Evolutionary characterization of the emerging porcine epidemic diarrhea virus worldwide and 2014 epidemic in Taiwan.
Since 2010, a new variant of PEDV belonging to Genogroup 2 has been transmitting in China and further spreading to the Unites States and other Asian countries including Taiwan. In order to characterize in detail the temporal and geographic relationships among PEDV strains, the present study systematically evaluated the evolutionary patterns and phylogenetic resolution in each gene of the whole PEDV genome in order to determine which regions provided the maximal interpretative power. The result was further applied to identify the origin of PEDV that caused the 2014 epidemic in Taiwan. Thirty-four full genome sequences were downloaded from GenBank and divided into three non-mutually exclusive groups, namely, worldwide, Genogroup 2 and China, to cover different ranges of secular and spatial trends. Each dataset was then divided into different alignments by different genes for likelihood mapping and phylogenetic analysis. Our study suggested that both nsp3 and S genes contained the highest phylogenetic signal with substitution rate and phylogenetic topology similar to those obtained from the complete genome. Furthermore, the proportion of nodes with high posterior support (posterior probability >0.8) was similar between nsp3 and S genes. The nsp3 gene sequences from three clinical samples of swine with PEDV infections were aligned with other strains available from GenBank and the results suggested that the virus responsible for the 2014 PEDV outbreak in Taiwan clustered together with Clade I from the US within Genogroup 2. In conclusion, the current study identified the nsp3 gene as an alternative marker for a rapid and unequivocal classification of the circulating PEDV strains which provides complementary information to the S gene in identifying the emergence of epidemic strain resulting from recombination.
['Sung|Ming-Hua|MH|', 'Deng|Ming-Chung|MC|', 'Chung|Yi-Hsuan|YH|', 'Huang|Yu-Liang|YL|', 'Chang|Chia-Yi|CY|', 'Lan|Yu-Ching|YC|', 'Chou|Hsin-Lin|HL|', 'Chao|Day-Yu|DY|']
D000818:Animals D001499:Bayes Theorem D018352:Coronavirus Infections D004196:Disease Outbreaks D019143:Evolution, Molecular D005814:Genes, Viral D005838:Genotype D014943:Global Health D049674:History, 21st Century D010802:Phylogeny D053485:Porcine epidemic diarrhea virus D064370:Spike Glycoprotein, Coronavirus D013552:Swine D013553:Swine Diseases D013624:Taiwan
Porcine epidemic diarrhea virus Taiwan Likelihood mapping Nsp3 Phylogenetic signal Evolutionary rate Spike