Molecular Characterization of the ORF3 and S1 Genes of Porcine Epidemic Diarrhea Virus Non S-INDEL Strains in Seven Regions of China, 2015

In an effort to trace the evolution of porcine epidemic diarrhea virus (PEDV), S1 and ORF3 genes of viruses identified in 41 pig farms from seven regions (North, Northeast, Northwest, Central, East, South West, and South, respectively) of China in 2015 were sequenced and analyzed. Sequence analysis revealed that the 41 ORF3 genes and 29 S1 genes identified in our study exhibited nucleotide homologies of 98.2%–100% and 96.6%–100%, respectively; these two genes exhibited low nucleotide sequence similarities with classical CV777 strain and early Chinese strain LZC. Phylogenetic analysis indicated that the identified PEDV strains belonged to global non S-INDEL strains, and exhibited genetic diversity; S1 gene of the HLJ2015/DP1-1 strain harbored an unique deletion of 12 nucleotides (A1130CAACTCCACTG1141); while the Chinese PEDV S-INDEL reference strains included two types of the “CV777” S-INDEL as well as the “US” S-INDEL, and all co-circulated with Chinese non S-INDEL strains. Of 29 identified S1 genes, the SS2 epitope (Y748SNIGVCK755) was highly conserved, while the SS6 epitope (L764QDGQVKI771) and pAPN receptor-binding region (aa 490–615) exhibited amino substitutions. Nine possible recombination events were identified between the 29 identifed S1 genes and the 3 S1 reference genes from early Chinese PEDV strains. The complete S genes of selected Chinese PEDV field strains (2011–2015) showed 5.18%–6.07% nucleotide divergence, which is far higher than the divergence observed in early Chinese PEDV strains (3.1%) (P为追踪猪流行性腹泻病毒（Porcine Epidemic Diarrhea Virus，PEDV）的进化历程，本研究对2015年采自中国7个地区（依次为华北、东北、西北、华中、华东、西南及华南）的41个猪场的病毒毒株的S1基因与ORF3基因进行了测序与分析。序列分析结果显示，本研究鉴定得到的41条ORF3基因与29条S1基因的核苷酸同源性分别为98.2%~100%与96.6%~100%；上述两个基因与经典毒株CV777以及中国早期毒株LZC的核苷酸序列相似性均较低。系统发育分析表明，本研究鉴定的PEDV毒株均属于全球非S-INDEL毒株，且存在遗传多样性；HLJ2015/DP1-1毒株的S1基因存在一段独特的12核苷酸缺失（A1130CAACTCCACTG1141）；中国PEDV S-INDEL参考毒株包含"CV777"型S-INDEL与"US"型S-INDEL两类，且均与中国非S-INDEL毒株共同流行。在29条鉴定得到的S1基因中，SS2表位（Y748SNIGVCK755）高度保守，而SS6表位（L764QDGQVKI771）以及pAPN受体结合区（氨基酸490~615）均存在氨基酸替换。本研究在29条S1基因与3条来自中国早期PEDV毒株的S1参考基因之间，共鉴定出9处潜在重组事件。本研究选取的2011~2015年中国PEDV田间毒株的完整S基因的核苷酸分歧率为5.18%~6.07%，远高于中国早期PEDV毒株的核苷酸分歧率（3.1%）（P