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

Abstract

In 2022/2023, Europe experienced its third consecutive season of high-pathogenicity avian influenza. During this period, the Czech Republic was again severely affected. For the first time, the number of culled birds approached one million, which was three times higher than in previous seasons. In parallel to the outbreaks in poultry, mass die-offs of gulls were also observed. In the present study, we performed whole-genome sequencing and phylogenetic analysis of 137 H5N1 strains collected in the Czech Republic in 2022/2023 (94.6% of all outbreaks or locations). The analysis revealed four distinct genotypes: AB, CH, BB and AF. Phylogenetic analysis suggested that the AF genotype persisted from the previous H5N1 season without reassortment. In addition, the genotype BB, which was detected mainly in gulls, showed a noticeable strain diversity at the local level. This virus was also responsible for a single outbreak in commercially bred turkeys. Finally, an interesting spatio-temporal cluster with three co-circulating H5N1 genotypes, AB, CH and AF, was identified with no evidence of intrasubtype reassortment. Highly sensitive molecular surveillance and the timely sharing of genomic sequences and associated metadata could greatly assist in tracking the spread and detecting molecular changes associated with the increased virulence of this potentially zoonotic pathogen.

Outbreaks of H5N1 High Pathogenicity Avian Influenza in South Africa in 2023 Were Caused by Two Distinct Sub-Genotypes of Clade 2.3.4.4b Viruses

“…In contrast, all the outbreaks in chickens were caused by sub-genotype SA15. SA15 is a unique southern African variant that was first associated with outbreaks in Botswana in mid-2022 [ 13 ] and was the cause of a single outbreak in commercial ostriches in South Africa’s Free State province in November 2022 [ 7 ]. Furthermore, the three clusters of SA15-associated poultry outbreaks in the Paardeberg and George areas and KZN were phylogenetically unrelated.…”

“…When the SA13 viruses from 2022 were compared to the SA13 viruses from 2023 using amino acid sequence distance matrices of the of H5 HA protein (576 aa; Table S4) and N1 NA (470 aa; Table S5), the mean number of mutations in the HA protein was 2.1 (1-5), but in the NA protein, it was 8.1 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). Percentagewise, the mean amino acid mutations in HA in SA13 increased by 0.36% between 2022 and 2023, and in NA, the value was 1.72%.…”

“…More alarmingly, in 2023, clade 2.3.4.4b viruses began to increasingly infect mammals in Europe and the Americas, raising fears that a pandemic human strain may soon emerge [ 10 ]. Aside from the catastrophic effects of clade 2.3.4.4b H5Nx HPAI on global poultry production, unprecedented outbreaks in wild birds and marine mammals have had dire ecological and conservation impacts [ 10 , 11 , 12 , 13 ].…”