Molecular analysis reveals a distinct subgenogroup of porcine epidemic diarrhea virus (PEDV) in Northern Vietnam in 2018–2019

Abstract Porcine epidemic diarrhea (PED) is known as a serious disease infecting all ages of pigs, with a mortality rate of up to 100% in piglets. The spike protein (S) of porcine epidemic diarrhea virus (PEDV), in particular, the S1-CTD (C-terminal domain), which contains the conservative neutralizing epitopes CO­26K equivalent (COE) (aa 499–638), exhibits a high degree of genetic and antigenic diversity. We obtained 26 Vietnamese PEDV-S1-CTD sequences (630 bp) from samples collected from seven northern provinces from June 2018 to January 2019 and analyzed them with 35 sequences from previous studies, representing the G1a and 1b, G2a and 2b, and recombinant (G1c) genotypes, and PEDV vaccines. The majority (73.1%) of strains (19/26) belonged to the subgroup G2b. With strong nodal support (98%), seven strains were clustered into an independent, “distinct subgenogroup” (named dis-subG), separate from both G1a and G1b and other G2a, 2b, and 1c (recombinant strains). When compared with the prototype CV777 strain (AF353511), sequence analysis revealed distinct changes of 513T>S, 520G>D, 527V>(I/L/M), 591L>F, 669A>(S/P), 691V>I in the COE and S1D regions of the S1-CTD protein that were only identified in these Vietnamese strains. This cluster is a new antigenic variant subgroup and further studies are required to investigate its anigenicity. The results in this study revealed the continuous evolution in the S1 region of the Vietnamese PEDV strains, which emphasizes the need for frequent updates of the vaccines for effective protection.