title: The genetic diversity and complete genome analysis of two novel porcine deltacoronavirus isolates in Thailand in 2015.
abstract: Porcine deltacoronavirus (PDCoV) was identified in intestinal samples collected from piglets with diarrhea in Thailand in 2015. Two Thai PDCoV isolates, P23_15_TT_1115 and P24_15_NT1_1215, were isolated and identified. The full-length genome sequences of the P23_15_TT_1115 and P24_15_NT1_1215 isolates were 25,404 and 25,407 nucleotides in length, respectively, which were relatively shorter than that of US and China PDCoV. The phylogenetic analysis based on the full-length genome demonstrated that Thai PDCoV isolates form a new cluster separated from US and China PDCoV but relatively were more closely related to China PDCoV than US isolates. The genetic analyses demonstrated that Thai PDCoVs have 97.0-97.8 and 92.2-94.0% similarities with China PDCoV at nucleotide and amino acid levels, respectively, but share 97.1-97.3 and 92.5-93.0 similarity with US PDCoV at the nucleotide and amino acid levels, respectively. Thai PDCoV possesses two discontinuous deletions of five amino acids in ORF1a/b region. One additional deletion of one amino acid was identified in P23_15_TT_1115. The variation analyses demonstrated that six regions (nt 1317-1436, 2997-3096, 19,737-19,836, 20,277-20,376, 21,177-21,276, and 22,371-22,416) in ORF1a/b and spike genes exhibit high sequence variation between Thai and other PDCoV. The analyses of amino acid changes suggested that they could potentially be from different lineages.
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
authors.forename: Athip
authors.initials: A
authors.lastname: Lorsirigool
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
authors.forename: Kepalee
authors.initials: K
authors.lastname: Saeng-Chuto
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
authors.forename: Adthakorn
authors.initials: A
authors.lastname: Madapong
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
authors.forename: Gun
authors.initials: G
authors.lastname: Temeeyasen
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, 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, 12120, Thailand.
authors.forename: Pavita
authors.initials: P
authors.lastname: Kaewprommal
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: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, 12120, Thailand.
authors.forename: Jittima
authors.initials: J
authors.lastname: Piriyapongsa
authors.affiliation: Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand. dachrit@gmail.com.
authors.forename: Dachrit
authors.identifier: http://orcid.org/0000-0002-7691-6790
authors.initials: D
authors.lastname: Nilubol
mesh_terms: D000818:Animals; D017934:Coronavirus / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D007422:Intestines / Q000473:pathology / Q000821:virology; D008969:Molecular Sequence Data; D010802:Phylogeny; D013552:Swine / Q000821:virology; D013553:Swine Diseases / Q000235:genetics* / Q000821:virology; D013785:Thailand
keywords: Full-length genome; Porcine deltacoronavirus; Thailand