Minayo-Martin, S. | Search bioRxiv

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

Dynamics and control of highly pathogenic H5 avian influenza in a threatened pelican population

The ongoing epizootic of highly pathogenic avian influenza (HPAI) continues to cause massive deaths in wildlife. Fundamental understanding of its disease ecology in natural populations is urgently needed. This knowledge has been hindered by the difficulty of acquiring data on epidemic dynamics. Here, using data collected from a threatened population of Dalmatian pelicans (Pelecanus crispus), we recover the epidemiological and evolutionary history of one of the largest HPAI wildlife mortality events. The results show that this devastating outbreak was likely seeded by a single introduction associated with movement of the species. By estimating epidemiological features of two consecutive outbreaks in the same population, we show that panzootic H5N1 since 2022 likely exhibits higher transmissibility and longer shedding time in non-reservoir birds, compared to previous H5NX subtypes. We also evaluate effectiveness of past and future control measures: carcass removal during the outbreak is shown to have surprisingly little impact on mitigating the mortality; and current H5 vaccines relying on capture and injection to deliver cannot establish herd immunity in a wildlife population. The results provide the first field evidence supporting the hypothesis that viral fitness difference of H5N1 to previous H5NX subtypes is the key cause of the expanded epizootic and panzootic since 2022, and on highly debated HPAI management strategies in wildlife populations. Author SummarySince late 2021, a panzootic of H5N1 highly pathogenic avian influenza (HPAI) has caused unprecedented mass mortality in wildlife. Many severely affected species are critical for ecosystem functions, including several threatened and endangered species. However, fundamental knowledge of HPAI disease ecology in natural populations is still lacking, and the effectiveness of potential controls is under debate. Here, using data collected from one of the largest HPAI outbreak in wild animals - over 1700 deaths (80% of the population) in a threatened population of Dalmatian pelicans in Greece, for the first time we recover the transmission dynamics of H5N1 in a migratory bird population. Based on the recovered dynamics, we show that removing carcasses during the outbreak was surprisingly ineffective, and future potential vaccination would require a novel delivery method to establish population immunity in wildlife. Our study provides new insight in the epidemiology of HPAI clade 2.3.4.4b in wildlife, and provides a foundation for assessing interventions within this complicated system.

ecology↗