1. Complete genomic characterization of PEDV CH/JSXZ/2015 strain
The genome length of the isolate CH/JSXZ/2015 (JSXZ) excluding the poly(A) tail was 28,044 nucleotides (nt) with 42% G+C content and 58% A+T content. The genomic organization of the virus was in the following order: 5’untranslated region (UTR), nucleotide 1 to 292; replicase polyprotein, nucleotide 293 to 12646 for ORF1a and nucleotide 12601 to 20637 for ORF1b; spike (S) protein, nucleotide 20634 to 24794; open reading frame 3 (ORF3), nucleotide 24794 to 25468; envelope (E) protein, nucleotide 25449 to 25679; membrane (M) protein, nucleotide 25687 to 26367; nucleocapsid (N), nucleotide 26379 to 27704; and 3’UTR, nucleotide 27705 to 28044.
Interestingly, compared with CH/JLDH/2016, strain CH/JSXZ /2015 had a single amino acid insertion in the S gene (1197T). The genome information of strain CH/JSXZ/2015 will conducive to understand the evolutionary characteristics and molecular epidemiology of PEDV in China.
2. Genome-wide sequence comparison
In this study, the complete genome sequences of PEDV strains from different locations and years were counted, and these data were analyzed comparatively. The results of the study revealed that CH/JSXZ/2015 had 99.5%-90.1% nucleotide identity with other PEDV complete genomes in GenBank (Table 2). CH/JSXZ/2015 showed the highest nucleotide identity (99.5%) with CH/GDZHDM/1401 strain (KR153326.1 and KR153326.1), and the lowest similarity (93.5%) to 85-7‐mutant1 strain (KX839247.1). CH/JSXZ/2015 shared 93.6% nucleotide correlation with CV777 and 98.9% nucleotide resemblance with JS‐HZ2012 (KC210147) strain, which was isolated from the identical province with PEDV CH/JSXZ/2015, and 98.6% nucleotide similarity to PEDV/MEX/PUE/01/2015 (MH004421), PC22A‐P100‐C6 (KU893871) and PC273/O (MG837058), respectively.
3. phylogenetic analysis of CH/JSXZ/2015
To analyze the evolution of PEDV, we performed phylogenetic tree based on the determined nucleotide sequences of the full-length CH/JSXZ/2015. Interestingly, phylogenetic analysis revealed that these PEDV strains cluster into two groups (Figture1). Viruses in group Ⅰ includes CV777, PEDV-SX, SH1302, 85-7 mutant1, and 85-7-140. CH/JSXZ/2015 and others belongs to group Ⅱ. CH/JSXZ/2015 is closely related to CH/GDZHDM/1401, PEDV-WS, and CH/HNLH/2015.
4. Characterization and phylogenetic analysis of S
S protein is a fibrotic glycoprotein located on the surface of PEDV and the largest structural protein of PEDV. PEDV S protein is a key determinant of a virus invading host cell and is a key target site of host antibody response. What's more, it also include viral neutralizing epitopes that can serve as an important target for vaccine development. Therefore, we conducted systematic development analysis of S proteins CH/JSXZ/2015 with 69 historic strains in GenBank. CH/JSXZ/2015 S amino acid identity was 90.8%‐99.8% compared with other strains.
To analyze the evolution of PEDV, phylogenetic analysis based on PEDV S gene was performed. We found phylogenetic tree cluster into two groups (Figure. 2). The S of CH/JSXZ/2015 is part of the group Ⅱ. The S of CH/JSXZ/2015 is closely related to CH/GDZHDM/1401 (KR153326.1 and KR153326.1).
5. Characterization and phylogenetic analysis of ORF3
ORF3 is the only adjuvant protein of PEDV, which is located between the S protein and the E protein, composed of 225 amino acids, and the relative molecular mass is about 25 kdα. PEDV ORF3 proteins show ion channel activity and enhance the copying ability of viruses. Besides, ORF3 plays a very important role in PEDV inhibiting host natural immune. We compared the amino acid of CH/JSXZ/2015 ORF3 identity with 69 historic PEDV strains. According to the research, the CH/JSXZ/2015 ORF3 amino acid identity was 91.2%‐100.0% compared with other PEDV strains. The results show that CH/JSXZ/2015 ORF3 protein is very similar to the remaining strains.
We performed phylogenetic tree based on the determined nucleotide sequences of ORF3 of CH/JSXZ/2015. These PEDV strains cluster into two different groups (Fiure 3). The result had an alike grouping structure as the tree grew out of the PEDV whole genomes and S. The ORF3 of CH/JSXZ/2015 is part of the group Ⅱ.