title: Characterization and evolution of porcine deltacoronavirus in the United States.
abstract: Porcine deltacoronavirus (PDCoV) was identified in multiple states across the United States (US) in 2014. In this study, we investigate the presence of PDCoV in diagnostic samples, which were further categorized by case identification (ID), and the association between occurrence, age, specimen and location between March and September 2014. Approximately, 7% of the case IDs submitted from the US were positive for PDCoV. Specimens were categorized into eight groups, and the univariate analysis indicated that oral fluids had 1.89 times higher odds of detecting PDCoV compared to feces. While the 43-56 day age group had the highest percentage of PDCoV positives (8.4%), the univariate analysis indicated no significant differences between age groups. However, multivariable analysis for age adjusted by specimen indicated the >147 day age group had 59% lower odds than suckling pigs of being positive for PDCoV. The percentage of PDCoV in diagnostic samples decreased to <1% in September 2014. In addition, 19 complete PDCoV genomes were sequenced, and Bayesian analysis was conducted to estimate the emergence of the US clade. The evolutionary rate of the PDCoV genome is estimated to be 3.8×10(-4) substitutions/site/year (2.3×10(-4)-5.4×10(-4), 95% HPD). Our results indicate that oral fluids continue to be a valuable specimen to monitor swineherd health, and PDCoV has been circulating in the US prior to 2014.
authors.affiliation: College of Veterinary Medicine, Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States.
authors.forename: Nitipong
authors.initials: N
authors.lastname: Homwong
authors.affiliation: College of Veterinary Medicine, Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Jarvis
authors.affiliation: College of Veterinary Medicine, Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States.
authors.forename: Ham Ching
authors.initials: HC
authors.lastname: Lam
authors.affiliation: College of Veterinary Medicine, Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States.
authors.forename: Andres
authors.initials: A
authors.lastname: Diaz
authors.affiliation: College of Veterinary Medicine, Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States.
authors.forename: Albert
authors.initials: A
authors.lastname: Rovira
authors.affiliation: Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, United States.
authors.forename: Martha
authors.initials: M
authors.lastname: Nelson
authors.affiliation: College of Veterinary Medicine, Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States. Electronic address: marth027@umn.edu.
authors.forename: Douglas
authors.initials: D
authors.lastname: Marthaler
mesh_terms: D000367:Age Factors; D000818:Animals; D005075:Biological Evolution; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D003967:Diarrhea / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D053485:Porcine epidemic diarrhea virus / Q000235:genetics / Q000502:physiology*; D017422:Sequence Analysis, DNA / Q000662:veterinary; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000821:virology; D014481:United States / Q000453:epidemiology
keywords: Bayesian analysis; Porcine deltacoronavirus; Swine oral fluid