Genesis and Spread of Novel Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus Genotype EA-2023-DG Reassortant, Western Europe

Abstract

In Europe, highly pathogenic avian influenza (HPAI) virus circulates in avian wildlife, undergoing frequent reassortment, sporadic introductions in domestic birds, and spillover to mammals. An H5N1 clade 2.3.4.4b reassortant, EA-2023-DG, affecting wild and domestic birds was detected in western Europe in November 2023. Six of its RNA segments came from the EA-2021-AB genotype, but the polymerase basic 2 and polymerase acidic segments originated from low pathogenicity avian influenza viruses. Discrete phylogeographic analyses of concatenated genomes and single polymerase basic 2 and polymerase acidic segments suggested reassortment in summer 2023 near the southwestern Baltic Sea. Subsequent continuous phylogeographic analysis of all concatenated EA-2023-DG genomes highlighted circulation in northwestern Europe until June 2024 and long-distance dispersal toward France, Norway, England, Slovakia, Switzerland, and Austria. Those results illustrate the value of phylodynamic approaches to investigate emergence of novel avian influenza virus variants, trace their subsequent dispersal history, and provide vital clues for informing outbreak prevention and intervention policies.

Keywords: Europe; H5­N1; HPAI; Influenza; highly pathogenic avian influenza virus; phylogeography; viruses; whole-genome sequencing; zoonoses.

Figure 1

Discrete phylogeographic analysis from study of genesis and spread of novel highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus genotype EA-2023-DG reassortant, western Europe. The maximum clade credibility (MCC) tree was obtained from discrete phylogeographic inference based on the analysis of the PB1-HA-NP-NA-MP-NS (polymerase basic 1, hemagglutinin, nucleoprotein, neuraminidase, matrix protein, nonstructural protein) concatenated alignment of EA-2023-DG samples and selected EA-2021-AB reference sequences sourced from GISAID EpiFlu (http://www.gisaid.org). Vertical gray shaded bars reflect the 95% highest posterior density interval associated with each internal node age estimate; internal nodes are colored according to their inferred location, and tip nodes are colored according to their sampling location. For the internal nodes, when a single location could not be inferred with a posterior probability >0.95, we used a pie chart to display the posterior probabilities associated with inferred locations with a posterior probability of >0.05. The gray transparent box highlights the position of the EA-2023-DG clade. The discrete phylogeographic reconstruction based on the analysis of the polymerase basic 2 and polymerase acidic segments are available as supplementary information (Appendix 1 Figures 1, 2).

Figure 2

Continuous phylogeographic analysis from study of genesis and spread of novel highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus genotype EA-2023-DG reassortant, western Europe. A) Time-scaled maximum clade credibility treeretrieved and annotated from the continuous phylogeographic inference based on analysis of 54 publicly available complete EA-2023-DG genomes and associated sampling metadata from GISAID EpiFlu (http://www.gisaid.org). The tree shows horizontal shaded bars reflecting the 95% highest posterior density (HPD) associated with each internal node age estimate. The tree and HPD estimates are based on 1,000 trees sampled from the posterior distribution of trees and are colored according to time of occurrence; internal nodes are displayed as dots and tip nodes are displayed as squares. Dotted vertical lines correspond to 2-month intervals beginning July 1, 2023. B­–F) Phylogeographic reconstruction of EA-2023-DG viral lineages across western Europe. We mapped the MCC tree and 80% HPD regions reflecting the uncertainty related to the Bayesian phylogeographic inference as of June 25, 2024 (B), and for other time points: C) September 1, 2023; D) November 1, 2023; E) January 1, 2024; and F) June 25, 2024. On the maps, the dispersal direction of viral lineages is indicated by the edge curvature in a counterclockwise direction.