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.

Keywords: H5N1; HPAI; avian influenza; highly pathogenic avian influenza; outbreak; poultry.

Figure 1

Distribution of AIV detections in the 2021/2022 season in the Czech Republic. Bar chart showing the number of HPAI/LPAI outbreaks detected per calendar week.

Figure 2

Phylogenetic analysis of H5 hemagglutinin. Species correlation ML tree consisting of Czech and selected Eurasian H5 HPAI sequences collected during 2021–2022 and rooted to A/guinea fowl/Nigeria/2019 H5N8 HA. The tree was calculated by the IQ-TREE program implementing TN + F + I as the best-fitting model selected according to the Bayesian information criterion. The tree was drawn to scale, with branch lengths measured in the number of substitutions per site. For each branch, bootstrap values (1000 replicates) were given in percentages. Subclades B1 and B2 were colored green and brown, respectively. The virus taxa of the H5N1 strains sequenced in the present study were highlighted according to origin: red-commercial; orange-backyard; and blue-wild. A more comprehensive H5 tree is provided in Supplementary Material file S1, Figure S1.

Figure 3

Genotyping of Czech H5N1 HP/LPAI strains detected during the 2021/2022 influenza season. The ML tree was calculated based on 59 concatenated genomes and rooted to A/ew/NL/1/2020 H5N1. The order of segments in the concatenated genomes is PB2, PB1, PA, H5, NP, N1, MP, and NS. The tree was computed using IQ-TREE (GTR + F + R2 as the best-fitting model selected according to the Bayesian information criterion) and scaled with branch lengths measured in the number of substitutions per site. For each branch, bootstrap values (based on 1000 replicates) were given in percentages. Three branches corresponding to discrete genotypes were labeled as A–F and LPAI and highlighted with a genotype-specific color. Further, the figure summarizes the segment constellations of the identified influenza virus genomes inferred from SIMs, SDCMs, and phylogenetic trees calculated individually for each segment (Supplementary Material file S1, Figure S1 and Supplementary Material file S2).

Figure 4

Geographical distribution of H5N1 genotypes. The figure shows the localities of H5N1 virus detections in the 2021/2022 season on a blind map of the Czech Republic. Solid dots indicate bird categories (wild, backyard, and commercial). Localities with available genotype information are surrounded by a halo indicating genotype assignment according to Figure 3. An interactive version of the map is available online at https://www.google.com/maps/d/u/0/edit?mid=1_pWrJqfuItU2UwgIuwHjJDsG-tugjU4q&usp=sharing (accessed on 20 November 2022).