High pathogenic avian influenza A(H5) viruses of clade 2.3.4.4b in Europe-Why trends of virus evolution are more difficult to predict

Abstract

Since 2016, A(H5Nx) high pathogenic avian influenza (HPAI) virus of clade 2.3.4.4b has become one of the most serious global threats not only to wild and domestic birds, but also to public health. In recent years, important changes in the ecology, epidemiology, and evolution of this virus have been reported, with an unprecedented global diffusion and variety of affected birds and mammalian species. After the two consecutive and devastating epidemic waves in Europe in 2020-2021 and 2021-2022, with the second one recognized as one of the largest epidemics recorded so far, this clade has begun to circulate endemically in European wild bird populations. This study used the complete genomes of 1,956 European HPAI A(H5Nx) viruses to investigate the virus evolution during this varying epidemiological outline. We investigated the spatiotemporal patterns of A(H5Nx) virus diffusion to/from and within Europe during the 2020-2021 and 2021-2022 epidemic waves, providing evidence of ongoing changes in transmission dynamics and disease epidemiology. We demonstrated the high genetic diversity of the circulating viruses, which have undergone frequent reassortment events, providing for the first time a complete overview and a proposed nomenclature of the multiple genotypes circulating in Europe in 2020-2022. We described the emergence of a new genotype with gull adapted genes, which offered the virus the opportunity to occupy new ecological niches, driving the disease endemicity in the European wild bird population. The high propensity of the virus for reassortment, its jumps to a progressively wider number of host species, including mammals, and the rapid acquisition of adaptive mutations make the trend of virus evolution and spread difficult to predict in this unfailing evolving scenario.

Keywords: Europe; high pathogenic avian influenza A(H5) viruses; phylodynamics; reassortments; spatial spread.

Figure 1.

Graphical representation of the A(H5Nx) genotypes identified in Europe during the first (2020–2021) and second (2021–2022) epidemic wave. A number and associated colour code is assigned to each gene based on its genetic clustering in the phylogenetic trees. The reference sequences represent the possible progenitor virus for each specific gene.

Figure 2.

Upper panel: distribution of total number of notified (grey) and genetically characterized (black) HPAI A(H5Nx) viruses in Europe by month of detection. Lower panel: monthly distribution of the A(H5Nx) genotypes identified in Europe between July 2020 and August 2022. Each colour represents a different genotype. The four main genotypes EA-2020-A, EA-2020-C, EA-2021-AB and EA-2022-BB are marked in the graph.

Figure 3.

Panel A—bars represent the distribution of the genetically characterized (complete genome) A(H5Nx) viruses collected from mammals in Europe from December 2020 to August 2022, by month of detection, coloured according to the genotype. Panel B—frequency of the molecular markers of mammalian adaptation in the PB2 protein (271A, 627K, 701N) identified in viruses collected from mammalian species in Europe between October 2020 and August 2022.

Figure 4.

Geographic distribution of the major A(H5Nx) genotypes (represented by at least three viruses) in Europe during the first (2020–2021, left panel) and second (2021–2022, right panel) epidemic wave. The pie charts display the frequency of the genotype in each country. The size of the circle is proportional to the number of sequences analysed.

Figure 5.

Distribution of the different genotypes by bird host categories during the first (2020–2021, left panel) and second (2021–2022, right panel) epidemic wave. The colours assigned to the four major genotypes are reported in the figure legend.

Figure 6.

Global migration rates among the geographic regions of clade 2.3.4.4b (2019–2022). The thickness of the lines representing the rates is proportional to the relative strength by which rates are supported: very strong (BF > 150, thick lines) and positive (5 < BF < 20, thin lines).

Figure 7.

Pattern of geographic jumps and hotspots obtained from the analyses of (A) global dataset, (B) European dataset—first wave (2020–2021), and (C) European dataset—second wave (2021–2022). The three heatmaps on the left indicate the frequency of transitions between locations estimated using a discrete trait phylogenetic model. The number of location transitions was determined using Markov jumps. The bar charts on the right indicate the proportion of time the virus spent in each location.

Figure 8.

Migration rates between European regions of clade 2.3.4.4b during the first (continuous lines) and second (dashed lines) epidemic wave. The thickness of the lines representing the rates is proportional to the relative strength by which rates are supported: very strong (BF > 150, thick lines), strong (20 < BF < 150, medium lines), and positive (5 < BF < 20, thin lines).