Results
- Showing results for:
- Reset all filters
Search results
-
Journal articleKoemen S, Faria NR, Bastos LS, et al., 2026,
Fast and trustworthy nowcasting of dengue fever: a case study using attention-based probabilistic neural networks in São Paulo, Brazil
, Epidemics, Vol: 54, ISSN: 1755-4365Nowcasting methods are crucial in infectious disease surveillance, as reporting delays often lead to underestimation of recent incidence and can impair timely public health decision-making. Accurate real-time estimates of case counts are essential for resource allocation, policy responses, and communication with the public. In this paper, we propose a novel probabilistic neural network (PNN) architecture, named NowcastPNN, to estimate occurred-but-not-yet-reported cases of infectious diseases, demonstrated here using dengue fever incidence in São Paulo, Brazil. The proposed model combines statistical modelling of the true number of cases, assuming a Negative Binomial (NB) distribution, with recent advances in machine learning and deep learning, such as the attention mechanism. Uncertainty intervals are obtained by sampling from the predicted NB distribution and using Monte Carlo (MC) Dropout. Using proper scoring rules for the prediction intervals, NowcastPNN achieves nearly a 30% reduction in losses compared to the second-best model among other state-of-the-art approaches. While our model requires a large training dataset (equivalent to two to four years of incidence counts) to outperform benchmarks, it is computationally cheap and outperforms alternative methods even with significantly fewer observations as input. These features make the NowcastPNN model a promising tool for nowcasting in epidemiological surveillance of arboviral threats and other domains involving right-truncated data.
-
Journal articleMcCain K, Vicco A, Morgenstern C, et al., 2026,
A systematic review and meta-analysis of Zika virus epidemiology
, Nature Health, Vol: 1, Pages: 355-367, ISSN: 3005-0693Zika virus (ZIKV), classified as a priority pathogen by the World Health Organization, is an Aedes-borne arbovirus that can cause neurological complications and birth defects in newborns of mothers infected during pregnancy. We conducted a systematic review of peer-reviewed studies reporting ZIKV epidemiological parameters, transmission models and outbreaks (PROSPERO CRD42023393345) to characterize its transmissibility, seroprevalence, risk factors, disease sequelae and natural history. We performed meta-analyses of the proportions of congenital Zika syndrome, pregnancy loss among ZIKV-infected mothers and symptomatic cases. We extracted information from 574 studies. Across 418 included studies assigned a high-quality score, we extracted 969 parameters, 127 outbreak records and 154 models. Using random-effects models, we estimated proportions of congenital Zika syndrome (4.65%, 95% confidence interval (CI): 3.38–6.67%), pregnancy loss (2.48%, 95% CI: 1.62–3.78%) and symptomatic cases (51.20%, 95% CI: 38.00–64.23%). Seroprevalence estimates (n = 354) were retrieved beyond South America and French Polynesia. Basic reproduction number estimates (n = 77) ranged between 1.12 and 7.4. We found 66 human epidemiological delay estimates, including the intrinsic incubation period (n = 11, range: 4–12.1 days), infectious period (n = 15, range: 3–50 days), extrinsic incubation period (n = 22, range: 5.1–24.2 days) and serial interval (n = 27, range: 7.4–32.9 days).These data are available in the R package ‘epireview’ (version 1.4.5). We provide a comprehensive systematic summary of ZIKV epidemiology, revealing large heterogeneities and inconsistencies in the reporting of parameter estimates, study designs and parameter definitions and underscoring the need for standardized epidemiological definitions.
-
Journal articleVerwilghen DR, Pelosi A, Abbas M, et al., 2026,
Surgical site infection definitions consensus: a first step toward improving prevention in veterinary medicine.
, Am J Vet Res, Vol: 87OBJECTIVE: To establish specific veterinary surgical site infection (SSI) terminology to support the creation of consistent, comparable, and repeatable clinical and research datasets. METHODS: Establishment of SSI definitions by iterative Delphi questionnaires leading to a convergence of consensus opinion by a multidisciplinary panel of 32 specialists in large- and small-animal surgery (European College of Veterinary Surgeons, American College of Veterinary Surgeons), veterinary internal medicine (American College of Veterinary Internal Medicine, European College of Veterinary Internal Medicine, European College of Equine Internal Medicine), anesthesia (European College of Veterinary Anesthesia and Analgesia), critical care (American College of Veterinary Emergency and Critical Care, European College of Veterinary Emergency and Critical Care), dentistry (European Veterinary Dental College), microbiology, preventive medicine (American College of Veterinary Preventive Medicine), animal welfare (European College of Animal Welfare and Behavioural Medicine), and human infection control. Consensus was defined as agreement by a minimum of 75% of panel members. RESULTS: The panel defined 18 terms for veterinary use, including those for superficial, deep, and organ/space infections; surgical procedure; pyrexia; wound classification and closure; and agreements on SSI monitoring timeframes. CONCLUSIONS: A common clinical and research language appropriate to the veterinary field useable in future SSI surveillance practice has been established through expert consensus. CLINICAL RELEVANCE: The use of a standard SSI language in veterinary practice is central to the future reliability of studies, their comparison, and the understanding of clinical risk factors in the development and prevention of SSI.
-
Journal articleDjaafara BA, Elyazar IRF, Silalahi FSM, et al., 2026,
Dengue transmission heterogeneity across Indonesia's archipelago: Climate-driven spatiotemporal patterns and policy implications.
, PLoS Negl Trop Dis, Vol: 20Indonesia has the highest dengue burden in Southeast Asia, with 488 of 514 districts reporting cases annually across its 17,000-island archipelago. Despite this substantial burden, spatiotemporal transmission patterns remain poorly characterised. We analysed province-level dengue surveillance data (2010-2024) from Indonesia's Ministry of Health alongside local and regional climate variables to characterise heterogeneity in dengue periodicity and identify provinces where climate-based early warning may be feasible. Using wavelet phase analysis, dynamic time warping clustering, and distributed lag non-linear models, we examined relationships between climate and dengue incidence across 34 provinces. A systematic west-to-east gradient in dengue wave timing was identified, with Northern Sumatran provinces peaking earlier than other provinces, aligning with Australian-Asian monsoon progression. This gradient was robust in western Indonesia (Spearman ρ = 0.7 between longitude and phase lag) but weakened in eastern provinces. Multi-annual outbreak peaks (2015-2016, 2023-2024) coincided with strong El Niño events, with mean incidence during strong El Niño years was 96% higher than other years. The Indian Ocean Dipole showed no significant association. Phase coherence analysis identified 18 provinces where precipitation-dengue timing was sufficiently consistent (coherence ≥0.85) for potential early warning applications and DLNM confirmed significant dose-response associations in 11 of these. Indonesia's dengue-climate relationships exhibit structured heterogeneity that precludes uniform national prediction approaches but may enable province-specific early warning in high-coherence areas. A two-tier system combining ENSO monitoring for strategic preparedness with local climate monitoring for tactical intervention timing could improve outbreak response across Indonesia's diverse epidemiological landscapes.
-
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.
-
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.
-
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
-
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.
-
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.
-
Journal articleGyuricza IG, Fola AA, Simkin A, et al., 2026,
Malaria control and the unexpected spread of diagnostic-resistant Plasmodium falciparum in Peru.
, bioRxivPlasmodium falciparum parasites with deletions of the histidine-rich protein 2 and 3 (hrp2 and hrp3) genes evade detection by common rapid diagnostic tests (RDTs) and pose a growing threat to malaria control. While these deletions have emerged in multiple regions globally, the evolutionary forces driving their spread remain unclear. Here, we analyze 1,215 P. falciparum samples collected between 2003 and 2018 in Loreto, Peru. This region experienced a major decline in malaria transmission following the Project for Malaria Control in Andean Border Areas (PAMAFRO) and now harbors a high proportion of hrp2/3 deleted parasites despite limited RDT use. Using molecular inversion probe (MIP) sequencing across > 2,000 genome-wide loci, we observed a marked reduction in genetic diversity, increased clonality, and fixation of parasites with deletions of both hrp2 and hrp3 genes (hrp2-/3-) over time. Identity-by-descent (IBD) analysis revealed rapid expansion of a single hrp2-/3- dominant lineage in the post-PAMAFRO period, consistent with clonal replacement after intense malaria control. Targeted sequencing of the hrp2/3 regions showed conserved deletion breakpoints across three different lineages, indicative of recombination of a common haplotype into distinct genetic backgrounds. To investigate the evolutionary forces driving the fixation of hrp2-/3- in Loreto, we simulated allele frequency trajectories under different selection coefficients. We found that fixation of hrp2-/3- due solely to genetic drift (selection coefficient s = 0) is unlikely; a selection coefficient of s ≥ 0.03 was required for fixation to occur consistently. However, our simulations also indicate that a genetic bottleneck caused by PAMAFRO increased the likelihood of fixation through drift by 4.5- to 17-fold depending on the population. These findings suggest that hrp2-/3- fixation was likely driven by a combination of demographic changes resulting from PAMAFRO and selective advantage unrelated to
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.
Contact us
For any enquiries related to the Centre please contact:
Scientific Manager
Susannah Fisher
mrc.gida@imperial.ac.uk
External Relationships and Communications Manager
Dr Sabine van Elsland
s.van-elsland@imperial.ac.uk