Journal of The Royal Society Interface

BackgroundVaccines can prevent severe disease by preventing infection or by reducing progression among those who become infected. Vaccine effectiveness against progression given infection is often used to quantify this second mechanism, but it conditions on infection, which is itself affected by vaccination. As a result, this estimand lacks a clear causal interpretation and may behave non-intuitively over time. MethodsWe introduce a conceptual framework that models protection against infection ...

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...

1The timeliness of infectious disease surveillance systems largely determines the speed at which mitigation interventions may be implemented. However, it is unclear how surveillance timeliness evolves during a pandemic with changing government policies, testing tools, and population-level infection and immunity landscapes. Here, we adapt an agent-based model for COVID-19 transmission to explore the timeliness of the surveillance signals obtained from polymerase chain reaction (PCR) and rapid ant...

Increasing human mobility and population connectivity have intensified the risks of global pathogen spread, while concurrent shifts in human demographic patterns, ecological factors, and climatic conditions have altered the global landscape of this risk. Genomic surveillance can serve as a critical tool for early detection of emerging pathogen threats; however, challenges remain in deciding where to monitor, in understanding trade-offs among surveillance modalities, and in translating detections...

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...

BackgroundStrikingly low allocation of SARS-CoV-2 vaccine to the African Continent limits its capacity to control transmission. Characterizing the trajectory of vaccination efforts and their impact on the expected burden of SARS-CoV-2 will help planning vaccine delivery strategies, and public health interventions more broadly. As the burden is strongly age-dependent, this requires an understanding of the age-structured dynamics of susceptible individuals, accounting for the combined effects of v...

Epigenetic clocks estimate biological age from DNA methylation patterns at CpG sites, providing robust predictions of mortality and morbidity risk. "Blue zones"--regions of exceptional longevity--offer a unique opportunity to investigate how biological aging diverges from chronological age. However, standard clocks are typically trained on large, heterogeneous datasets, reflecting average population trends rather than region-specific dynamics. Using data from the Costa Rican Longevity and Health...

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 ...

Wastewater-based epidemiology provides a low-cost, scalable view of community infection dynamics, but converting these signals into actionable epidemiological insights remains difficult. Mechanistic models offer interpretability, yet, assumptions such as a constant transmission rate limit realism over long simulation horizons and heterogeneous settings. We present a susceptible-exposed-infectious-recovered (SEIR) universal differential equation (UDE) that links wastewater viral loads to case cou...

Human contact network structure fundamentally shapes infectious disease transmission and control. Most COVID-19 epidemic models assumed approximately homogeneous contact patterns, yet real-world networks are highly heterogeneous. We analysed 59,585 daily non-household contact reports from Germanys COVIMOD study (2020-2021) using a novel heavy-tail regression framework. Throughout the pandemic, contact distributions remained strongly heavy-tailed despite substantial non-pharmaceutical interventio...

The COVID-19 pandemic has presented severe challenges in understanding and predicting the spread of infectious diseases, necessitating innovative approaches beyond traditional epidemiological models. This study introduces an advanced method for automated model discovery using the Sparse Identification of Nonlinear Dynamics (SINDy) algorithm, leveraging a dataset from the COVID-19 outbreak in Thuringia, Germany, encompassing over 400,000 patient records and vaccination data. By analysing this dat...

Pathogenic organisms are typically thought to be constrained by a tradeoff between the rate and duration of transmission, an assumption that underpins a considerable body of evolutionary theory. Here we test for a transmission-duration tradeoff using detailed historical malaria infection data from an era prior to widespread use of antibiotics when humans were deliberately infected with malaria parasites as treatment for neurosyphilis (malariatherapy). These time series follow individual human in...

Infection with pnuemococcus bacteria is generally mild but can be more severe in the young and elderly, causing invasive pneumococcal disease (IPD) and community-acquired pneumonia (CAP). Although paediatric pneumococcal conjugate vaccine (PCV) programmes and elderly pneumococcal polysaccharide vaccine (PPV) programmes have reduced cases, we estimate that pneumococcal infection still leads to direct health care costs of around {pound}68M and approximately 16 thousand QALY losses in England per y...

The two largest US measles outbreaks in over two decades (2025 Gaines County, Texas: 414 cases, contained; 2025-2026 Spartanburg County, South Carolina: 923+ cases, ongoing) occurred in counties with similar sub-threshold K-12 MMR coverage (85.1% vs 88.8%), yet their trajectories diverged dramatically. Using kernel density estimation with a common bandwidth and bootstrap uncertainty quantification, we compared sub-county vaccination data at the district level for Texas (3 districts, 3,560 studen...

BackgroundRoutine immunization (RI) is widely used to increase population immunity against measles. In low-resource settings, achieving immunity goals using RI alone has proved challenging and supplemental immunization activities (SIAs), large community-based vaccination campaigns conducted every few years, have been used to close immunity gaps. Although effective at covering the population unreached by RI and boosting the population immunity, SIAs are labor-intensive and expensive, allowing for...

Schistosomiasis is a neglected parasitic disease caused by various trematode species of the genus Schistosoma for which 251 million people needed treatment in 2021. Many mathematical models of Schistosoma mansoni transmission incorporate the effect of chemoprophylaxis on parasite burden within the human host. While praziquantel is the most commonly implemented pharmaceutical used to control schistosomiasis, due to its applicability over several species and its negligible side effects, it is not ...

A concern in infectious disease modelling is how accurately population mixing is incorporated, as it shapes the type and frequency of contacts through which infection spreads, and consequently, estimated intervention effectiveness. Although synthesizing mixing patterns from diary-based surveys is an established framework, geographical information is poorly or sparsely captured. Here we propose a generalizable workflow to quantify geographical connectivity from job registry data covering over 8 m...