Ticks are temporary ectoparasites that serve as vectors for a wide range of pathogens affecting both wildlife and humans. In Greece, research on the prevalence of tick-borne pathogens in wildlife is limited. This study investigates the presence of pathogens, including Anaplasma spp., Babesia spp., Bartonella spp., Rickettsia spp., as well as tick-borne encephalitis (TBE), and Crimean–Congo hemorrhagic fever (CCHF) viruses, in ticks collected from 28 wild animals across 10 different animal species. Ticks were manually harvested and identified using molecular methods, with sequencing confirming the presence of Hyalomma aegyptium, H. marginatum, H. anatolicum, Ixodes frontalis, and I. ventalloi. Among the pathogens detected, R. aeschlimannii was the most prevalent, particularly in H. aegyptium ticks from tortoises. Additionally, R. africae was identified in H. aegyptium from tortoises, marking the first report of this pathogen in this tick species in Greece. Hemolivia mauritanica, an apicomplexan parasite commonly found in Testudo tortoises, was also detected. No evidence of Babesia spp., Anaplasma spp., Bartonella spp., or viral nucleic acid was found. Phylogenetic analysis revealed close genetic relationships between the detected Rickettsia species and those previously reported in neighboring regions. These findings underscore the role of wildlife in the epidemiology of tick-borne pathogens in Greece and highlight the need for comprehensive surveillance to prevent future outbreaks.

Continuous genomic surveillance of influenza virus is critical for monitoring viral evolution, detecting emerging variants, and informing vaccine strain selection. While partial-gene Sanger sequencing has traditionally underpinned national surveillance programs, whole-genome sequencing (WGS) enables simultaneous characterization of all eight genomic segments, providing resolution not achievable through conventional approaches. This is the first published, systematic, whole-genome-based influenza surveillance study reported from Greece. We sequenced and characterized influenza viruses circulating in Southern Greece (S. Greece) during two consecutive influenza seasons, 2024–2025 and 2025–2026, using Oxford Nanopore Technologies (ONT) sequencing. A total of 40 samples were analyzed, with complete or near-complete genome assembly achieved in the vast majority of them. During 2024–2025, co-circulation of A(H1N1)pdm09 (subclades C.1.9.3 and D.3.1), A(H3N2) (subclades J.1.1 and J.2.2), and B/Victoria (C.5 subclades, predominantly C.5.7) influenza viruses was confirmed, with the detection of an oseltamivir-resistant H1N1 variant carrying NA H275Y as a clinically significant finding. Extension of surveillance into 2025–2026 revealed a complete inter-seasonal lineage transition in A(H1N1)pdm09 from subclade C.1.9.3 to D.3.1/D.3.1.1, and the rapid emergence and geographic dissemination of A(H3N2) subclade K across multiple regions of Southern Greece. Phylogenetic analysis characterized the HA subclade composition across the two seasons and positioned the Greek strains within the European and global context. Sequences of subclade K strains from S. Greece were phylogenetically concordant with the updated 2026–2027 vaccine strains, in line with ECDC and WHO surveillance data. Whole-genome analysis confirmed the absence of virulence-associated polymerase markers in all isolates with fully assembled polymerase segments, and identified conserved internal segment substitution patterns co-segregating with circulating subclades. These findings provide the first published whole-genome evolutionary dataset for influenza in Southern Greece, contributing insight into subtype and clade-level evolutionary dynamics and demonstrating the public health value of sustained genomic surveillance at a national reference laboratory level.