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

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.

Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018

“…The HPAI H5N8 epidemic that occurred during January 2014 in South Korea, infecting 161 commercial poultry flocks, led to the culling of 14,000,000 birds; subsequently, the virus was detected continuously in Germany, England, and the Netherlands in early November 2014. Soon afterward, in early 2015, HPAI H5 had threatened Canada, along with various states in the USA, with more than 200 confirmed cases and 48,000,000 birds affected [ 60 ]. Certain HPAI H5 clade 2.3.4.4 viruses isolated from North America were proven to possess the HA gene originating from Asian lineages [ 61 , 62 ].…”

Global subtype diversity, spatial distribution patterns, and phylogenetic analysis of avian influenza virus in water

“…Multiple AIV subtypes have been detected from poultry and wild birds in Africa, Australia, Europe, and America (Alexander, 2007; Araujo et al., 2018; I. H. Brown, 2010; Grillo et al., 2015; Hansbro et al., 2010; Jiménez‐Bluhm et al., 2018; Senne, 2007). Even, environmental sampling has been performed over early, mid and late phases of influenza outbreaks on poultry (Nonthabenjawan et al., 2016); for instance, the HPAI H5N2 AIVs reported in turkey barns from the United States. However, our global analysis of AIV evidenced a lack of sequences isolated from environmental water in Africa, Oceania, and South America, as well as, in Europe.…”