title: Evolutionary and epidemiological analyses based on spike genes of porcine epidemic diarrhea virus circulating in Thailand in 2008-2015.
abstract: Porcine epidemic diarrhea (PED) has been endemic causing sporadic outbreaks in Thailand since 2007. In 2014-2015, several herds had experienced severe PED outbreaks and the reason of the re-current outbreaks was unknown. Whether or not the introduction of exotic strains or continual evolution of existing PEDV, genetic analyses would provide a more understanding in its evolutionary pattern. In the study, 117 complete spike gene sequences of Thai PED virus (PEDV) collected from 2008 to 2015 were clustered along with 95 references of PEDV spike sequences, and analyzed with the US sequences dataset (n=99). The phylogenetic analysis demonstrated that Thai PEDV spike sequences were genetically diverse and had been influenced by multiple introduction of exotic strains. Although Thai PEDV have been evolved into 6 subgroups (TH1-6), Subgroup TH1 strains with the unique 9 nucleotides (CAA GGG AAT) insertion between 688th-689th position of spike (changing amino acid from N to TREY) insertion has become the dominant subgroup since 2014. Thai PEDV spike gene have higher evolutionary rate compare to that of the US sequences. One contributing factor would be the intra-recombination between subgroups. Thailand endemic strain should be assigned into new subclade of G2 (Thai pandemic variant).
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Thailand.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Stott
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Thailand.
authors.forename: Gun
authors.initials: G
authors.lastname: Temeeyasen
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Thailand.
authors.forename: Thitima
authors.initials: T
authors.lastname: Tripipat
authors.affiliation: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand.
authors.forename: Pavita
authors.initials: P
authors.lastname: Kaewprommal
authors.affiliation: Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Thailand.
authors.forename: Angkana
authors.initials: A
authors.lastname: Tantituvanont
authors.affiliation: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand.
authors.forename: Jittima
authors.initials: J
authors.lastname: Piriyapongsa
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Thailand. Electronic address: ndachrit@chula.ac.th.
authors.forename: Dachrit
authors.initials: D
authors.lastname: Nilubol
mesh_terms: D000818:Animals; D005075:Biological Evolution; D003001:Cloning, Molecular; D018352:Coronavirus Infections / Q000453:epidemiology / Q000635:transmission / Q000662:veterinary* / Q000821:virology; D004196:Disease Outbreaks; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D016679:Genome, Viral; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D011110:Polymorphism, Genetic; D053485:Porcine epidemic diarrhea virus / Q000145:classification / Q000235:genetics*; D011994:Recombinant Proteins / Q000235:genetics; D011995:Recombination, Genetic; D064370:Spike Glycoprotein, Coronavirus / Q000235:genetics*; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000635:transmission / Q000821:virology; D013785:Thailand / Q000453:epidemiology
chemical_list: D011994:Recombinant Proteins; D064370:Spike Glycoprotein, Coronavirus
keywords: Epidemiology; Evolutionary rate; Porcine epidemic diarrhea virus; Thailand