title: Full-length genome analysis of two genetically distinct variants of porcine epidemic diarrhea virus in Thailand.
abstract: Porcine epidemic diarrhea virus (PEDV) has continued to cause sporadic outbreaks in Thailand since 2007 and a pandemic variant containing an insertion and deletion in the spike gene was responsible for outbreaks. In 2014, there were further outbreaks of the disease occurring within four months of each other. In this study, the full-length genome sequences of two genetically distinct PEDV isolates from the outbreaks were characterized. The two PEDV isolates, CBR1/2014 and EAS1/2014, were 28,039 and 28,033 nucleotides in length and showed 96.2% and 93.6% similarities at nucleotide and amino acid levels respectively. In total, we have observed 1048 nucleotide substitutions throughout the genome. Compared to EAS1/2014, CBR1/2014 has 2 insertions of 4 ((56)GENQ(59)) and 1 ((140)N) amino acid positions 56-59 and 140, and 2 deletions of 2 ((160)DG(161)) and 1 ((1199)Y) amino acid positions 160-161 and 1199. The phylogenetic analysis based on full-length genome of CBR1/2014 isolate has grouped the virus with the pandemic variants. In contrast, EAS1/2014 isolate was grouped with CV777, LZC and SM98, a classical variant. Our findings demonstrated the emergence of EAS1/2014, a classical variant which is novel to Thailand and genetically distinct from the currently circulating endemic variants. This study warrants further investigations into molecular epidemiology and genetic evolution of the PEDV in Thailand.
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Bangkok, Thailand.
authors.forename: Thaniwan
authors.initials: T
authors.lastname: Cheun-Arom
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Bangkok, Thailand.
authors.forename: Gun
authors.initials: G
authors.lastname: Temeeyasen
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Bangkok, 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: 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 Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand.
authors.forename: Suchada
authors.initials: S
authors.lastname: Sukrong
authors.affiliation: Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand.
authors.forename: Wanchai
authors.initials: W
authors.lastname: Chongcharoen
authors.affiliation: Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand.
authors.forename: Angkana
authors.initials: A
authors.lastname: Tantituvanont
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Bangkok, Thailand. Electronic address: dachrit@gmail.com.
authors.forename: Dachrit
authors.initials: D
authors.lastname: Nilubol
mesh_terms: D000818:Animals; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary; D014644:Genetic Variation; D016679:Genome, Viral; D010802:Phylogeny; D053485:Porcine epidemic diarrhea virus / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D012641:Selection, Genetic; D013552:Swine; D013553:Swine Diseases / Q000821:virology; D013785:Thailand / Q000453:epidemiology
keywords: Antigenic index; Classical; Full-length genome; Pandemic; Porcine epidemic diarrhea virus; Thailand