Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines

Abstract

To trace the possible route of introduction of porcine epidemic diarrhea virus (PEDV), the phylogenetic relationships of PEDV strains in the regions of epidemicity in the Philippines to PEDV strains that are endemic in other countries were investigated. Partial nucleotide sequences of the S1 spike gene was determined from the PEDV-positive samples and compared with S1 sequences from other countries. Phylogenetic analysis indicated that PEDV strains in the Philippines segregate into two groups. Members of group 1 are related to strains from the USA, Taiwan, Japan and Canada, while those in group 2 are related to strains from China and Vietnam.

Fig. 1

Molecular phylogenetic analysis of PEDV in the Philippines. Phylogenetic tree showing PEDV strains from “hotspot” provinces of the Philippines along with the other strains from China, Taiwan, Vietnam, Korea, Japan, the USA, Austria and Germany. Phylogeny was based on partial spike S1 gene sequences. Evolutionary history was inferred using the maximum-likelihood method based on the Kimura 2-parameter model [16]. The initial tree for the heuristic search was generated automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the maximum composite likelihood (MCL) approach. Evolutionary analysis was conducted using MEGA7 [8]