Abstract
The outbreaks of the highly pathogenic avian influenza (HPAI) in 2016–2017 and 2017–2018, caused by novel reassortant clade 2.3.4.4 H5N6 viruses, resulted in the loss of one billion birds in South Korea. Here, we characterized the H5N6 viruses isolated from wild birds in South Korea from December 2017 to August 2019 by next-generation sequencing. The results indicated that clade 2.3.4.4 H5N6 viruses isolated in 2017 and 2019 shared almost identical nucleotide sequences with the HPAI H5N6 viruses from 2016 in South Korea. This repeated detection of evolutionarily identical H5N6 viruses in same region for more than three years may suggest indigenization of the HPAI H5N6 virus in South Korea. Phylogenetic analysis demonstrated that the clade 2.3.4.4 H5N6 viruses isolated in 2017 and 2019 were evolutionarily distinct from those isolated in 2018. Molecular analysis revealed that the H5N6 viruses isolated in 2017 and 2019 had features associated with an increased risk of human infection (e.g. a deletion at position 133 of HA and glutamic acid residue at position 92 of NS1). Overall, these genomic features of HPAI H5N6 viruses highlight the need for continuous monitoring of avian influenza viruses in wild migratory birds as well as in domestic birds.
Highlights
Pathogenic avian influenza (HPAI) viruses cause disease in poultry and humans as well as in some other mammals and wild birds, demonstrating a serious threat to the economy and public
Since 2016, the novel reassortant clade 2.3.4.4 H5N6 viruses have appeared in migratory birds and have caused large outbreaks in poultry in South Korea, posing a serious threat to both poultry and the public
We revealed that the clade 2.3.4.4 H5N6 viruses isolated in 2017 and 2019 in Eumseong shared almost identical nucleotides with highly pathogenic avian influenza (HPAI) H5N6 viruses that caused large outbreaks in domestic poultry during the 2016/17 winter season in South Korea[9]
Summary
Pathogenic avian influenza (HPAI) viruses cause disease in poultry and humans as well as in some other mammals and wild birds, demonstrating a serious threat to the economy and public. Novel HPAI virus reassortant for the HA gene in the H5 clade 2.3.4.4 with different neuraminidase (NA) subtypes have been isolated in animals and humans worldwide[2], and are divided into four genetically distinct subgroups, A-D, based on phylogenetic analysis[3,4,5,6]. The outbreaks in the winter seasons of 2016–2017 and 2017–2018, caused by novel reassortant clade 2.3.4.4 H5N6 viruses[5,9,10,11], resulted in the loss of one billion birds in 440 farms in South Korea[12]. HPAI counts were obtained from the Korea Animal Health Integrated System (https://www.kahis.go.kr/)
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