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Journal articleLong MB, New JM, Stobo J, et al., 2026,
Design and rationale of the AIR-NET trial: a randomised, open-label, multifactorial, multicentre, adaptive platform trial using a range of repurposed anti-inflammatory treatments to improve outcomes in patients with bronchiectasis within the EMBARC clinical research network.
, ERJ Open Res, Vol: 12, ISSN: 2312-0541BACKGROUND: Neutrophilic airway inflammation is associated with disease severity and exacerbation frequency in bronchiectasis. Neutrophil protease inhibition significantly reduced exacerbation rates in phase II and III trials in bronchiectasis, highlighting this disease feature as an important therapeutic target. Additional neutrophil targeting therapeutics are needed to reduce the burden of the disease. Herein, we describe the protocol for the AIR-NET trial, the first randomised, open-label, multifactorial, multicentre, adaptive platform trial for people with bronchiectasis, run via the EMBARC (European Multicentre Bronchiectasis Audit and Research Collaboration) network, to investigate the safety and efficacy of several repurposed anti-inflammatory treatments. METHODS AND ANALYSIS: Participants with bronchiectasis confirmed by computed tomography, daily sputum production and evidence of active airway neutrophilic inflammation (based on a positive lateral flow test for neutrophil elastase (NE) activity), across 10 sites in the UK, will be randomised to one of several repurposed drugs with published evidence of effects on neutrophilic inflammation and acceptable safety profile (oral dose: disulfiram 400 mg once daily; dipyridamole 200 mg twice daily; doxycycline 100 mg once daily; n=42 per arm) or usual care, according to arm-specific eligibility criteria, and treated for 28 days. New arms will be added to the trial through an adaptive design. The primary end-point is change from baseline in sputum NE activity (a validated biomarker and surrogate of exacerbation risk) at day 28. Key secondary end-points include time-to-first exacerbation, quality of life questionnaires, neutrophil function and safety. SUMMARY: AIR-NET will establish a multi-centre network with integrated clinical and translational capabilities for the investigation of therapies in bronchiectasis aiming to identify key anti-inflammatory mechanisms and effective re-purposed treatments.
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Journal articleWang Y, Calzolari M, Calvi G, et al., 2026,
Association of avian biodiversity and West Nile Virus circulation in Culex mosquitoes in Emilia-Romagna, Italy.
, PLoS Negl Trop Dis, Vol: 20BACKGROUND: West Nile Virus (WNV) is a zoonotic arbovirus maintained in a transmission cycle between Culex mosquitoes and birds, occasionally spilling over into humans. The impact of avian biodiversity on WNV circulation remains debated, with studies reporting both negative and positive correlations (dilution and amplification effects respectively) across different settings. In Europe, this relationship remains largely unexplored, particularly in regions with high WNV transmission, such as Emilia-Romagna in Northern Italy. METHODS: We explored the association between avian biodiversity and WNV circulation in Culex mosquitoes in Emilia-Romagna using 11 years (2013-2023) of entomological surveillance data paired with two avian data sources. We calculated avian biodiversity indices (Shannon's, Simpson's, and Chao2) from observation records from the Farmland Bird Index project and applied linear regression models to assess their relationship with WNV detection frequency. Moreover, we used Bayesian spatiotemporal regression models and gridded weekly avian abundance estimates from the eBird project to analyse the associations between avian species richness indices and WNV transmission risk quantified by vector index (VI) at 68 geolocated mosquito traps across the region. RESULTS: We observed consistent negative associations between WNV detection frequency in the Culex population and avian biodiversity indices, supporting the dilution effect hypothesis (DEH). We found that non-passerine species richness was negatively associated with VI while passerine species richness showed a positive association after adjusting for covariates and spatial random effects. These findings suggest that passerines may amplify WNV transmission, whereas the presence of non-passerine species is associated with reductions in WNV circulation. SIGNIFICANCE: This study provides the first empirical evidence supporting the DEH for WNV in Europe. These findings have important implications for biodivers
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Journal articleYan X, Grassly NC, Pons-Salort M, 2026,
Impact of COVID-19 on the transmission dynamics of HFMD associated enterovirus serotypes in Japan: A modelling study of surveillance data.
, Epidemics, Vol: 54A notable decline in incidence of hand, foot, and mouth disease (HFMD) was observed globally since the beginning of the COVID-19 pandemic, indicating a change in the transmission dynamics of enteroviruses (EVs) causing HFMD. This study estimates the impact of COVID-19 non-pharmaceutical interventions (NPIs) on the transmission of EVs in Japan. Japan has a well-established sentinel surveillance system for enteroviruses and HFMD. A susceptible-infected-recovered stochastic transmission model was fitted to the time-series of weekly reported number of HFMD enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16), and CVA6 cases from January 2005 to December 2024, to estimate the impact of government containment interventions during the COVID-19 pandemic. Compared to pre-pandemic levels, the transmission rate decreased by 7.86 % (95 % Credible Interval (CrI): 6.31 %, 10.3 %) for EV-A71, 12.0 % (10.3 %, 14.1 %) for CVA16, and 20.1 % (16.3 %, 24.0 %) for CVA6 on average from January 2020 to December 2022. The reduction in transmission rate during this period correlated with the COVID-19 Stringency Index, such that 49.3 %, 19.9 % and 25.5 % of the reduction for each serotype respectively was explained by the index, with the biggest reductions occurring during "State of Emergency" periods. Enterovirus serotypes with higher transmissibility (R0) and therefore, a younger mean age at infection, were estimated to experience a bigger reduction in transmission that was more strongly associated with COVID-19 non-pharmaceutical interventions captured by the Stringency Index. This has implications for the impact of NPIs on other viral pathogens.
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Journal articleSymons TL, Moran A, Balzarolo A, et al., 2026,
Projected impacts of climate change on malaria in Africa.
, Nature, Vol: 651, Pages: 390-396The implications of climate change for malaria eradication this century remain poorly resolved1,2. Many studies focus on parasite and vector ecology in isolation, neglecting the interactions between climate, malaria control and the socioeconomic environment, including disruption from extreme weather3,4. Here we integrate 25 years of African data on climate, malaria burden and control, socioeconomic factors, and extreme weather. Using a geotemporal model linked to an ensemble of climate projections under the Shared Socioeconomic Pathway 2-4.5 (SSP 2-4.5) scenario5, we estimate the future impact of climate change on malaria burden in Africa, including both ecological and disruptive effects. Our findings indicate that climate change could lead to 123 million (projection range 49.5 million to 203 million) additional malaria cases and 532,000 (195,000-912,000) additional deaths in Africa between 2024 and 2050 under current control levels. Contrary to the prevailing focus on ecological mechanisms, extreme weather events emerge as the primary driver of increased risk, accounting for 79% (50-94%) of additional cases and 93% (70-100%) of additional deaths. Most increases stem from intensification in existing endemic areas rather than range expansion, with significant regional variation in impact. These results highlight the urgent need for climate-resilient malaria control strategies and robust emergency response systems to safeguard progress towards malaria eradication.
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Journal articleDellicour S, Faria NR, Rose R, et al., 2026,
SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements.
, Bioinformatics, Vol: 42SUMMARY: We report the second version of the R package "seraphim", a toolbox developed to process and analyze the output of spatially explicit phylogeographic reconstructions. This approach - also known as continuous phylogeographic inference - is commonly used in molecular epidemiology to reconstruct the dispersal history and spatiotemporal dynamics of rapidly evolving pathogens. The "seraphim" package now implements a broad range of features including (i) visualization of phylogeographic inferences, (ii) estimation of lineage dispersal metrics, (iii) several phylogeographic simulators, and (iv) hypothesis testing procedures to investigate the impact of environmental factors on variables such as diffusion velocity, dispersal location, and dispersal frequency of phylogenetic lineages. AVAILABILITY AND IMPLEMENTATION: The package is openly available (https://github.com/sdellicour/seraphim) along with a series of tutorials describing the different analytical procedures it implements.
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Journal articleLeuba SI, Verity R, Gutman JR, et al., 2026,
The burden of malaria-attributable maternal anaemia and the impact of preventive treatment across sub-Saharan Africa
, Nature Health, ISSN: 3005-0693Malaria in pregnancy is a major but poorly quantified contributor to maternal anaemia in sub-Saharan Africa. We combined individual-level data on haemoglobin (Hb), gravidity, gestational age and PCR-confirmed Plasmodium falciparum infection from 12,608 pregnancies in 7 African countries with a gravidity-specific model of malaria exposure and immunity linked to contemporary maps of transmission and fertility. For 2023, we estimate that 13.1 million pregnancies in malaria-endemic African regions were exposed to P. falciparum. In the absence of preventive measures, this exposure would have resulted in 2.41 million (95% credible interval 1.98–3.04 million) cases of moderate or severe anaemia (Hb < 9 g dl−1), including 600,000 (408,000–906,000) severe cases (Hb < 7 g dl−1). A counterfactual scenario using 2,000 transmission levels suggests that a 32% reduction in exposure during pregnancy translated into only a 22% decline in intrinsic anaemia burden, reflecting a shift from a concentration of risk in primigravidae to a more even distribution across gravidities as multigravid women acquire less pregnancy-specific immunity. Calibrating our model to randomized trials, we estimate that under current coverage, intermittent preventive treatment of malaria in pregnancy using sulfadoxine-pyrimethamine averted around 1.10 million (0.72–1.61 million) cases of moderate or severe anaemia and 330,000 (225,000–523,000) severe cases in 2023. These findings show that although burden has declined substantially, malaria remains a major driver of maternal anaemia risk. Meanwhile, lower immunity across multigravidae means any interruption to intermittent preventive treatment of malaria in pregnancy using sulfadoxine-pyrimethamine, or other population-based malaria control efforts, risks rapid resurgence of severe maternal anaemia, with substantial consequences for maternal and neonatal
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Journal articleDixon-Zegeye M, Walker M, Ramani A, et al., 2026,
HISTONCHO: A dataset of intervention histories for onchocerciasis control & elimination in sub-Saharan Africa
, Scientific Data, ISSN: 2052-4463In sub-Saharan Africa (SSA), onchocerciasis control has been implemented for many decades, beginning in 1974 under the Onchocerciasis Control Programme in West Africa (OCP) and in 1995 in Central and East Africa (plus Liberia) under the African Programme for Onchocerciasis Control (APOC). Since the establishment of the Expanded Special Project for Elimination of Neglected Tropical Diseases (ESPEN) in 2016, data on mass drug administration (MDA) with ivermectin has been centrally compiled for all endemic countries at implementation unit (IU) level, beginning in 2013. This paper presents HISTONCHO, a dataset collating detailed information on interventions, including vector control, from 1975 through to 2022, using the ESPEN portal (2013-2022), regional and country reports, implementation partners’ records, and published literature. Reconstructing such intervention histories is crucial for an understanding of their evolution, modelling their impact, and tailoring future interventions. We discuss strengths and limitations associated with the ESPEN database, and how HISTONCHO can be improved to support modelling of intervention strategies as well as onchocerciasis control and elimination efforts by endemic country programmes.
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Journal articleFaria N, Zé-Zé L, Borges V, et al., 2026,
Detection of dengue virus serotype 2 in local Aedes aegypti populations, Madeira Island, Portugal, 2025
, Parasites and Vectors, Vol: 19, ISSN: 1756-3305BackgroundSince 2010, dengue virus (DENV) has caused sporadic outbreaks across Europe, namely in Croatia, Spain, France, Italy and the Portuguese island of Madeira. Aedes aegypti mosquito is established in the Autonomous Region of Madeira, and along the eastern Black Sea coast of Cyprus. In Madeira Island, an outbreak of DENV serotype 1 occurred between 2012 and 2013, resulting in 1080 confirmed cases. Despite ongoing entomological surveillance, no further local transmission was detected in the following decade.MethodsIn January 2025, following two suspected dengue cases on Madeira Island, increased entomological surveillance efforts were implemented to confirm a local event transmission of DENV. A network of mosquito traps was complemented by targeted surveillance using 17 BG-PRO traps positioned in the vicinity of suspected human cases. Daily collections of adult A. aegypti, collected from 10 January to 31 March 2025, were screened by reverse transcription polymerase chain reaction (RT-PCR) for Aedes-borne viruses in the reference laboratory. Viral sequencing was performed using target enrichment and bioinformatics with INSaFLU-TELEVIR. The climate-driven suitability for dengue transmission by A. aegypti was also investigated. Serological and molecular tests were conducted on samples from suspected human cases.ResultsOut of 80 analysed A. aegypti pools (N = 393 mosquitoes), 1 pool, with 9 mosquitoes collected near the home of suspected human cases, tested positive for DENV. The dengue whole genome sequence from this sample was determined and classified as DENV-2 lineage 2II_F.1.1.3. The same virus was retrospectively confirmed in one of the clinical cases. Analysis of mosquito abundance and climate data confirmed the occurrence of this local transmission event during a period of low mosquito abundance and low climatic suitability.ConclusionsHere, we report an in-depth analysis of a local dengue transmission event that occurred in Funchal, the capital
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Journal articleTwumasi-Ankrah S, Owusu M, Owusu-Ansah M, et al., 2026,
Statistical methods for predicting the presence of Salmonella Typhi in wastewater samples at Asante Akyem Agogo, Ghana
, PLoS Neglected Tropical Diseases, Vol: 20, Pages: e001973-e001973, ISSN: 1935-2727BackgroundMonitoring wastewater is vital for tracking typhoid fever in endemic areas. This study evaluated the performance of both spatial and non-spatial models in predicting Salmonella Typhi detection in wastewater from the Asante Akim North district in Ghana and identified key environmental risk factors.MethodsWe collected wastewater samples of Moore swabs at 40 sites across Agogo, Juansa, Hwidiem, and Domeabra over a period of 27 months. Multiplex PCR was used to detect Salmonella Typhi, focusing on the ttr, tviB, and staG genes. An Aquaprobe AP-2000 was also used to measure different physicochemical factors, such as pH, temperature, dissolved oxygen, and salinity. Three non-spatial models, namely Generalized Estimating Equations (Logistic), Mixed-Effects Models, and Random Forest, as well as four spatial models, including Bayesian Generalized Additive Models (GAM) and Spatial Generalized Linear Mixed Models (GLMM), were fitted to the wastewater dataset. Model fitting was done using 5-fold cross-validation, stratified by site. Model performance was evaluated using accuracy, sensitivity, and specificity. We also used SHapley Additive exPlanations (SHAP) analysis to find the most important predictors.FindingsIn general, 44.13% of the samples tested positive for S. Typhi. Detection was much higher during wet seasons (50.17% vs. 35.11%; p < 0.001), with fast flows (64.45%), and in channels that were 1–2 meters wide (58.70%). Positive samples had relatively higher pH (7.46 vs. 7.40; p < 0.001), dissolved oxygen (46.97% vs. 36.77%; p < 0.001), and rainfall (3.92mm vs. 3.30mm; p = 0.022). In comparing both non-spatial and spatial models, the non-spatial Random Forest model demonstrated the highest performance with an accuracy of 0.993, sensitivity of 0.997, and specificity of 0.989. In the SHAP analysis of the preferred non-spatial random forest model, it was found that pH, season, dissolved oxygen
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Journal articleChindelevitch L, Hedman ÅK, Bichko D, et al., 2026,
ReverseGWAS identifies combined phenotypes associated with a genotype in GWA studies
, Bioinformatics, ISSN: 1367-4803MotivationTraditional genome-wide association studies (GWAS) aim to uncover the genetic variants associated with a single phenotype of interest (typically a disease), and to elucidate its genotypic architecture. However, many of today’s GWAS simultaneously measure multiple related phenotypes, leading to the possibility of pursuing the reverse aim of elucidating the “phenotypic architecture” of a single genetic variant. In other words, we may ask what combination of measured phenotypes is associated with a given genotypic variant. ReverseGWAS is an algorithmic platform for answering such questions in the context of large-scale multi-phenotype GWAS.ResultsWe demonstrate the effectiveness of ReverseGWAS on simulated data, showing its ability to identify logical combinations of phenotypes with a reasonable amount of noise. We then apply it to a selection of combined phenotypes from the UK Biobank, obtaining 719 candidate associations using autoimmune diseases and 205 using common ICD10 codes. We find that the majority of these associations (546/719 and 111/205, respectively) successfully replicate in an independent cohort, FinnGen.AvailabilityThe source code of ReverseGWAS is freely available to non-commercial users as an installable R package at https://github.com/Leonardini/rgwas.Supplementary informationSupplementary data are available at Bioinformatics online.
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