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Journal articleSilhol R, Booton R, Mitchell K, et al., 2025,
Identifying priority populations for HIV interventions using acquisition and transmission indicators: a combined analysis of 15 mathematical models from 10 African countries
, The Lancet HIV, ISSN: 2352-3018Background. Characterising disparities in HIV infection across populations by gender, age, and HIV risk is key information to guide intervention priorities. We aimed to assess how indicators measuring HIV acquisitions, transmissions, or potential long-term infections influence estimates of the contribution of different populations to new infections, including key populations (KPs, including female sex workers (FSW), their clients, men who have sex with men).Methods. Using 9 models representing 15 different settings across Africa, we evaluated four indicators: I1) acquisition indicator measuring the annual fraction of all new infections acquired by a specific population, I2) direct transmission indicator measuring the annual fraction of all new infections directly transmitted by a specific population, I3) 1-year and I4) 10-year transmission population-attributable fractions (tPAFs). tPAFs measure the fraction of new infections averted if transmission involving a specific population was blocked over a specific time period. We compared estimates of the four indicators across 7 populations and 15 settings and assessed if the contribution of specific populations is ranked differently across indicators for 10 settings.Findings. Indicators identified distinct priority populations as the largest contributors: The acquisition indicator (I1) identified women aged 25+ years outside KPs as contributing the most to acquired infections in 8/10 settings in 2020, but to direct transmissions (I2) in only two settings. In 6/10 settings, the 10-year tPAFs (I4) identified non-KP men aged 25+ years and clients of FSW as the largest contributors to HIV transmission. Notably, non-KP women aged 15-24 years acquired (I1) more infections in 2020 (median of 1·7-fold across models) than they directly transmitted (I2), while non-KP men aged 25+ years and clients of FSWs transmitted more infections than they acquired in all but one model (median: 1·4 and 1·6-fold, respective
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Journal articleWilliams LR, Voysey M, Pollard AJ, et al., 2025,
A statistical method for evaluating vaccine-induced immune correlates of protection against infection and disease progression: application to the ChAdOx1-S nCoV-19 phase 3 trial
, Vaccine, Vol: 67, ISSN: 0264-410XBackground: Correlates of protection (CoPs), defined as immune markers statistically correlated with vaccine efficacy (VE), can be used to accelerate vaccine development. Different components of the immune response may be important for protection against infection and against progression from asymptomatic infection to symptomatic or severe disease. However, CoPs are typically evaluated for these outcomes separately, which can lead to some CoPs not being identified. We propose a novel statistical framework for the integrated evaluation of CoPs for infections with multiple potential outcomes.Methods: We developed a model of the natural history of an infection that can identify CoPs at each stage of infection and disease progression and implemented this model in a Bayesian estimation framework. We validated the model on simulated data then applied it to individual-level clinical and serum neutralising and binding antibody data from COV002 (NCT04400838), a phase II/III trial of the ChAdOx1 nCoV-19 (AZD1222) vaccine. We explored logistic and non-parametric (cubic spline) relationships between VE and the candidate CoPs.Results: Both parametric and non-parametric forms of the model accurately estimated the relationships between the immune CoP and VE against infection (VEin) and against progression to symptoms given infection (VEpr) in 1000 simulated trial datasets. In the COV002 correlates subset (2227 participants, 5315 samples), SARS-CoV-2 spike-specific IgG was positively associated with both VEin and VEpr (average proportion of VE mediated by spike specific IgG, 27 % (95 % CI 2–88 %) for VEin and 41 % (95 % CI 0–96 %) for VEpr). Pseudoneutralisation antibody titres and receptor binding domain (RBD) specific serum IgG showed similar correlations.Conclusion: Integrated analysis of multiple disease outcomes and candidate CoPs enables the identification of CoPs that operate at different stages of disease progression, which are missed when evaluating outcomes se
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Journal articleParag K, Lambert B, Donnelly CA, et al., 2025,
Asymmetric limits on timely interventions from noisy epidemic data
, Communications Physics, ISSN: 2399-3650Deciding on when to initiate or relax an intervention in response to an emerging infectious disease is both difficult and important. Uncertainties from noise in epidemiological surveillance data must be hedged against the potentially unknown and variable costs of false alarms anddelayed actions. Here we clarify and quantify how case under-reporting and latencies in case ascertainment, which are predominant surveillance noise sources, can restrict the timeliness of decision-making. Decisions are modelled as binary choices between responding or not that are informed by reported case curves or transmissibility estimates from those curves. Optimal responses are triggered by thresholds on case numbers or estimate confidence levels, with thresholds set by the costs of the various choices. We show that, for growing epidemics, both noise sources induce additive delays on hitting any case-based thresholds and multiplicative reductions in our confidence in estimated reproduction numbers or growth rates. However, for declining epidemics, these noise sources have counteracting effects on case data and limited cumulative impact on transmissibility estimates. We find this asymmetry persists even if more sophisticated feedback control algorithms that consider the longer-term effects of interventions are employed. Standard surveillance data therefore provide substantially weaker support for deciding when to initiate a control action or intervention than for determining when to relax it.This information bottleneck during epidemic growth may justify proactive intervention choices.
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Journal articleBerden J, Hanley-Cook GT, Chimera B, et al., 2025,
Synergies between food biodiversity, processing levels, and the EAT-Lancet diet for nutrient adequacy and environmental sustainability: a multiobjective optimization using the European Prospective Investigation into Cancer and Nutrition cohort.
, Am J Clin NutrBACKGROUND: Diets have become increasingly monotonous and high in ultraprocessed foods (UPFs), contributing to poor health outcomes and environmental degradation. Although sustainable diets, food biodiversity, and food processing levels have each been linked to nutritional and environmental outcomes, their combined impact has not been assessed. OBJECTIVES: This study aims to examine whether food biodiversity, intakes of UPFs, and adherence to the EAT-Lancet diet can simultaneously optimize nutrient adequacy while reducing environmental impacts. METHODS: Using data from 368,733 adults in the European Prospective Investigation into Cancer and Nutrition, we assessed associations and interactions between dietary species richness (DSR) (disaggregated into DSRPlant and DSRAnimal), food processing levels (Nova categories; % g/d), and adherence to EAT-Lancet recommendations [healthy reference diet (HRD) score; 0-140 points] with the Probability of Adequate Nutrient Intake Diet (PANDiet) score, dietary greenhouse gas emissions (GHGe; kg CO2-eq/d), and land use (m2/d). Regression models subsequently informed multiobjective optimization to identify optimal dietary patterns balancing nutritional and environmental outcomes. RESULTS: Compared with observed diets, optimal diets showed a mean HRD score increase of 13.91 (95% confidence interval: 13.89, 13.93) points; DSRPlant increased by mean of 1.36 (1.35, 1.37) species, and a mean substitution of 12.44 (12.40, 12.49) percentage points of UPFs with unprocessed or minimally processed foods. Correspondingly, the mean PANDiet score increased by 4.12 (4.10, 4.14) percentage points, whereas GHGe and land use reduced by 1.07 (1.05, 1.09) kg CO2-eq/d and 1.43 (1.41, 1.45) m2/d, respectively. CONCLUSIONS: Diets that adhere to the EAT-Lancet diet, are more biodiverse, and prioritize unprocessed and minimally processed foods over UPFs, have the potential to synergistically enhance nutrient adequacy while minimizing environmental impacts. T
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Journal articleEilerts-Spinelli H, Romero-Prieto JE, Herbst K, et al., 2025,
Pregnancy reporting and biases in under-five mortality in three African HDSSs
, POPULATION STUDIES-A JOURNAL OF DEMOGRAPHY, ISSN: 0032-4728 -
Journal articleHayes S, Lushasi K, Changalucha J, et al., 2025,
Generalizing an outbreak cluster detection method for two groups: an application to rabies
, ROYAL SOCIETY OPEN SCIENCE, Vol: 12, ISSN: 2054-5703 -
Journal articleMills C, Falconi-Agapito F, Carrera J-P, et al., 2025,
Multi-model approach to understand and predict past and future dengue epidemic dynamics
, ROYAL SOCIETY OPEN SCIENCE, Vol: 12, ISSN: 2054-5703 -
Journal articleJiao B, Sato R, Mak J, et al., 2025,
Financial risk protection from vaccines in 52 Gavi-eligible low- and middle-income countries: A modeling study
, PLOS MEDICINE, Vol: 22, ISSN: 1549-1277 -
Journal articleJohnson R, 2025,
Competing societal objectives in epidemic mitigation: A modelling study of COVID-19 in the Philippines
, Frontiers in Public Health, ISSN: 2296-2565 -
Journal articleGrimm SL, Kaufman JT, Rice DP, et al., 2025,
Inferring the sensitivity of wastewater metagenomic sequencing for early detection of viruses: a statistical modelling study
, Lancet Microbe, Vol: 6Background Metagenomic sequencing of wastewater (W-MGS) can in principle detect any known or novel pathogen in a population. We aimed to quantify the sensitivity and cost of W-MGS for viral pathogen detection by jointly analysing W-MGS and epidemiological data for a range of human-infecting viruses. Methods In this statistical modelling study, we analysed sequencing data from four studies of untargeted W-MGS to estimate the relative abundance of 11 human-infecting viruses. Corresponding prevalence and incidence estimates were obtained or calculated from academic and public health reports. We combined these estimates using a hierarchical Bayesian model to predict relative abundance at set prevalence or incidence values, allowing comparison across studies and viruses. These predictions were then used to estimate the sequencing depth and concomitant cost required for pathogen detection using W-MGS with or without use of a hybridisation capture enrichment panel. Findings After controlling for variation in local infection rates, relative abundance varied by orders of magnitude across studies for a given virus. For instance, a local SARS-CoV-2 weekly incidence of 1% corresponded to a predicted SARS-CoV-2 relative abundance ranging from 3·8 × 10<sup>−10</sup> to 2·4 × 10<sup>−7</sup> across studies, translating to orders-of-magnitude variation in the cost of operating a system able to detect a SARS-CoV-2-like pathogen at a given sensitivity. Use of a respiratory virus enrichment panel in two studies greatly increased predicted relative abundance of SARS-CoV-2, lowering yearly costs by 27-fold (from US$7·87 million to $287 000) and 29-fold (from $1·98 million to $69 100) for a system able to detect a SARS-CoV-2-like pathogen before reaching 0·01% cumulative incidence. Interpretation The large variation in viral relative abundance after controlling for epidemiological factors indicates that ot
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