Time-space analysis of highly pathogenic avian influenza H5N2 outbreak in the US

Nutthawan Nonthabenjawan, Carol Cardona, Alongkorn Amonsin, Srinand Sreevatsan

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


Background: 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. Methods: 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. Results: 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. Conclusions: 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.

Original languageEnglish (US)
Article number147
JournalVirology journal
Issue number1
StatePublished - Aug 30 2016

Bibliographical note

Funding Information:
The authors would like to thank Chulalongkorn University for a Dutsadi Phiphat scholarship to NN and TRF senior scholar to AA (RTA5680006). We also thank Drs. Toremorrell, Murtaugh, Marthaler and Mor for samples and critical discussions on our analysis. This project was funded by Agricultural Experiment Station grants expended as Rapid Agricultural Response fund awarded to CC.

Publisher Copyright:
© 2016 The Author(s).


  • Evolutionary
  • H5N2
  • Highly pathogenic avian influenza
  • Minnesota

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