Based on the complete genome sequences, PEDV are classified into GI and GII groups [13, 14]. The GI group contains classic strains; it includes the subgroups GI-a and GI-b. The GII group comprises so-called variant strains; it also includes two subgroups, GII-a and GII-b. In China, the highly virulent variant strains of the GII group are dominant pandemic strains in the pig population [14–16].
Point mutations, insertions, or deletions in structural proteins and non-structural proteins have resulted in changes in tropism and virulence of coronaviruses [17–19]. In the case of PEDV, deletions or insertions are frequently observed in the spike protein or ORF3 [20–22]. For example, HM2017 has two insertions in the S gene [20], HLJBY has a 133-aa deletion in ORF3 [21], and 15 novel field PEDV variants with large genomic deletions have been identified in Japan [22]. Point mutation is a common phenomenon in coronaviruses. In this study, we isolated a novel PEDV strain, SC-YB73, in China, which was confirmed by PCR assay and pathology. Sequencing analysis found that six nucleotides were inserted in the E gene and did not disrupt the ORF, which resulted in two extra amino acids. This is the first report of an insertion in the E gene. However, the Mouse hepatitis virus E and M proteins result in the formation and secretion of particles [23, 24]. Further experiments are required to reveal the biology and function of the E protein of SC-YB73. Comparing SC-YB73 with another 27 strains demonstrated 50 unique positions in the complete genome. In general, in different countries or regions, there will be some unique characteristics of the loci. However, these positions of SC-YB73 are distinct from any other Chinese and non-Chinese strains, which suggests that the strain has antigenic variation or different biological activity.
Recombination plays an important role in the evolution of PEDV, resulting in the occurrence of variant strains with high virulence and immunogenicity. It is hypothesized that PEDV may have originated from bats; some PEDV strains are more closely related to the bat coronavirus than to transmissible gastroenteritis virus and human coronavirus [25]. In this study, SC-YB73 was found to show potential recombinants events from GDS47, TW/Yunlin550/2018, and COL/Cundinamarca/2014. The analysis confirmed the probable occurrence of recombination in the E, M, and N genes of SC-YB73. Our results indicated that recombination within subgroups is a common phenomenon, and is the driving force of PEDV evolution. In general, PEDV strains utilize point mutation, insertion, deletion, and recombination to generate field strains, ensuring that the current vaccines cannot provide complete protection.