Characterisation of porcine epidemic diarrhea virus isolates during the 2014-2015 outbreak in the Philippines

Abstract

The viral agent of the porcine epidemic diarrhea (PED) was investigated during the reported 2014-2015 outbreaks in commercial farms in Central Luzon, Philippines. The study covered detection of PED virus (PEDV) in fecal and intestinal samples through reverse transcription PCR and sequence analysis of the nucleocapsid (N) gene. Results showed that 10 out of 34 fecal and intestinal samples examined were positive for PEDV. The partial nucleotide sequence of the N gene of the field samples showed 98-99% homologous to PEDV sequences registered in the GenBank. It was also noted that N gene sequences between field samples were 98% homologous. Interestingly, the partial sequences of the N genes of the field samples were genetically similar to the PEDV isolates from USA, China, Mexico, Canada and Japan. The phylogenetic tree analysis revealed that the Philippine samples clustered in group 2-1 of the PEDV, wherein the isolates of this group were responsible for the outbreaks in Asia and the USA. Analysis of the partial nucleotide and amino acid sequences revealed polymorphisms, deletions and insertions in the N-gene of the PEDV. Amino acid sequence alignment also showed deletions and insertion in the PEDV detected in the Philippines.

Keywords: Nucleocapsid gene; Nucleotide polymorphisms; Phylogenetic tree analysis; Porcine epidemic diarrhea virus.

Fig. 1

Amplified N gene of PEDV from intestinal samples of suspected animals. Lane lad (1 kb + ladder), lanes 1–14 (PED samples), lane 15 (PED vaccine) and lane 16 (negative control)

Fig. 2

Phylogenetic analysis of Philippine samples and other PEDV based on N gene nucleotide sequence