Molecular analysis reveals a distinct subgenogroup of porcine epidemic diarrhea virus in northern Vietnam in 2018-2019

Abstract

The spike protein (S) of porcine epidemic diarrhea virus (PEDV), in particular, the C-terminal domain of the S1 subunit (S1-CTD), which contains the conserved CO-26K-equivalent (COE) region (aa 499-638), which is recognized by neutralizing antibodies, exhibits a high degree of genetic and antigenic diversity. We analyzed 61 PEDV S1-CTD sequences (630 nt), including 26 from samples collected from seven provinces in northern Vietnam from 2018 to 2019 and 35 other sequences, representing the G1a and 1b, G2a and 2b, and recombinant (G1c) genotypes and vaccines. The majority (73.1%) of the strains (19/26) belonged to subgroup G2b. In a phylogenetic analysis, seven strains were clustered into an independent, distinct subgenogroup named dsG with strong nodal support (98%), separate from both G1a and G1b as well as G2a, 2b, and G1c. Sequence analysis revealed distinct changes (513^T>S, 520^G>D, 527^V>(L/M), 591^L>F, 669^A>(S/P), and 691^V>I) in the COE and S1^D regions that were only identified in these Vietnamese strains. This cluster is a new antigenic variant subgroup, and further studies are required to investigate the antigenicity of these variants. The results of this study demonstrated the continuous evolution in the S1 region of Vietnamese PEDV strains, which emphasizes the need for frequent updates of vaccines for effective protection.

Fig. 1

Maximum-likelihood phylogenetic tree based on the alignment of 61 S1-CTD nucleotide sequences (630 nucleotides) of PEDV G1a, 1b, 2a, 2b isolates and recombinant strains (or G1c) [34], including 26 Vietnamese strains from this study and 35 reference strains. The phylogenetic tree reconstruction was performed in MEGA X using the maximum-likelihood method with the general time-reversible GTR + G + I model. Support for each node was tested by 1000 bootstrap resamplings [35], and only bootstrap values greater than 30% are shown. The Vietnamese PEDV strains in this study are indicated by a diamond symbol, and the reference strains representing different genogroups are indicated by a square symbol. A cluster formed by seven Vietnamese strains that are distinct from the other PEDV sequences is designated as the “dsG” subgroup, which is bracketed between the G1 and G2 genogroups. For each sequence, following the accession number is the abbreviation of the country’s name (two-letter: https://www.iban.com/country-codes) and the strain designation. The year of isolation is given at the end of each sequence name. The scale bar represents the number of substitutions per site.

Fig. 2

Alignment of the partial S1-CTD protein sequences (deduced from 630 nt) of 27 PEDV strains, including 26 clinical strains from this study and the classical C777 strain (AF353511/BE/CV777/2001), representing genogroup 1a (G1a). The top line is the amino acid sequence for the C777 strain. Residues in the aligned sequences that are identical to those of the C777 strain are indicated by dots, and differences are indicated by single letters. The highly conserved core neutralizing epitope (COE) (aa 499–638) and S1^D domain are indicated at the top. The aligned sequences of seven Vietnamese PEDV strains identified as belonging to a distinct subgenogroup (designated as dsG) are shaded in gray, and the distinct residues are colored and vertically boxed. Accession numbers and subgenotypes are shown at the start of the sequences.