Molecular Surveillance and Partial Genetic Characterization of Low-Pathogenic Avian Influenza A Viruses in Migrating...

Wild migratory birds are the principal natural reservoir of influenza A viruses (IAVs) and play a central role in their evolution and global dissemination. Ukraine lies along the Black Sea-Mediterranean Flyway, making surveillance of avian influenza viruses in wild birds essential within a One Health framework, although genomic data from the region remain limited. Between October 2025 and January 2026, 604 cloacal and oropharyngeal swabs and environmental fecal samples were collected from migratory birds and mixed-species flocks in the Tuzlivski lymany National Nature Park and surrounding areas, together with samples from nearby domestic poultry. Influenza A virus was detected by real-time RT-PCR targeting the matrix gene, followed by H5/H7 screening, Oxford Nanopore sequencing of complete hemagglutinin genes, and phylogenetic analysis. Influenza A virus RNA was identified in 30/604 samples (4.97%), whereas all samples were negative for H5 and H7 subtypes. Complete hemagglutinin sequences revealed three low-pathogenic subtypes (H1, H4, and H6) that clustered within established Eurasian lineages closely related to contemporary avian viruses circulating across Europe, Asia, and North America. No influenza A virus or Newcastle disease virus was detected in domestic poultry. These findings provide an important genomic baseline for avian influenza surveillance in Ukraine and demonstrate the value of portable nanopore sequencing and integrated One Health surveillance for monitoring viral diversity and supporting early detection of emerging influenza threats.