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

Nutthawan Nonthabenjawan,Srinand Sreevatsan,Carol Cardona,Alongkorn Amonsin

doi:10.1186/s12985-016-0605-4

Nutthawan Nonthabenjawan, Srinand Sreevatsan + Show 2 more

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https://doi.org/10.1186/s12985-016-0605-4

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Abstract

BackgroundIn 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.MethodsIn 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.ResultsThe 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.ConclusionsData 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0605-4) contains supplementary material, which is available to authorized users.

Highlights

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
Avian influenza virus (AIV) can be divided into low pathogenic avian influenza viruses (LPAI) and highly pathogenic avian influenza viruses (HPAI) by its ability to cause disease in poultry which is identified by intravenous pathogenicity
TS, CS and Envi stand for tracheal swab, cloacal swab and environmental sample, respectively representative clustering pattern by using a tree annotator with 10 % discarding of the chains as burn-in and the resulting maximum clade credibility tree was visualized with FigTree software (v1.4.2) (Molecular evolution, phylogenetics and epidemiology, Edinburgh, Scotland, UK). First case of this series of outbreaks in the Midwest area was confirmed on March 4th, 2015 in Pope county, Minnesota and last case on June 17th, 2015 in Iowa [12]

Summary

Introduction

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. Hemagglutinin (HA) and neuraminidase (NA) are surface proteins that are used to classify AIV into subtypes. 16 HA and 9 NA subtypes have been identified in aquatic wild birds which are a natural reservoir of these viruses [2]. AIV can be divided into low pathogenic avian influenza viruses (LPAI) and highly pathogenic avian influenza viruses (HPAI) by its ability to cause disease in poultry which is identified by intravenous pathogenicity. Outbreaks HPAI H5 in Guangdong, China in 1996 have likely origins from goose Guangdong lineage HPAI viruses [4]. In 2003, a re-emergence of HPAI H5N1 in China and South East Asia was reported. The H5 clade 2.3.4.4 has demonstrated an ability to reassort with multiple neuraminidase subtypes including N1, N2, N3, N5, N6 or N8 [7]

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