New porcine epidemic diarrhoea virus variant with a large deletion in the spike gene identified in domestic pigs

Abstract

From October 2013 to date, approximately 1,000 outbreaks of porcine epidemic diarrhoea virus (PEDV) have occurred in Japan. Porcine epidemic diarrhoea with non-lethal effects in piglets was identified in Tottori prefecture in October 2014. Complete genome analysis revealed that the causative pathogen, Tottori2, is a new PEDV variant with a large (582 nt) deletion in the spike gene. Phylogenetic analysis indicated that the Tottori2 PEDV strain might have been derived from the current PEDV strains circulating in domestic pigs. Moreover, the Tottori2 PEDV strain was successfully isolated in Vero cells by serial passage.

Fig. 1

Amino acid sequence alignments of partial S proteins (aa 1–420) from the Tottori2 PEDV strain and two reference US PEDV strains, Colorado/USA/2013 (highly virulent type of PEDV) and PC177/USA/2013 (197-aa deletion). Deletions are labelled as ‘-’. The conserved amino acid residues are labelled as ‘*’

Fig. 2

Phylogenetic trees based on full-length nucleotide sequences of the spike gene (A) and complete genome sequences (B) of pig epidemic diarrhoea virus (PEDV) strains, including recent PEDV strains identified worldwide. TGEV and PRCV were used as outgroup controls. Dendrograms were constructed by using the maximum-likelihood method in the MEGA 6 program. A bootstrap test was performed with 1,000 replicates; bootstrap values >70 % are indicated on each branch. Reference PEDV strains were obtained from GenBank: common names of strains, country and year of collection, and accession number are shown in parentheses. Types of PEDV strains are represented on the right. Scale bars indicate nucleotide substitutions per site