title: Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus.
abstract: Porcine epidemic diarrhea virus (PEDV) has caused severe economic losses both recently in the United States (US) and historically throughout Europe and Asia. Traditionally, analysis of the spike gene has been used to determine phylogenetic relationships between PEDV strains. We determined the complete genomes of 93 PEDV field samples from US swine and analyzed the data in conjunction with complete genome sequences available from GenBank (n=126) to determine the most variable genomic areas. Our results indicate high levels of variation within the ORF1 and spike regions while the C-terminal domains of structural genes were highly conserved. Analysis of the Receptor Binding Domains in the spike gene revealed a limited number of amino acid substitutions in US strains compared to Asian strains. Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. These finding suggest that significant genetic events outside of the spike region have contributed to the evolution of PEDV.
authors.affiliation: Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Jarvis
authors.affiliation: Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
authors.forename: Ham Ching
authors.initials: HC
authors.lastname: Lam
authors.affiliation: Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH, USA.
authors.forename: Leyi
authors.initials: L
authors.lastname: Wang
authors.affiliation: Kansas State Veterinary Diagnostic Laboratory and Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, USA.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Hesse
authors.affiliation: Kansas State Veterinary Diagnostic Laboratory and Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, USA.
authors.forename: Ben M
authors.initials: BM
authors.lastname: Hause
authors.affiliation: Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, The Ohio State University, Wooster, OH, USA.
authors.forename: Anastasia
authors.initials: A
authors.lastname: Vlasova
authors.affiliation: Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, College of Food Agriculture and Environmental Sciences, The Ohio State University, Wooster, OH, USA.
authors.forename: Qiuhong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
authors.forename: Jianqiang
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Martha I
authors.initials: MI
authors.lastname: Nelson
authors.affiliation: Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Murtaugh
authors.affiliation: Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA. Electronic address: marth027@umn.edu.
authors.forename: Douglas
authors.initials: D
authors.lastname: Marthaler
mesh_terms: D000818:Animals; D005075:Biological Evolution; D018352:Coronavirus Infections / Q000662:veterinary* / Q000821:virology; D003967:Diarrhea / Q000662:veterinary* / Q000821:virology; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D053485:Porcine epidemic diarrhea virus / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000662:veterinary; D013552:Swine; D013553:Swine Diseases / Q000821:virology*; D014481:United States
keywords: Bayesian analysis; Complete genome; Molecular analysis; Porcine epidemic diarrhea virus