11 May 2026
During the 2022–2023 epizootic season, France experienced a peculiar "biphasic" epidemic in its southwestern poultry-dense regions. After an initial wave of 11 outbreaks ended in January 2023, the region saw 99 consecutive days without a single detection. However, the virus suddenly returned in May 2023, leading to 88 additional outbreaks. Remarkably, the first cases of this second wave appeared just two days after authorities lifted the national requirement to shelter poultry, raising urgent questions: was this a new introduction from migratory birds, or had the virus been "hiding" on the farms?
To solve this mystery, researchers performed whole-genome sequencing on 82 viral samples belonging to the EA-2022-CC genotype. By analyzing the substitution rate, the speed at which the virus's genetic code mutates over time, the team made a striking discovery. Based on the estimated substitution rate observed in the first wave, the virus should have accumulated between 9 and 33 mutations during the 99-day hiatus. Instead, the viruses in the second wave showed a genetic distance of only 1 to 5 nucleotides from the first wave. This minimal divergence suggests the virus was not actively circulating in birds during those three months. Instead, it likely persisted in a "latent" state within the environment, likely in manure or feathers, waiting for poultry to be let back out to pasture. Phylogenetic analysis confirmed that the second wave viruses formed a monophyletic cluster, and no wild bird sequences from the period were directly related to these farm outbreaks. The study highlights a critical vulnerability in current control measures. Clearing an outbreak requires more than just depopulating the birds; it requires rigorous, long-term environmental management and disinfection.
Briand et al. (2026). Re-emergence of a highly pathogenic avian influenza H5N1 virus of clade 2.3.4.4b in poultry in France. Infection, Genetics and Evolution
