Genotype Diversity, Wild Bird-to-Poultry Transmissions, and Farm-to-Farm Carryover during the Spread of the Highly Pathogenic Avian Influenza H5N1 in the Czech Republic in 2021/2022

Abstract

In 2021/2022, the re-emergence of highly pathogenic avian influenza (HPAI) occurred in Europe. The outbreak was seeded from two sources: resident and reintroduced viruses, which is unprecedented in the recorded history of avian influenza. The dominant subtype was H5N1, which replaced the H5N8 subtype that had predominated in previous seasons. In this study, we present a whole genome sequence and a phylogenetic analysis of 57 H5N1 HPAI and two low pathogenic avian influenza (LPAI) H5N1 strains collected in the Czech Republic during 2021/2022. Phylogenetic analysis revealed close relationships between H5N1 genomes from poultry and wild birds and secondary transmission in commercial geese. The genotyping showed considerable genetic heterogeneity among Czech H5N1 viruses, with six different HPAI genotypes, three of which were apparently unique. In addition, second-order reassortment relationships were observed with the direct involvement of co-circulating H5N1 LPAI strains. The genetic distance between Czech H5N1 HPAI and the closest LPAI segments available in the database illustrates the profound gaps in our knowledge of circulating LPAI strains. The changing dynamics of HPAI in the wild may increase the likelihood of future HPAI outbreaks and present new challenges in poultry management, biosecurity, and surveillance.

Enzootic Circulation, Massive Gull Mortality and Poultry Outbreaks during the 2022/2023 High-Pathogenicity Avian Influenza H5N1 Season in the Czech Republic

“…In general, the outbreaks in Czech commercial poultry followed the same scenario as observed in previous years [ 36 , 37 ] and reported elsewhere in Europe [ 38 , 39 , 40 ]. The disease has always appeared suddenly, even in commercial poultry farms with a high level of biosecurity [ 41 ].…”

“…The 2022/2023 H5N1 HPAI season was the most serious for the poultry industry ever recorded in the Czech Republic. Despite the number of outbreaks in poultry being roughly comparable to the previous seasons [ 36 , 37 ], for the first time, the number of culled birds approached one million. This was circa three times higher than in previous years and was mainly due to an outbreak in a single poultry farm of ~750,000 laying hens.…”

“…This has been suggested at the local level using the reappearance of genotype AF in domestic poultry in the Czech Republic. In addition, this genotype showed a much wider geographical distribution compared to the previous season [ 36 ]. Similarly, but from a broader perspective, enzootic circulation is clearly evident, at least for the genotype BB, which was first identified in May 2022 and has since persisted in colony-breeding seabirds in northern Europe [ 17 ].…”

Detection of clade 2.3.4.4 highly pathogenic avian influenza H5 viruses in healthy wild birds in the Hadeji‐Nguru wetland, Nigeria 2022

“…[8][9][10][11][12][13] The Hadejia-Nguru wetlands are located about 220 km from the first HPAI H5N1 outbreaks reported in Kano State in January 2015 and could be a source of infection and maintenance of the virus. 2,8,14 Although there is low transmissibility of HPAIV from birds to humans and high fatality has been reported in humans in previous epidemics, the potential for a mutant strain of HPAIV to become pandemic through spillover from infected migratory birds poses a threat to public health. 15 Several phylogenetically distinct sub-lineages of the HPAIV have been reported in wild migratory birds.…”

“…Nigeria within the sub‐Saharan agroecological region has witnessed several introductions of avian influenza virus (AIV) since 2006, and there is strong evidence of the role of wild birds in the ecology and epidemiology of HPAI 8–13 . The Hadejia‐Nguru wetlands are located about 220 km from the first HPAI H5N1 outbreaks reported in Kano State in January 2015 and could be a source of infection and maintenance of the virus 2,8,14 . Although there is low transmissibility of HPAIV from birds to humans and high fatality has been reported in humans in previous epidemics, the potential for a mutant strain of HPAIV to become pandemic through spillover from infected migratory birds poses a threat to public health 15 …”