Molecular characterization of porcine epidemic diarrhoea virus (PEDV) in Poland reveals the presence of swine enteric coronavirus (SeCoV) sequence in S gene

Abstract

Porcine epidemic diarrhoea (PED) is a highly contagious enteric viral disease of pigs with a high morbidity and mortality rate, which ultimately results in huge economic losses in the pig production sector. The etiological agent of this disease is the porcine epidemic diarrhoea virus (PEDV) which is an enveloped, positive single-stranded RNA virus. The aim of this study was to perform molecular characterization of PEDV to identify the strains circulating in Poland. In this study, 662 faecal samples from 2015 to 2021 were tested with reverse transcription quantitative real-time PCR (RT-qPCR) and the results showed that 3.8% of the tested samples revealed a positive result for PEDV. A phylogenetic analysis of the complete genome and complete S gene sequences showed that Polish PEDV strains belonged to the G1b (S-INDEL) subgroup and were closely related to the European PEDV strains isolated from 2014 to 2019. Furthermore, RDP4 analysis revealed that the Polish PEDV strains harboured a recombinant fragment of ~400 nt in the 5' end of S gene with PEDV and swine enteric coronavirus (SeCoV) being the major and minor parents, respectively. Antigenic analysis showed that the aa sequences of neutralizing epitopes were conserved among the Polish PEDV strains. Only one strain, #0100/5P, had a unique substitution in the COE epitope. However, Polish PEDV strains showed several substitutions, especially in the COE antigen, as compared to the classical strain CV777. To the best of our knowledge, this is the first report concerning the molecular characterization of porcine epidemic diarrhoea virus strains, as well as the first phylogenetic analysis for PEDV in Poland.

Fig 1. Phylogenetic relationship between the sequences of the PEDV Polish strains and the sequences of the reference strains obtained from GenBank.

The phylogenetic tree was constructed on the basis of the complete genome sequences with MEGA6 software using the neighbor-joining method. Bootstrap values >70 are shown. The numbers of each branch represent the bootstrap value calculated using 1000 replicates. The scale bars indicate nucleotide substitutions per site. The S gene sequences from the PEDV isolates identified in this study are indicated with filled black circles.

Fig 2. Phylogenetic relationship between the sequences of PEDV Polish strains and sequences of reference strains obtained from GenBank.

The phylogenetic tree was constructed on the basis of the complete S gene sequences with MEGA6 software using the neighbor-joining method. Bootstrap values >70 are shown. The numbers of each branch represent the bootstrap value calculated using 1000 replicates. The scale bars indicate nucleotide substitutions per site. The S gene sequences from the PEDV isolates identified in this study are indicated with filled black circles.

Fig 3. Amino acid alignment of the neutralizing epitope SS2, SS6 and 2C10 located in the S protein of the Polish PEDV strains and reference strains.

The dots (.) represent amino acids that are identical. Alignment was constructed using the Clustal W method. Stars indicate the Polish PEDV sequences described in this study.

Fig 4. Amino acid alignment of the neutralizing epitope COE located in the S protein of the Polish PEDV strains and reference strains.

The dots (.) represent amino acids that are identical. Alignment was constructed using the Clustal W method. Stars indicate the Polish PEDV sequences described in this study.

Fig 5. Potential recombination breakpoints in the S gene of the Polish PEDV strains.

The potential minor parent was the SeCoV Spanish strain MU2 (MN692770) and the major parent was the recombinant PEDV Spanish strain 1556 (MN692763) or the South Korean strain DR13 (JQ23161). The analysis was performed using the pairwise distance model with a window size of 200, step size of 20 and 1,000 bootstrap replicates by the RPD4 program.