title: Time-space analysis of highly pathogenic avian influenza H5N2 outbreak in the US.
abstract: In early 2015, highly pathogenic avian influenza H5N2 caused outbreaks in commercial poultry farms in Minnesota and neighboring states where more than 48 million birds were affected. To date, the origin and transmission pathways of HPAI H5N2 have not been conclusively established.
  
  
  
  In this study, we analyzed forty-six samples from turkeys and their environment that were collected at different time-points of the outbreak to identify origins and within outbreak evolutionary changes. We performed de-novo whole genome sequencing from primary samples and the most recent common ancestors of the PB2, PA, HA5, M and NS segments were traced back to Japanese HPAI H5N8 isolates. These segments appeared to have diverged from the ancestor around June and November 2014.
  
  
  
  The time to most recent common ancestor analysis for PB1, NP and NA2 segments suggest two likely possibilities of reassortant HPAI H5N2 origin - either a reassortment in Alaska area or multiple reassortments with North American low pathogenic avian influenza strains, before the HPAI H5N2 outbreak strain emerged. Within the outbreak, viruses clustered into two and three subgroups suggesting high substitution rates of 0.702x10-2 - 1.665x10-2 (subs/site/year), over the 5-month outbreak period.
  
  
  
  Data are suggestive of a fast evolving HPAI strain within an outbreak that should be taken into consideration in developing appropriate control strategies in the future.
authors: Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.|Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.|Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Rm 301E, St. Paul, MN, 55108, USA.
authors: Nutthawan
authors: N
authors: Nonthabenjawan
authors: Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Rm 301E, St. Paul, MN, 55108, USA.|Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Rm 301E, St. Paul, MN, 55108, USA.
authors: Carol
authors: C
authors: Cardona
authors: Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.|Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
authors: Alongkorn
authors: A
authors: Amonsin
authors: Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Rm 301E, St. Paul, MN, 55108, USA. sreev001@umn.edu.|Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Rm 301E, St. Paul, MN, 55108, USA. sreev001@umn.edu.
authors: Srinand
authors: 0000-0002-5162-2403
authors: S
authors: Sreevatsan
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D004196:Disease Outbreaks; D004783:Environmental Microbiology; D016679:Genome, Viral; D053125:Influenza A Virus, H5N2 Subtype / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000821:virology*; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D062211:Spatio-Temporal Analysis; D014422:Turkeys / Q000821:virology; D014481:United States / Q000453:epidemiology; D014764:Viral Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins
keywords: Evolutionary; H5N2; Highly pathogenic avian influenza; Minnesota