Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus

Matthew C Jarvis; Ham Ching Lam; Yan Zhang; Leyi Wang; Richard A Hesse; Ben M Hause; Anastasia Vlasova; Qiuhong Wang; Jianqiang Zhang; Martha I Nelson; Michael P Murtaugh; Douglas Marthaler

doi:10.1016/j.prevetmed.2015.10.020

Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus

Prev Vet Med. 2016 Jan 1:123:175-184. doi: 10.1016/j.prevetmed.2015.10.020. Epub 2015 Nov 10.

Authors

Affiliations

¹ Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
² Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH, USA.
³ Kansas State Veterinary Diagnostic Laboratory and Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, USA.
⁴ 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.
⁵ Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
⁶ Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
⁷ Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
⁸ Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA. Electronic address: marth027@umn.edu.

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.

Keywords: Bayesian analysis; Complete genome; Molecular analysis; Porcine epidemic diarrhea virus.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Biological Evolution
Coronavirus Infections / veterinary*
Coronavirus Infections / virology
Diarrhea / veterinary*
Diarrhea / virology
Genome, Viral*
Molecular Sequence Data
Phylogeny
Porcine epidemic diarrhea virus / genetics*
Sequence Analysis, DNA / veterinary
Swine
Swine Diseases / virology*
United States