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Acta Tropica

Elsevier BV

Preprints posted in the last 7 days, ranked by how well they match Acta Tropica's content profile, based on 13 papers previously published here. The average preprint has a 0.02% match score for this journal, so anything above that is already an above-average fit.

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Operational insights for larval source management programs: An exploratory study of Anopheles breeding habitat dynamics across urban wards in Ibadan, Nigeria

Bamgboye, E.; Adeleke, M. A.; Surakat, O.; Mhlanga, L.; Fasasi, K.; Rufai, A. M.; Popoola, K. O.; Aminu, U. M.; Ogbulafor, N.; Ozodiegwu, I. D.

2026-07-18 public and global health 10.64898/2026.07.16.26358299 medRxiv
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Larval source management (LSM) is a complementary malaria control intervention, yet evidence to guide context-specific implementation remains limited. Nigeria's recent national commitment to LSM scale-up makes the need for operational evidence particularly urgent. Informal settlements embedded within wards of differing dominant settlement archetypes may present distinct Anopheles larval habitat profiles with implications for how LSM strategies should be tailored. We evaluated Anopheles larval habitats within informal settlement areas across wards with contrasting settlement archetypes in Ibadan metropolis, Nigeria, to inform targeted larval source management. Potential breeding habitats were surveyed in dry and wet seasons within informal settlement areas across three wards -- Olopomewa, Challenge, and Agugu -- representing formal, informal, and slum settlement-dominant archetypes respectively. Habitats were characterized and assessed for Anopheles larval presence. Pareto analysis identified habitats accounting for 80% of larval abundance. Breeding habitat density per km{superscript 2} was estimated using a simulated pathway technique. Associations between mosquito dispersal scale and household malaria infections identified through Rapid Diagnostic Testing were evaluated using kernel-based distance-decay weighting. Environmental drivers of habitat suitability were modeled in MaxEnt. Of 420 potential breeding habitats identified, 31 (7.4%) contained Anopheles larvae, predominantly during the wet season (26, 83.9%). Puddles, dug wells, drainages/gutters/ditches and canals accounted for 80% of site-level larval abundance when standardized by sampling effort. Larval and breeding habitat density were highest in Agugu, the slum-dominant ward, across both seasons. Modeled mosquito dispersal scale showed best fit at 30-32m in Challenge (OR 1.41, 95% CI: 1.05-1.89) during the wet season and 16-18m in Agugu (OR 1.29, 95% CI: 1.04-1.60) during the dry season. Habitat suitability in Agugu was higher farther from large water bodies and in areas with higher population density and positive Normalized Difference Water Index values. In Challenge, suitability was higher in areas with lower nighttime light levels, positive Normalized Difference Water Index values, and negative Normalized Difference Moisture Index values. Further studies incorporating multiple wards across diverse urban settings are needed to determine whether differences in larval ecology between settlement archetypes provide a reliable basis for planning larval source management.

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Molecular and phylogenetic insights into the novel Brugia sp. in Sri Lanka with new evidence for zoonotic transmission

Nimalrathna, S. U.; Harischandra, H.; Kimber, M.; Chandrasena, N.; De Silva, N.; Mallawarachchi, H.; De Silva, B. G. D. N. K.

2026-07-21 infectious diseases 10.64898/2026.07.20.26358473 medRxiv
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The World Health Organization (WHO) validated Sri Lanka had eliminated lymphatic filariasis as a public health problem in 2016, the second country in Southeast Asia to attain this status. However, post-validation surveillance has identified sporadic cases of brugian filariasis. The reemergence of Brugia malayi infections in Sri Lanka warrants urgent investigations. Recent studies have shown that the parasite responsible for the reemergence is a novel zoonotic Brugia sp. maintained among dogs that is closely related but distinct to the human-infecting B. malayi species. The current study employed morphological and morphometric assessments, revealing that this novel zoonotic Brugia sp. is within the B. malayi morphological range. Molecular characterization of three genomic regions, the nuclear genomic region SLXI, the non-coding region HhaI, and the mitochondrial genomic region COXI confirmed it as a genetic variant more closely related to B. malayi than to B. pahangi. Phylogenetic analysis further indicated it as a distinct genomic variant, closely related to a B. malayi-like parasite reported from India. Notably, that same parasite was identified in infected humans, animals, and potential vector mosquitoes. This, together with the detection of both human and animal blood within the same brugian infective mosquitoes, and delineating the canine origin of the parasites in human infections, provides compelling evidence supporting zoonotic transmission of this parasite. To our knowledge, this is the first report demonstrating the presence of the same brugian parasite in humans, domestic animals, and potentially infective mosquitoes in Sri Lanka, supported by multi-genomic evidence. The recent identification of multiple potential mosquito vector species suggests that this parasite may have undergone adaptive changes, facilitating its ability to overcome the species barrier. These findings substantiate the long-held hypothesis of zoonotic transmission of the reemerged brugian parasite, highlighting significant implications for ongoing surveillance and control strategies.

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Rising dengue burden in high-altitude central Nepal: evidence from a population-based longitudinal serosurvey, 2019-2023

Shrestha, A.; Thapa, M.; Shrestha, S.; Tamrakar, S.; Ranjitkar, U.; Katuwal, N.; Shahi, S. B.; Naga, S. R.; Andrews, J. R.; Shrestha, R.; Aiemjoy, K.; Tamrakar, D.

2026-07-16 infectious diseases 10.64898/2026.07.14.26357903 medRxiv
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Background Dengue is intensifying globally due to climate change, urbanization, and land use changes. In Nepal, dengue has expanded from lowland regions to higher altitudes, with record outbreaks in 2022 and 2023. However, reliance on passive surveillance and hospital-based studies may underestimate community level infection burden. Methods We conducted a population-based serologic cohort study in Kathmandu and Kavrepalanchok districts, Nepal, enrolling a geographically representative, age stratified random sample of residents aged 0 to 25 years from pre-defined hospital catchment areas. Enrollment occurred in two phases: Phase I (February 2019 to April 2021) with follow-up visits at approximately 3, 6, and 12 months, and Phase II (February to June 2023) revisiting the original cohort. At each household visit, we collected capillary blood samples by finger-prick onto filter paper and tested the samples for IgG responses against dengue-derived recombinant antigen using InBios DENV DetectTM ELISA. Serostatus was classified using the manufacturer's recommended immune status ratio (ISR) cutoffs. We calculated seroprevalence at each time point and estimated seroincidence rates by identifying seroconversion events per 1,000 person-years. We assessed risk factors using multivariable regression models. Results Between 2019 and 2023, we enrolled 840 participants and collected 2,082 blood samples. The overall seroincidence rate was 33.8 per 1,000 person-years (95% CI [24.9 to 45.0]), with the highest rates in urban Kathmandu ([105.7], 95% CI [75.1 to 144.4]). Seroincidence increased with age and over time from 46.1 in 2019 to 51.0 in 2023. Participants living with a dengue-positive individual in the same household (adjusted RR [4.65], 95% CI [2.72 to 8.0]) and households with water-filled flower basins (adjusted RR [2.53], 95% CI [1.28 to 5.74]) had significantly higher risk of seroconversion. Conclusions This study reveals a significant and increasing burden of dengue infection in the Kathmandu Valley between 2019 and 2023. highlighting an urgent need for immediate public health interventions to mitigate dengue's rise in Nepal's higher-altitude regions.

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Profile of red blood cell disorders among healthy schoolchildren in the low malaria-endemic region in Indonesia

Pasaribu, A. P.; Nanine, I.; Ainur, F.; Jimanto, V.; Hutagalung, A. P.; Panggalo, L. V.; Devin, D.; Siregar, O. R.; Hasibuan, B. S.; Fahmi, F.; Trianty, L.; Coutrier, F. N.; Sasmono, R. T.; Satyagraha, A. W.

2026-07-21 epidemiology 10.64898/2026.07.20.26358521 medRxiv
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Red blood cell (RBC) disorders arose as an advantageous evolutionary response to malaria infections. In a heterozygous condition, such as in Southeast Asian Ovalocytosis (SAO), hosts are protected against severe malaria. In malaria-endemic regions, RBC disorders are presumed to be highly prevalent. Tanjung Leidong, a moderately endemic area in North Sumatra (API 1.13 in 2024), lacks comprehensive data on RBC disorder prevalence beyond G6PD deficiency. Therefore, this study aims to characterize the RBC disorders in this region as well as to characterize the anemia status in children living in Tanjung Leidong. Schoolers attending D. I. Panjaitan elementary to high school were recruited and screened for malaria by microscopy and G6PD deficiency using the STANDARD G6PD Assay. The DNA of the participants was also extracted to be genotyped for SAO, Hemoglobin E (HbE), and -thalassemia. Exclusively, G6PD-deficient DNA samples were genotyped further to determine variants. The proportion of G6PD deficiency, SAO, HbE, -thalassemia one-gene deletion, and two-gene deletion were 0.90%, 0.90%, 2.40%, 6.26%, and 0.30%, respectively. Anemia prevalence was approximately 14%, and RBC disorders were observed across children with normal to obese BMI. No malaria infections were detected by microscopy. The predominance of asymptomatic RBC disorders highlights that they are protective against malaria infection, although their protective role against malaria could not be directly assessed in this study. Both nutritional and genetic factors are found to contribute to anemia in this cohort. These findings underscore the importance of integrated screening strategies for RBC disorders and anemia in malaria-endemic settings.

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Combining vaccination with wMel for dengue control in Brazil

Finch, E.; Huang, A. T.; McCormack, C.; Vicco, A.; Croda, J.; Ferguson, N. M.; Dorigatti, I.; Salje, H.

2026-07-15 infectious diseases 10.64898/2026.07.12.26357821 medRxiv
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Dengue virus is a severe threat to global health. Novel vaccine and Wolbachia technologies offer a potential path to dengue control; however, it remains unclear how to use these approaches in tandem. Using metapopulation transmission models, we simulated future dengue burden in Brazil. We estimated that wMel releases in 300 municipalities could avert 12-22% of cases over the next 10 years, while a national vaccination campaign could avert 8-10% of cases in the total population and 39-45% within the vaccinated cohort. Projecting forward 40 years, we found wMel releases would drive up the mean age of cases beyond increases due to the ageing population and increase population susceptibility to dengue. Finally, wMel releases can help mitigate the future burden in southern Brazil where climate change is rapidly increasing dengue virus risk. These findings highlight the need to consider the two technologies in parallel to optimise efforts to combat future dengue burden.

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Mortality in Eastern Democratic Republic of the Congo: A Population-Based Survey Following the 2025 M23 Offensive and Humanitarian Funding Withdrawal

OKeeffe, J.; Karume, A. G. B.; Roberts, L.

2026-07-15 public and global health 10.64898/2026.07.10.26357778 medRxiv
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Introduction: In early 2025, North and South Kivu Provinces in the Democratic Republic of the Congo (DRC) underwent a major geopolitical shift marked by the concurrent abrupt withdrawal of humanitarian support and large-scale military takeover by the M23 armed group. This study sought to quantify mortality before and after the humanitarian and security collapse. Methods: We conducted a retrospective, two-stage cluster household survey comparing mortality in the pre- and post-crisis periods. Difference-in-differences were analyzed using survey-weighted Poisson regression with a log-link and person-time offset to estimate adjusted incident rate ratios for crude, under-five, and sex-specific mortality. We interviewed community leaders and health facility staff as key informants to provide qualitative data. Results: The adjusted risk of death was 2.02 times higher in the post-crisis than the pre-crisis period (95% CI 1.07, 3.80; p=0.03). Crude mortality rose from a pre-crisis adjusted marginal mean of 0.38 (95% CI 0.22, 0.53) to 0.74 (95% CI 0.56, 0.92) deaths/10,000/day. The increase in mortality was consistent across DRC-Government and M23 controlled areas. Results indicate that 165,391 (95%CI: 63,557, 267,225) excess deaths occurred in the post-crisis period, equating to 245,397 annual excess deaths. Conclusion: The crisis in DRC is driven by the convergence of humanitarian funding withdrawals and escalating conflict. Averting further preventable deaths requires large-scale restoration of humanitarian assistance. The resources needed to do so represent a small fraction of global economic capacity.

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Malaria Pre-screening Technology Using Artificial Intelligence (AI)

Ibeto, O. O.; Nwoye, E. O.

2026-07-17 infectious diseases 10.64898/2026.07.15.26357432 medRxiv
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Malaria remains a severe health problem in endemic regions because people lack adequate diagnostic tools, leading to delayed medical care and elevated death rates. This research introduces a dual-mode artificial intelligence system that uses two complementary models to enhance malaria pre-screening and diagnosis. The patient-centered model uses multivariate logistic regression to analyze biosignals, including heart rate, body temperature, and oxygen saturation, collected through a wearable sensor prototype and a mobile interface for symptom analysis. The system enables patients to begin self-assessment to determine their level of need before scheduling a doctor's appointment. The clinician-centered model represents a customized convolutional neural network that uses annotated microscopy images of red blood cells to achieve 94.84% accuracy, 95.71% precision, 93.87% recall, 94.78% F1 score, and 0.84 Area Under Curve (AUC). The patient model achieved 94.6% accuracy and an AUC of 0.985 using a 70/30 train-test split. These systems work together to create a layered diagnostic system that can operate independently or together to detect malaria at an early stage, especially in areas with limited resources. The findings demonstrate that wearable biosignal data integration with image-based deep learning can produce dependable, scalable, and user-friendly systems for malaria pre-screening. Keywords - malaria diagnosis, artificial intelligence (AI), convolutional neural networks (CNN), wearable biosensors, multivariate logistic regression

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A global assessment of dengue seasonality: Applying a novel, proportion-based method to case time series from 1990 to 2024

Joshi, K.; Susong, K. M.; Lim, A.; Liu, Y.; Brady, O. J.

2026-07-16 epidemiology 10.64898/2026.07.13.26358002 medRxiv
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Dengue is a mosquito-borne, viral disease of increasing public health significance. Currently, most public health interventions target the vector, with efficacy dependent on timing within the season. Whilst seasonal profiles have been characterised in some endemic settings a global assessment is lacking. Here, we develop and apply a proportion-based measure of dengue seasonality to reported case time series from 1990 to 2024 across 106 countries and territories, the largest assessment of this phenomenon to date. We identify regional differences in seasonality such that every month of the year saw cases peak in at least one country or territory. Latitude was identified as influencing seasonality, with cases peaking between March and April in the southern hemisphere and July and October in the northern hemisphere. Equatorial locations displayed flat seasonality, and amplitude increased with distance from the equator. K-means clustering identified three seasonal profile types: two with pronounced seasonal outbreaks (with distinct peak timing and shape) and one with flatter, more endemic transmission. Peak month timing covaried among locations within the same seasonality cluster, with phase differences meaning that information on shifts in peak timing may be available several months in advance in some settings, of potential significance for prediction and intervention planning. Beyond aiding public health planning, identification of seasonal clusters suggests that information on dynamics in one location could be leveraged to improve forecasting power in others with similar seasonal dynamics.

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Malaria burden and care in hard-to-reach indigenous communities in the Peruvian Amazon during the COVID-19 pandemic: A mixed-methods study

Fernandez, S. P.; Rojas, L. M.; Gomez, J.; Sandoval-Bances, J.; Condori-Catachura, S.; Garcia, P. D.; Abrams, S.; Anthierens, S.; Bastiaens, H.; Chenet, S. M.; Delgado-Ratto, C.

2026-07-15 infectious diseases 10.64898/2026.07.12.26357900 medRxiv
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Background The COVID-19 pandemic was associated with reported disruptions to healthcare delivery and malaria control activities in remote, malaria-endemic indigenous communities with limited access to healthcare. Remote indigenous communities in the Peruvian Amazon may have been especially vulnerable due to interruptions in malaria surveillance, diagnosis, and treatment. We investigated the impact of the COVID-19 pandemic on malaria burden, healthcare access, and community perceptions in hard-to-reach indigenous communities in the Amazonas region of Peru. In malaria-endemic regions, these lessons are particularly important because future health emergencies may similarly affect surveillance, diagnosis, prevention, and treatment activities, potentially reversing gains achieved through malaria control programs. Methods A convergent parallel mixed-methods study was conducted in 2021 and 2022 across four indigenous communities in the Rio Santiago district, Amazonas region, Peru. Quantitative data were collected through cross-sectional malaria surveys, and qualitative data were obtained through semi-structured interviews with inhabitants, community health workers, and local health personnel. Malaria infections were detected by microscopy and confirmed by PCR. Factors associated with the occurrence of malaria infection were studied based on a generalized estimating equation (GEE) approach applied to clustered binary outcome data and accounting for repeated observations within participants across study years. Qualitative data were analyzed thematically, and both components were integrated using the Pillar Integration Process framework. Results A total of 514 participants were included. PCR-based malaria prevalence was 17.6% in 2021 and 26.09% in 2022. P. falciparum prevalence was particularly high in the Alianza Progreso community (2021: 24.19%, 2022: 16.16%) compared to the other studied communities. Previous malaria infection and chills were associated with PCR-confirmed malaria infection. Qualitative findings indicated that COVID-19-related disruptions affected malaria control activities by interrupting diagnosis and treatment availability, reducing community follow-up, and prioritizing COVID-19 response activities over malaria control. Participants also described fear of COVID-19, temporary migration to farm areas, and reliance on herbal medicine during the pandemic. Conclusions The COVID-19 pandemic may have contributed to exacerbated pre-existing challenges to malaria control in remote indigenous communities in the Peruvian Amazon. Strengthening malaria surveillance, ensuring continuity of diagnosis and treatment, and improving healthcare access in geographically isolated communities will be critical to supporting malaria elimination efforts in Peru.

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Assessing the performance and costs of female genital schistosomiasis screening methods in Ondo and Kebbi States, Nigeria.

Osinoiki, O.; Trotignon, G.; Oluwole, A. S.; Imhansoloeva, M.; Jeyam, A.; Jones, I.; Selby, R.; Schmidt, E.

2026-07-15 epidemiology 10.64898/2026.07.12.26357899 medRxiv
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Female Genital Schistosomiasis (FGS) is a gynaecological condition, arising from complication from schistosomiasis - a neglected tropical disease (NTD). FGS shares overlapping symptoms with several sexually transmitted infections, making it challenging to diagnose and manage especially in primary health care settings where diagnostic tools are often unavailable. In response to this challenge, an FGS screening tool (COUNTDOWN screening tool) was developed to support primary health care workers in identifying persons at risk of FGS. We investigated the sensitivity and specificity of adapted versions of the COUNTDOWN screening tool and evaluated the costs associated with providing these services in two Nigerian schistosomiasis endemic states (Ondo and Kebbi). Using three adapted versions of the screening tool against colposcopy and unit costs of activities, performance of the tool and cost-effectiveness analysis were evaluated. Compared to the colposcopy, the performance of the FGS screening tool varied using different screening definitions. When only direct and indirect contact with surface water was considered it demonstrated a sensitivity of 66.7% (95%CI: 60.1-72.8) and specificity of 35.4% (30.2-40.9); and when water contact together with any self-reported urogenital symptom was considered, the sensitivity and specificity were 50.2% (95%CI: 43.5 - 56.9) and 48.0% (95%CI: 42.5 - 53.6) respectively. Activity based micro-costing, showed that the FGS screening tool could screen individuals for approximately US$11 per woman, compared with US$20 per woman when using colposcopy. The screening tool detected far fewer true positive cases than the reference standard, assuming colposcopy did not miss true positives. The sub-optimal performance of the screening tool indicates the need for further refinement, to balance cost and effectiveness.

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Clinical Manifestations and Risk Factors of Pediatric Leptospirosis: A Cross-Sectional Study at a Tertiary Care Center in Northern Vietnam

Thuy, N. T.; Huong, T. T. T.; Long, H. B.; Lam, N. V.; Taylor-Robinson, A. W.

2026-07-21 infectious diseases 10.64898/2026.07.19.26357440 medRxiv
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Background: Leptospirosis causes around 1 million cases and 60,000 deaths globally annually, predominantly affecting flood-prone tropical regions. Transmitted through contact with water or soil contaminated by animal urine infected with Leptospira spp., this bacterial zoonosis is classified as a high-risk Group B infectious disease in Vietnam. However, epidemiological and clinical data are scarce, particularly in pediatric populations. This study evaluated clinical and laboratory characteristics of leptospirosis cases at the National Children's Hospital, Hanoi, from January 2023 to August 2025. Methodology : All children admitted with probable or confirmed leptospirosis were enrolled. Clinical and laboratory data were analyzed to characterize disease manifestations and identify risk factors for severe leptospirosis. This was defined by the presence of organ dysfunction, including liver or renal failure, hemorrhage (particularly pulmonary), aseptic meningitis, cardiac arrhythmias, pulmonary insufficiency, or hemodynamic collapse. Principal Findings : Of 84 patients (37 confirmed, 47 probable), the mean age was 9.4 years, with 52.4% male and over half aged [≥] 10 years. Fever was the most common presenting symptom (85.7%); gastrointestinal and renal manifestations were frequent, including oliguria in 26.2% of cases. Key laboratory abnormalities included elevated D-dimer (81.8%), elevated C-reactive protein (75.6%), hypoalbuminemia (74.3%), increased liver enzymes (AST 63.3%, ALT 53.2%), and renal impairment ({approx} 46%). Severe disease developed in 48.8% of patients, most frequently as acute kidney injury. Hematuria was independently associated with increased severity (OR = 4.89). Conversely, fever, higher baseline albumin, and longer symptom duration prior to hospitalization were associated with a significantly reduced risk of severe disease. Conclusions : Pediatric leptospirosis in this cohort frequently presented with systemic inflammation and multi-organ involvement, particularly renal impairment. Nearly half the patients developed severe disease. Early recognition of renal signs, especially hematuria, and careful monitoring of albumin levels are critical to identifying children at risk for severe progression and optimizing clinical management.

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Temporal and Spatial Patterns of Snakebite Envenoming in Ghana, 2020-2025: A Nationwide Surveillance Analysis

Nyarko, E.; Antwi, P.; Amponsah, E. B.; Ofori-Boadu, L.; Oduro-Mensah, E.; Oliver-Commey, J. A.; Haruna, M.; Serwaa, C.; Dadzie, G.

2026-07-16 epidemiology 10.64898/2026.07.12.26357875 medRxiv
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Snakebite envenoming is a major neglected tropical disease disproportionately affecting rural populations in sub-Saharan Africa. In Ghana, evidence on the spatial and temporal distribution of risk remains limited, constraining targeted prevention and resource allocation. This study quantified district-level snakebite risk across Ghana, identified persistent hotspots and environmental drivers, and evaluated the relationship between snakebite burden and geographic access to treatment. Monthly district-level snakebite cases from Ghana's District Health Information Management System (2020 to 2025) were analyzed across all 261 districts using a Bayesian spatio-temporal model incorporating spatial effects, a temporal random effect, and a space-time interaction, fitted via Integrated Nested Laplace Approximation. Environmental covariates including rainfall, temperature, humidity, and NDVI quantified associations with risk. Relative risks, exceedance probabilities, Local Indicators of Spatial Association, and geographic accessibility identified priority districts. Snakebite risk showed strong spatial clustering and temporal variation. Persistent high risk districts were concentrated in Upper West (Daffiama Bussie Issa, Wa East, Wa West, Sissala East), Savannah (Bole, Gonja), North East (Mamprugu Moagduri), Western North (Bia East), Bono (Banda), Oti (Krachi Nchumuru), Western (Wassa East), and Eastern Region (Nsawam Adoagyiri, Fanteakwa North), though patterns evolved. Fanteakwa North emerged as the highest risk district nationally in 2025. Humidity and temperature were associated with increased risk, while rainfall and NDVI showed no significant effect. High risk districts often had poor treatment access, revealing inequities. This first nationwide Bayesian spatio temporal assessment provides an evidence base for surveillance, antivenom distribution, and interventions supporting WHO's 2030 snakebite reduction goals.

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Mathematical Modeling of Rift Valley Fever in the Sahelian Zone

Djimramadji, H.; Ndonane, B.; Djaouga, P.; MARKHOUS, H. M.; Djoumountanan, E.; TOBAYE, K.; Abakar, F. M.

2026-07-17 epidemiology 10.64898/2026.07.15.26358164 medRxiv
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We develop a mathematical model of Rift Valley Fever integrating mosquito vectors, ruminants, and humans, based on an SEIR-type structure with vertical transmission in vectors. Local data from the Sudanian and especially the Sahelian zones are used to capture the impact of climatic variations on mosquito population dynamics. The mathematical analysis establishes the models positivity, determines the basic reproduction number R0, and demonstrates the local and global stability of the disease-free equilibrium. Sensitivity analysis (PRCC) highlights the most influential parameters, while the stochastic approach using a continuous-time Markov chain confirms the major role of seasonal rainfall. Numerical simulations reveal a peak in animal and human infections around the 9th month, correlating with periods of heavy rainfall. This model provides a relevant tool for surveillance and prevention within a "One Health" approach in Chad.

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Emergence of Genetic Mutations associated with Malaria Diagnostic and Artemisinin Partial Resistance in Somalia: A Genomic Surveillance Study

Arale, A. M.; Hassan, A. H.; Mahmoud, A. I.; Rey, J.; la Fuente, I. M.-d.; Chopo-Pizarro, A.; Yap, T.; Hassen, A. M.; Amran, J.; Cunningham, J.; Warsame, M.; Beshir, K.

2026-07-21 infectious diseases 10.64898/2026.07.19.26357122 medRxiv
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Histidine-rich protein 2 (HRP2)-based rapid diagnostic tests (RDTs) are central to malaria case management in Africa but fail when Plasmodium falciparum parasites lack the pfhrp2 or pfhrp3 genes. Widespread deletions have been reported in Eritrea, Ethiopia, and Djibouti, yet no systematic data have been available from Somalia. Between May and October 2023, we collected 7148 dried blood spot (DBS) samples from patients with suspected malaria attending eight health facilities across seven regions in Somalia. Field HRP2/pan-lactate dehydrogenase (LDH) RDTs and microscopy were performed, and DNA was extracted from 301 RDT-positive and 173 RDT-negative DBS samples. A multiplex quantitative PCR assay targeting pfldh, pfhrp2, and pfhrp3 was used to identify deletions in pfldh-positive samples lacking pfhrp2 or pfhrp3 amplification, with mixed infections inferred from delta cycle threshold ({Delta}Ct) differences. Of 474 analysed samples, 301 (4.2%, 95% CI 3.7-4.7) were RDT or microscopy positive, and 159 (33.5%) were confirmed pfldh-positive by qPCR. Among these, six (3.8%, 95% CI 1.4-8.1) carried pfhrp2 deletions and 59 (37.1%, 95% CI 29.6-45.1) carried pfhrp3 deletions. Eleven infections (6.9%, 95% CI 3.5-12.1) produced discordant RDT outcomes, HRP-/LDH+ or RDT-negative despite pfldh positivity. Deletions were most frequent in Dolow, Luq, and Bosaso. A single isolate carried the pfk13 R622I mutation, confirming the first report of the emergence of an artemisinin partial resistance-associated in Dolow, Gedo region, Somalia. Pfhrp2/3 deletions causing false RDT results remain low in Somalia and the confidence interval overlaps with the 5% policy threshold for changing RDTs, indicating uncertainty that warrants larger-scale assessment. Pfhrp3 deletions are widespread and compromise the diagnostic redundancy of HRP2-based tests. Most deletion-carrying parasites remain detectable through the pan-LDH line, minimising immediate clinical risk but leading to systematic misclassification of P. falciparum as non-falciparum malaria. These findings support the continued use of HRP2/Pan-LDH RDTs but highlight high risk areas and emphasise the need for periodic and expanded molecular surveillance for prevalence trends to guide timely future diagnostic policy.

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Comparative effectiveness of sulfadoxine-pyrimethamine plus amodiaquine versus other antimalarial regimens for paediatric malaria chemoprevention in the context of drug resistance: a systematic review and meta-analysis

Cuomo-Dannenburg, G.; Mousa, A.; Simmons, O. S.; Cairns, M.; Staedke, S. G.; Chico, R. M.; Roper, C.; Walker, P.; Okell, L. C.

2026-07-17 infectious diseases 10.64898/2026.07.16.26356047 medRxiv
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Each year, over 50 million children receive preventive malaria treatment. However, to date there has been no consensus on the most effective antimalarial drugs to use, especially given geographic differences in drug resistance. Here, we conduct a systematic review comparing the effectiveness of the most commonly used antimalarial chemopreventive regimen, sulfadoxine-pyrimethamine plus amodiaquine (SP+AQ), with other antimalarial drugs in preventing new infections. We searched MEDLINE, Embase, Global Health, PubMed and WWARN clinical trial databases until 06 December 2025 for studies satisfying the inclusion criteria. Studies were included if they were peer-reviewed, randomised-controlled studies in Africa, measuring incidence of infection or clinical episodes of Plasmodium falciparum malaria for at least 28 days post-treatment. We also compiled data on the prevalence of markers of resistance in the parasite dhfr, dhps and mdr1 genes in the study areas. We conducted meta-analyses of incidence rates, with subgroup analyses by drug resistance levels. This review is registered on PROSPERO (CRD42024577149). We identified 27 studies representing 38,252 participants in 32 sites across 13 countries. In pooled analysis, SP+AQ reduced incidence of malaria by 54.6% (95% CI: 33.8-68.8%) compared to SP alone, including significantly outperforming SP even in areas with low SP resistance. These findings suggest that countries currently using SP alone for chemoprevention should consider switching to SP+AQ. Where AQ resistance remains low, available evidence suggests SP+AQ remains efficacious for malaria chemoprevention. SP+AQ was comparable to the artemisinin-based treatment, dihydroartemisinin-piperaquine across all studies (incidence rate ratio 0.93; 95% CI 0.78-1.11). By resistance levels, SP+AQ had slightly higher efficacy in areas with low SP and AQ resistance but had comparable or slightly lower efficacy in areas with higher resistance. Using artemisinin-based treatments for chemoprevention must be balanced against the risk of worsening artemisinin resistance in Eastern and Southern Africa. This study was funded by the UK Royal Society.

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A New Method to Predict the Effect of an Intervention in the Host Population to Reduce the Magnitude of an Outbreak of a Vector-Borne Infection

Coutinho, F. A. B.; Amaku, M.; Kallas, E. G.; Massad, E.

2026-07-19 epidemiology 10.64898/2026.07.16.26358272 medRxiv
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In this paper, we propose a new model to estimate the impact of an intervention on human hosts of a vector-borne infection, such as dengue, which occurs in yearly outbreaks of different magnitudes. The model applies to these outbreaks and, in fact, is independent of their intensity, that is, it does not require the steady-state assumption. The model takes as input the officially reported age-dependent number of cases of a vector-borne infection. It is deterministic and does not account for stochasticity. Our objective is to estimate the impact of the intervention (the efficacy), and we rely on the observed fact that the age distribution of the proportion of cases of the infections transmitted by the same vector is independent of both the intensity of transmission and the geographic area studied, at least for Brazilian regions. This finding is highlighted in the main text and forms the basis of our calculations. A hypothetical intervention is simulated using a dengue vaccine, which allows the determination of the optimal strategy for a vaccination campaign.

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Factors associated with delayed access of care among children under five with malaria and their outcomes at a regional referral hospital in Eastern Uganda

Yung, K. M. M.; Ssenyonga, L. V.; Oboth, P.; Lyagoba, I.; Olowo, S.; Adongo, P. R.

2026-07-18 health systems and quality improvement 10.64898/2026.07.16.26358296 medRxiv
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Introduction: Uganda has the highest number of Malaria cases in East and Southern Africa and accounted for 3% of deaths in 2020. This calls for prevention, early diagnosis and treatment of Malaria most especially among children whose condition can progress to severe Malaria within 24 hours. While numerous interventions have been put into place to prevent malaria transmission, delays in diagnosis and treatment of Malaria when ill can lead to further mortality. Therefore, factors associated with delayed access of care among children under five with malaria and their outcomes need to be explored. Methods: A cross sectional study was carried out. The target population was parents/caretakers to children under five with malaria at Mbale Regional Referral Hospital. A consecutive sampling technique was used on the target population. Quantitative data was collected using researcher administered questionnaires designed consistent with the research objectives. Collected data was analyzed using STATA version 15. Results: Among the 216 children under five admitted at Mbale regional referral hospital with Malaria, 59.26% received care from a health facility 24 hours after symptom onset. The most significant predictors of delay in seeking care were the caregiver/ parent having attained tertiary education (AOR=7.1, p value=0.02) and initially implementing other measures other than giving medication/herbs before taking a child to the health center (AOR=4.1, p value=0.00). Conclusion: Despite the numerous interventions put into place to curb the spread of malaria and to manage malaria, delayed access of care remains a significant contributor to the adverse effects of malaria among children under five. Health education on the impact of delayed access of care should be intensified at all levels of healthcare.

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Classification of scenarios based on the determinants of childhood vaccination coverage in Brazil

Schrarstzhaupt, I. N.; Diaz-Quijano, F. A.; Fontana Sutile Tardetti Fantinato, F.; Guzman-Barrera, L. S.

2026-07-20 public and global health 10.64898/2026.07.17.26358349 medRxiv
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ABSTRACT Background: Vaccination coverage in Brazil declined between 2015 and 2022, followed by a recovery in 2023 and 2024. Given this instability, driven by multiple determinants, we sought to identify factors associated with childhood vaccination and group Brazilian municipalities into scenarios that could guide interventions to improve coverage. Methods: In this ecological study of 5,274 Brazilian municipalities, we assessed the rate of children under 1 year unvaccinated with the third dose of the Inactivated Poliovirus Vaccine (IPV) in 2024, chosen for its high correlation with other tracer vaccines such as Diphtheria, Tetanus and Pertussis (DTP) and Measles, Mumps and Rubella (MMR). We applied a hierarchical model with three levels of determinants (socioeconomic, health service structure, and operational), using Poisson regression to estimate standardized Rate Ratios (RR), followed by a K-means cluster analysis to identify municipal profiles. Results: Several determinants were associated with higher rates of unvaccinated children, most notably the proportion of the population not covered by Community Health Workers (CHW) (RR = 1.15; 95% CI 1.14-1.15) and inequality measured by the Gini Index (RR = 1.33; 95% CI 1.32-1.34). We identified six municipal profiles that differed in tracer-vaccine coverage up to four years of age and in the composite Vaccination Needs Index (VNI). Conclusion: Multiple socioeconomic, structural and operational factors were associated with unvaccinated rates, highlighting the relevance of healthcare service organization even in favorable social contexts. Classifying municipalities into risk profiles may support more targeted interventions aligned with local needs. Keywords: Vaccination coverage, Childhood vaccination, Primary Health Care, Determinants, Scenarios, Profiles.

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West Nile virus in Italy: history and evolving transmission patterns

Giovanetti, M.; Cella, E.; Fonseca, V.; Moir, M.; Oude Munnink, B.; de Martinis, C.; Moreno, A.; Rizzo, A.; Mileto, D.; Caccuri, F.; Caruso, A.; Tramontano, E.; Nanev Slavov, S.; Bispo de Filippis, A. M.; de Oliveira, T.; Alcantara, L. C. J.; Marcello, A.; Colizzi, V.; Rezza, G.; Ciccozzi, M.; Castilletti, C.; Holmes, E. C.; Maggi, F.; Barzon, L.; Lourenco, J.

2026-07-15 infectious diseases 10.64898/2026.07.12.26357540 medRxiv
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West Nile virus (WNV) has become an important public health concern in Europe. Italy is one of the most affected countries, yet our understanding of WNV epidemiology, genomics, and dispersal across hosts and geographic regions is incomplete. AIM: To reveal the history of WNV in Italy by integrating epidemiological, genomic, and environmental data into descriptive and quantitative assessments of its past spatio-temporal surveillance and expansion. We collated vertebrate and mosquito WNV records from national surveillance and the scientific literature spanning multiple decades. Historical serological and molecular data were summarized by host and region, climatic associations with case trends were assessed using regression models, and phylodynamic and phylogeographic analyses reconstructed viral introductions and dispersal within Italy.WNV circulation in Italy has changed markedly over time, with increasing human case reporting and expansion beyond historically affected northern regions. Climate-informed regression models explained recent reporting trends, supporting an environmental contribution to transmission. Phylodynamic analyses identified multiple independent introductions and sustained local transmission with increasing regional connectivity. Wavefront analyses revealed lineage-specific dispersal patterns associated with seasonal climatic gradients. Discrepancies between epidemiological records and genomic sampling highlighted uneven surveillance across regions and host species.WNV emergence in Italy reflects repeated viral introductions, local persistence, heterogeneous surveillance, and environmentally associated dispersal dynamics. Strengthening integrated surveillance combining epidemiological, environmental, and genomic data will improve early detection, the monitoring of transmission dynamics, and public health preparedness under ongoing environmental change.

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Bayesian shared-component spatiotemporal modeling of sexually transmitted infection co-occurrence: identifying geographic vulnerability across 204 countries, 1990-2023

Ma, Q.; Zhang, T.; Lin, D.; Zou, W.

2026-07-21 epidemiology 10.64898/2026.07.19.26358422 medRxiv
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Objectives: Although HIV incidence has declined in some settings, the overall global burden of sexually transmitted infections remains a major public health concern. In the context of the World Health Organization's call for people-centred STI prevention and care, identifying the shared geographic pattern of multiple STIs using data-driven analysis may help detect vulnerable areas and inform integrated prevention strategies. Methods: We analysed country-level incidence counts from the Global Burden of Disease 2023 study for 204 countries and territories over 1990-2023. A Bayesian shared-component spatiotemporal model was fitted, decomposing each disease's log-rate into a shared spatial component (scaled intrinsic conditional autoregressive prior), disease-specific spatial deviations, disease-specific first-order random walk temporal effects, and five socioeconomic covariates, with a negative binomial likelihood to accommodate overdispersion. The shared spatial score - the posterior mean of the shared spatial component - was used as a continuous index of STI co-occurrence burden. Posterior exceedance probabilities quantified directional stability. External validity was assessed via Spearman correlation with the Socio-demographic Index and generalised estimating equation regression of HIV/AIDS mortality on the shared score. Results: The shared spatial score exhibited marked geographic heterogeneity. The five highest-scoring countries were Eswatini (2.25), Lesotho (2.13), Malawi (1.90), Mozambique (1.89), and South Africa (1.85), all in southern Africa. Fifty-seven countries had high directional stability (posterior exceedance probability >0.95), concentrated in sub-Saharan Africa and the Caribbean. The score correlated negatively with SDI (Spearman rho = -0.619, p = 6.4 x 10^-23) and positively with HIV/AIDS mortality (incidence rate ratio = 14.64 per standard deviation, 95% CI: 11.90-18.01). Prior sensitivity analysis confirmed near-perfect ranking stability (rho >= 0.9999). Conclusions: STI co-occurrence is geographically concentrated, with the highest shared burden in sub-Saharan Africa and persistently elevated shared spatial signals also observed in parts of mainland Southeast Asia and the Caribbean. The shared spatial score provides a data-driven tool for prioritising integrated STI screening and prevention resources across countries.