First detection and transatlantic introduction of Influenza A(H3N2) subclade K (J.2.4.1) into Ecuador: insights from genomic sentinel surveillance

Abstract

Background The rapid evolution of Influenza A(H3N2) requires constant global monitoring. This study analyzes the genomic characteristics and the first introduction of the emerging subclade K (J.2.4.1) in Ecuador, utilizing publicly available data to trace its intercontinental movement. Methods The hemagglutinin (HA) protein of an Influenza A(H3N2) strain isolated from an Ecuadorian patient was analyzed. A Bayesian phylogenetic reconstruction was performed using BEAST v1.10.4 with 251 global sequences. A molecular clock was applied to estimate the time of most recent common ancestor (TMRCA). Substitutions were screened using the FluSurver tool. Results Phylogenetic analysis clustered the Ecuadorian isolate within a monophyletic group of European origin (Northern Spain). The estimated introduction occurred in late November 2025, aligning with epidemiological links to Ecuadorian migrants travelling from Spain for Christmas holidays. Molecular screening identified HA1 substitutions annotated in FluSurver as mutations of interest, including S160N, N174D, I176K, Q189R, and Y211F. S160N was associated with the creation of a potential N-glycosylation site. The NA protein harbored the N358D substitution, which was annotated in FluSurver as having a reported association with neuraminidase inhibitor susceptibility. Conclusion The introduction of subclade K into South America illustrates the high efficiency of transatlantic travel as a conduit for viral dispersal. This study supports the use of open-access genomic surveillance as a critical sentinel tool for global health security.