LC107-19, LC107-16). Other81strains and Chinese strain DX, LJB-03, HuN, JS-2004-2belonged to cluster3. While cluster1and cluster4are composed of other reference strains.To analyse the S genes, S gene of25strains composed of4161nucleotides, nine of4158nucleotides, four of4149nucleotides, one of4176nucleotides, one of4164nucleotides, one of4140nucleotides, and encoded1387,1386,1383,1392,1388,1380amino acids respectively. The S gene of41PEDV strains had94.8%-100%(94.1%-100%) nucleotide (deduced amino acid) identity with each other and89.3%-99.4%(91.1%-99.4%) with the domestic and foreign reference strains. By phylogenetic analysis, all strains were divided into three groups. Four strains from our study (LC55-9, LC55-5, GP35-7and GP35-8) and European strains CV777, Attenuated-DR13belong to group1, and then others37strains were in a group3, whereas group2were only composed of reference strains, containing Korean strains (Chinjiu99and KPED-9), Japan strains (83P-5and MK), Chinese strains (LJB-03, JS-2004-2, DR13and LZC) and European strain Brl-87.To compared with the vaccine strain CV777, there are many amino acid changes at five linear antigenic epitopes, neutralizing epitopes(S1D) and receptor binging domain(MRR). Eight mutations of33amino acids at S1P1(248-499aa) were found in all strains from our study and contained eight mutations of58amino acids at S1P2(442-499aa), seven mutations of46amino acids at S1P3(697-742aa), one mutation of7amino acids in one strain at SS5 (748-755aa), one mutation of7amino acids at SS6(764-771aa), eighteen mutations of153amino acids at SlD(636-789aa), fifty-four mutations of280amino acids at MRR(249-529aa). The S protein contained27to29Asn-Xaa-Ser/Thr sequons, including addition, deletion or substitution of N-glycosylation sites. Compared with the vaccine strain CV777, twelve mutations of amino acid sequence changed the type of N-linked glycosylation sites, and then eight mutations destroyed N-linked glycosylation sites, whereas another five mutations created five new glycosylation sites.It is a great difference between strains in Guangxi and European strains (CV777and Brl-87) and early domestic strains (CH/S, LZC, LJB-03, DX and JS-2004-2). By the epitope region comparing with Chinese vaccine strain CV777, we concluded that the current vaccine has not played a effective role in immunization.