Biology subjects

Abrantes, J.

Publications and source records attributed to Abrantes, J..

3 recordsLinked to original sources

bioRxiv2026

Post-outbreak surveillance reveals contrasting circulation dynamics of West Nile, Usutu and Bagaza viruses in southern Portugal, 2021 - 2023

Mosquito-borne orthoflaviviruses pose a significant threat to human and animal health worldwide. In Europe, West Nile (WNV), Usutu (USUV) and Bagaza (BAGV) viruses have expanded their geographic distribution and are detected with increasing frequency. Following the emergence of BAGV in 2021, we investigated the circulation dynamics and genomic diversity of orthoflaviviruses in southern Portugal, where their epidemiology remains poorly understood. Active Orthoflavivirus surveillance was conducted in birds and mosquitoes during 2021-2023 using serological and molecular assays, complemented by viral genome sequencing and phylogenomic analyses. Viral RNA was detected in 3.5% (41/1,171) of birds, while seroneutralization assays identified an overall seroprevalence of 55.3% (503/910). WNV RNA (lineage-1, strains WMed-1.2 and WMed-1.3) was detected annually in resident birds, including Alectoris rufa, Cyanopica cooki and Garrulus glandarius (1.5%, 18/1,171), and in Culex univittatus mosquitoes (0.8%, 2/255). Together with a WNV-specific seroprevalence of 28.5% (259/910) in birds, these findings support sustained local circulation. USUV RNA (Africa 3.1 sub-lineage) was detected in A. rufa in 2021 and 2023 (0.2%, 2/1,171), but seroprevalence was low (1.3%, 8/623), consistent with intermittent circulation. BAGV RNA (genotype-2) was detected only during the 2021 outbreak in A. rufa and Emberiza calandra (1.8%, 21/1,171), although BAGV-specific antibodies (6.6%, 60/910) were detected for up to two years after the outbreak, suggesting continued exposure or low-level circulation. Overall, our findings reveal contrasting circulation dynamics of orthoflaviviruses in southern Portugal. Sustained WNV circulation implies the need to strengthen avian and human surveillance in Portugal to better assess its public health risk, while the sporadic detection of USUV and BAGV underscores the value of long-term, integrated One Health surveillance for improving early warning and preparedness for emerging mosquito-borne diseases.

genetics↗

bioRxiv2026

Cartilaginous fish inform the lineage-specific evolution and MHC association of the TLR family

Chondrichthyans (sharks, rays and chimaeras) diverged from other vertebrate lineages over 400 million years ago and possess fully functional innate and adaptive immune systems. They comprise over 1,200 species occupying diverse aquatic habitats, from fresh to marine waters and from shallow to deep seas. Exposure to diverse pathogens through time, together with contemporary ocean warming and habitat degradation driven by climate change, has likely shaped unique immune mechanisms in these species. Toll-like receptors (TLRs) are central components of innate immunity, recognizing conserved pathogen-associated molecular patterns and initiating immune responses, yet their diversity remains poorly characterized in Chondrichthyans. Here, we characterize the TLR gene repertoire in elasmobranchs (sharks and rays) using genomic and transcriptomic data. We identify orthologs spanning all known vertebrate TLR families, including genes shared with agnathans as well as gnathostome-specific genes, and detect lineage-specific patterns of TLR duplication and loss, particularly in squaliform sharks and rays. Molecular evolution analyses indicate that most elasmobranch TLRs are under strong purifying selection, with positively selected sites in all genes, consistent with ongoing adaptation to pathogen-and environment-driven pressures. Several TLRs co-localize with genomic regions enriched in immune genes, including MHC paralogous regions, suggesting an ancestral genomic hotspot for vertebrate immunity.

evolutionary biology↗

bioRxiv2024

Usutu virus African 3.1 lineage, Portugal, 2021-2023

BackgroundUsutu virus (Orthoflavivirus usutuense, USUV), a neurotropic arthropod-borne RNA virus of the family Flaviviridae, is a zoonotic virus that has spread throughout the European continent over the last three decades, since its emergence in Italy in 1996. However, no cases of USUV have been reported in Portugal so far. Material and methodsIn the scope of an active surveillance program for Orthoflavivirus, we collected growing feather samples from 249 red-legged partridges (Alectoris rufa) hunted in southern Portugal during the 2021-2023 hunting seasons. Samples positive for USUV were subjected to whole genome sequencing and strain characterization. ResultsTwo partridges tested positive for USUV. Phylogenetic analyses of whole and partial genomes assigned the USUV strains to the African 3 lineage, specifically the African 3.1 sub-lineage. ConclusionsOur study confirms, for the first time, the circulation of USUV in wild birds in Portugal. Active surveillance of hunted partridges proved to be a useful, accessible, and cost-effective method for USUV monitoring, further supporting their value as effective sentinels for Orthoflavivirus surveillance. Given the ongoing circulation of USUV and the increasing risk of its spillover to other domestic and wild animals, and humans, additional efforts are needed to improve virus surveillance in Portugal from a One Health perspective.

microbiology↗