title: Evolutionary characterization of the emerging porcine epidemic diarrhea virus worldwide and 2014 epidemic in Taiwan.
abstract: 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.
authors.affiliation: Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; Taichung City Animal Protection and Health Inspection Office, Taichung 408, Taiwan.
authors.forename: Ming-Hua
authors.initials: MH
authors.lastname: Sung
authors.affiliation: Animal Health Research Institute, Council of Agriculture, New Taipei City 25158, Taiwan.
authors.forename: Ming-Chung
authors.initials: MC
authors.lastname: Deng
authors.affiliation: Taichung City Animal Protection and Health Inspection Office, Taichung 408, Taiwan.
authors.forename: Yi-Hsuan
authors.initials: YH
authors.lastname: Chung
authors.affiliation: Animal Health Research Institute, Council of Agriculture, New Taipei City 25158, Taiwan.
authors.forename: Yu-Liang
authors.initials: YL
authors.lastname: Huang
authors.affiliation: Animal Health Research Institute, Council of Agriculture, New Taipei City 25158, Taiwan.
authors.forename: Chia-Yi
authors.initials: CY
authors.lastname: Chang
authors.affiliation: Department of Health Risk Management, School of Public Health, China Medical University, Taichung, Taiwan.
authors.forename: Yu-Ching
authors.initials: YC
authors.lastname: Lan
authors.affiliation: Department of Health Risk Management, School of Public Health, China Medical University, Taichung, Taiwan.
authors.forename: Hsin-Lin
authors.initials: HL
authors.lastname: Chou
authors.affiliation: Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan. Electronic address: dychao@nchu.edu.tw.
authors.forename: Day-Yu
authors.initials: DY
authors.lastname: Chao
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D018352:Coronavirus Infections / Q000453:epidemiology* / Q000266:history / Q000821:virology*; 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 / Q000145:classification / Q000235:genetics*; D064370:Spike Glycoprotein, Coronavirus; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000266:history / Q000821:virology*; D013624:Taiwan / Q000453:epidemiology
chemical_list: D064370:Spike Glycoprotein, Coronavirus
keywords: Evolutionary rate; Likelihood mapping; Nsp3; Phylogenetic signal; Porcine epidemic diarrhea virus; Spike; Taiwan