Journal of Theoretical Biology

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...

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 ...

We describe a fast, noninvasive, low-cost survey method designed to understand the mode of transmission of an emerging pathogen. It is inspired from the standard household prevalence survey consisting in sampling households and counting the total number of people infected in each household, but refines it with the aim of improving diagnosis and estimating more parameters of the model of intra-household transmission. The survey was carried out in May-June 2020, during part of the first national ...

The prospective design of vaccine efficacy trials for deployment in outbreaks requires advance consideration of plausible outbreak scenarios, anticipated vaccine characteristics, and logistical and ethical constraints. As part of CEPIs 100 Days Mission to accelerate vaccine development against a novel Disease X, we evaluated trial designs for a hypothetical Nipah-X outbreak. We assumed Nipah-X would share key features with Nipah, including high case fatality rates and substantial super-spreading...

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...

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...

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 ...

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...

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...

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 ...

In the three years since Omicron emergence, SARS-CoV-2 dynamics have exhibited persistent twice-yearly waves in the United States, peaking in late summer and winter, with heterogeneity in timing and intensity across states. This semiannual pattern sharply contrasts with typical annual respiratory pathogen dynamics in the US, yet their underlying mechanisms and whether this pattern will persist remain poorly understood. Here, we tested several hypothesized mechanisms and found that a combination ...

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 ...

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...

The UK Biobank (UKB) Brain Imaging cohort contains data from almost 100,000 subjects and has yielded invaluable understanding of the links between the brain and health outcomes and lifestyles. Much of the understanding of these links has come from exploring the association between Imaging Derived Phenotypes (IDPs) and other variables that are unrelated to brain imaging, so called non-Imaging Derived Phenotypes (nIDPs). When performing analysis of this kind, it is very important to control for we...

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...

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...

The COVID-19 pandemic exposed major vulnerabilities of hospital capacity and management worldwide, particularly in intensive care units (ICUs) and emergency rooms (ER), imposing prompt adaptation and resource reallocation. Although SARS-CoV-2 is no longer endangering healthcare systems, winter seasons continue to bring recurrent overload of critical care services, primarily due to respiratory infections. In France e.g., this pattern led to the reactivation of the national emergency response plan...

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-...