Journal of The Royal Society Interface

Biological fitness quantifies the efficiency and selective advantage of pathogens and hosts in their bilateral interaction. Key questions--such as how much more infectious an emerging variant is compared with its predecessor, or how much protection vaccination offers relative to no vaccination--require fitness to be measured systematically, in real time, and ideally beyond controlled laboratory settings. We propose an approach that infers biological fitness from mostly non-biological data on inf...

With significant population fractions in many societies who refuse vaccines, it is important to reconsider how vaccination is incorporated into compartmental epidemiology models. It is still most common to apply the vaccination rate to the entire class of susceptibles, rather than to use the more realistic assumption that the vaccination rate function should depend only on the population of susceptibles who are willing and able to receive a vaccination. This study uses a simple generic disease m...

Background: Human-to-human transmission of pathogens fundamentally depends on interactions among infectious and susceptible individuals, yet traditional population-scale models often overlook the stochastic, behaviour-driven, and highly heterogeneous nature of these interactions. Methods: Here, we develop a large-scale actor-based model capturing early epidemic dynamics of a novel respiratory pathogen on dynamic contact networks. We build these networks upon explicitly integrating detailed demog...

Nipah virus (NiV) is a sporadic yet extremely deadly zoonotic pathogen, with reported case fatality rates of 40%-75% in impacted areas. Prolonged incubation, documented relapse, and delayed-onset encephalitis following apparent recovery indicate that NiV dynamics are influenced by intricate temporal processes. However, mechanistic contributions of these processes to epidemic persistence remain poorly understood. In this study, we develop and analyze a delay differential equation model for NiV tr...

Visceral leishmaniasis (VL) is considerably more severe among individuals infected with human immunodeficiency virus (HIV), leading to higher parasite loads, frequent relapse, and increased mortality. To examine the epidemiological interaction between the two diseases, we develop a comprehensive VL-HIV co-infection model that incorporates transmission pathways, treatment effects, and relapse dynamics. The model is parameterized using real-time data from Bihar, India, including monthly VL-only an...

Wastewater is increasingly being recognized as an important data stream that can contribute to infectious disease surveillance and forecasting. With this recognition, a growing number of statistical inference approaches are being developed to use wastewater data to provide quantitative insights into epidemiological dynamics. However, few existing approaches have allowed for systematic integration of data streams for inference, for example by combining case incidence data and/or serological data ...

We present results from the second season of Influcast, a multi-model collaborative forecasting hub focused on influenza in Italy. During the 2024/25 winter season, Influcast collected one-to four-week-ahead probabilistic forecasts of influenza-like illness (ILI) incidence alongside influenza A and B ILI+ incidence signals. New ILI+ targets were constructed integrating syndromic surveillance data with virological detections collected weekly by the Italian National Institute of Health. Forecasts ...

We introduce PerTexP (Pertussis Time Exploration), an interactive modelling tool designed to investigate pertussis transmission dynamics and to support the evaluation of vaccination strategies and short-term projections. PerTexP allows users to explore and compare maternal, infant, and non-infant booster vaccination scenarios and to assess their potential impact on disease transmission, with a particular focus on the Italian epidemiological context. The tool is based on a discrete-time, stage-st...

Biological ageing begins before birth, with early-life exposures shaping late-life health. These exposures drive health inequities early, yet specific exposures and the composition of the ageing exposome remain largely undefined. This gap may persist as the field lacks agnostic investigations accounting for non-linearity, interactions and subtle signals. We aimed to identify exposures predictive of epigenetic ageing accumulated during childhood and adolescence and explore the composition of the...

Hybrid controlled trials (HCTs) incorporate real-world data into randomized controlled trials (RCTs) by augmenting the internal control arm with patients receiving the same treatment in routine care. Beyond increasing power, HCTs may improve recruitment by supporting unequal randomization ratios that increase patient access to experimental treatments. However, HCT validity is threatened by bias from unmeasured confounding due to lack of randomization of external controls, leading to outcome non-...

Abstract This protocol is reported in accordance with the SPIRIT 2025 guidelines for clinical trial protocols. Introduction: Young children, from birth to age 5 y are particularly vulnerable to indoor air pollutants and respiratory pathogens. Portable air purifiers (or filtration) and upper-room ultraviolet germicidal irradiation (UVGI) are two widely used interventions with the potential to improve indoor air quality (IAQ) and reduce sick-related absences. However, a review of the literature re...

Ambient air pollution has been associated with increased incidence of chronic disease and is estimated to contribute towards 4.2 million early deaths annually. Whilst the health impacts are well described, less is understood about the underlying biological mechanisms, particularly when considering the co-occurrence of multiple pollutants. Using an atmospheric chemistry transportation model (EMEP4UK), we generate pre-baseline sampling pollution exposure estimates for eight pollutants in Generatio...

BackgroundThe widespread insecticide resistance increasingly threatens malaria elimination, prompting a reassessment of vector control strategies. As Tanzania transitions from standard pyrethroid-only insecticide-treated nets (ITNs) to new-generation nets, evaluating the impact of this shift on malaria transmission and resistance is critical. MethodsUsing the agent-based malaria model, EMOD, we assessed the impact of three ITN types, standard pyrethroid-only nets, pyrethroid-PBO nets (Olyset(R)...

BackgroundLarval source management (LSM) was once central to malaria control before insecticide-treated nets and indoor residual spraying dominated. Renewed interest in LSM raises questions about its effectiveness in rural Africa, where habitats are dispersed, and vector species contribute unequally, and whether species-targeted larviciding could offer greater gains than broadcast approaches. MethodsThis modelling study quantified the potential impact of larviciding in African settings where mu...

Background and ObjectivesAssociations of common infections with Alzheimer disease (AD) risk have been reported. A hypothesized mechanism to explain these is cerebral amyloid-beta (A{beta}) aggregation as a defence in response to infection, with subsequent tau accumulation. However, few studies have assessed associations of infections with tau and A{beta} pathology. We investigated associations of serological measures of several common infections with plasma p-tau217 and A{beta} status measured b...

Suicide is one of the worlds leading public health problems, with more than 720,000 deaths annually. Suicide has traditionally been studied from an individual perspective. However, research has increasingly highlighted the influence of community-level factors on suicide risk. This study aimed to (1) analyse the spatial distribution of suicide mortality at the provincial level in Spain (2018-2022); (2) perform stratified analyses by sex and age group; and (3) compare suicide risk across differen...

BackgroundMeasurement of human antibodies against Anopheles salivary proteins that are injected during mosquito bites may serve as biomarkers of mosquito biting exposure. These biomarkers have been suggested as surrogate outcomes in trials of vector control intervention effectiveness, however, studies to-date have been largely descriptive and do not directly quantify the instantaneous nor cumulative effects of the intervention on antibody outcomes. In this study, we sought to explore the use of ...

The spread of Anopheles stephensi into the Horn of Africa represents one of the main challenges for malaria control, given the species ecological plasticity and resistance to multiple insecticides. In response to the World Health Organizations 2022 vector alert, an adaptive, model-based spatial surveillance framework was developed and evaluated to improve detection, mapping accuracy, and operational responsiveness during invasion. Adaptive surveillance utilises initial observations to guide subs...

BackgroundArtemisinin-based combination therapies (ACTs) are the most widely used treatment for Plasmodium falciparum malaria. Kelch 13 mutations associated with artemisinin partial resistance (ART-R) have emerged in Sub-Saharan Africa (SSA) and are now reported in an increasing number of countries. ACT treatment failure rates are at risk of unprecedented increase. To summarise existing surveillance data and guide future surveillance, we produce modelled estimates of the spatiotemporal distribut...

Students who frequently miss school are at greater risk for academic difficulty. High levels of absenteeism as early as kindergarten have been associated with long-term consequences, such as low reading proficiency in Grade 3 and low academic achievement in Grade 5, both of which have been associated with lower rates of high school graduation and enrollment in post-secondary education. The prevalence of school absenteeism has increased significantly since the COVID-19 pandemic and there have bee...