Cocirculation of endemic and recently introduced West Nile Virus lineage 1 clades in Southern Spain

In 2024, Andalusia (Southern Spain) reported its largest recent West Nile virus (WNV) outbreak, with 106 confirmed human cases and 16 deaths. Genomic analysis of 27 WNV isolates revealed the co-circulation of multiple WNV lineage 1 clades, including both endemic and recently introduced strains, reflecting a marked increase in viral genetic diversity. These findings underscore the critical role of integrated genomic surveillance systems in monitoring pathogen evolution and supporting timely public health responses to emerging zoonotic threats. • Genomic analysis of 27 WNV isolates reveals the co-circulation of endemic and newly introduced lineage 1 clades in Southern Spain. • Phylogenetic analysis identifies persistent WNV strains from previous outbreaks alongside novel variants. • The findings highlight Spain's role in the circulation of WNV between Africa and Europe. • Findings also underscore the need for enhanced One Health surveillance in Spain.