Equine influenza subtype H3N8 (equine influenza virus, EIV) is one of the most common respiratory diseases in horses. Although infection rarely leads to death, the virus’s high contagiousness has led to the introduction of effective and widely used preventive vaccination. For this reason, molecular testing for EIV is limited.
In April of this year, we detected the EIV H3N8 virus in nasal swabs from two horses from different regions of the Czech Republic. Genetic analysis showed that both Czech isolates are nearly identical and belong to the globally dominant American sublineage. Another surprising finding was that, according to available database information, there is almost no genetic data available on European EIV strains from the past five years, with the exception of approximately 90 genomes from England and one isolate from Italy.
Another significant finding is that the Czech viruses differ markedly from these European EIVs and show the closest relationship to recent viruses from the US and Japan detected in 2024–2025. These results highlight significant gaps in the current understanding of the genetic heterogeneity of European EIV H3N8 viruses. Both Czech H3N8 genomes were subsequently entered into an international genetic database.