Journal of The Royal Society Interface

Mathematical models of infectious disease dynamics are routinely fitted to surveillance data to estimate epidemiological parameters and inform public health decisions. Such data are typically discrete and noisy, but before attempting estimation, it is essential to ask whether the model structure itself permits unique parameter identification at least under perfect (continuous, noise-free) observations. This mathematical property of a model with respect to observation(s), known as structural iden...

The risk of highly pathogenic avian influenza infection to humans is challenging to estimate because many human avian influenza virus (AIV) infections are undetected as they may be asymptomatic, symptomatic but not tested, and as contact tracing is difficult because human-to-human spread is rare. We derive equations that consider the evolutionary mechanisms that give rise to pandemics and are parameterized to be consistent with records of past pandemics. We estimate that thousands of human AIV i...

Biological and behavioral differences between genders influence infectious disease dynamics. Yet, most epidemiological models overlook these aspects in favor of age stratification alone. Here, we systematically evaluate the impact of incorporating gender-specific features into an age-structured epidemic compartmental model, calibrated to COVID-19 mortality data from the second wave in Italy (Autumn 2020-Winter 2021). We develop eight model versions representing different combinations of three da...

Assessing epidemic risk following pathogen introduction is crucial in infectious disease epidemiology. Risk is commonly encoded through reproduction ratios, which underpin operational decision-making. In spatially structured populations, both local and cross-community transmission shape epidemic trends, a feature that standard reproduction ratios fail to capture simultaneously. Here, we use multitype branching processes to define the outbreak reproduction ratio Rob, a reformulation applicable ac...

Human African Trypanosomiasis (HAT) remains a persistent public health threat in sub-Saharan Africa, with transmission dynamics tightly coupled to the ecology and physiology of its tsetse fly vector. Despite growing evidence that temperature strongly modulates vector survival, development, and biting behavior, most existing transmission models assume static environmental conditions. We develop a model for HAT that incorporates temperature-dependent vector recruitment, mortality, and biting rates...

During an outbreak, infectious disease can spread among populations through host movement, potentially fueling local outbreaks with their own epidemiological dynamics. However, it is difficult to know how often infections between populations are transmitted by diseased travelers infecting healthy residents when abroad, rather than by diseased residents infecting healthy travelers, who later return home with the new pathogen. In this paper, we introduce a phylogeographic model where pathogens spr...

BackgroundCOVID-19 epidemic waves display pronounced temporal structure in mortality, with substantial variation in wave shape, duration, and asymmetry across regions. These dynamics are commonly interpreted within transmission-based compartmental models, in which epidemic growth is driven by interactions between infectious and susceptible individuals. However, several empirical features of observed mortality curves, including prolonged declines, asymmetric wave shapes, and coherent temporal pat...

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 ...

Most models for infectious disease spread simplify contact heterogeneity by assuming constant rates within a week. However, empirical studies show clear variation, such as reduced workplace contacts on weekends. In this work, we investigate the effects of daily variation in workplace contacts on the spread of respiratory infections using the individual-based framework GEMS (German Epidemic Micro-Simulation System) with a synthetic population of 5 million individuals. We compare a baseline scenar...

BackgroundViral interference, in which infection with one pathogen reduces susceptibility to another, may influence respiratory virus dynamics. Inference from surveillance data is complicated by time-varying testing behavior that can induce correlated detection patterns independent of biological interaction. MethodsWe developed a multi-pathogen renewal model augmented with a ratio penalty that constrains interference estimates to be consistent with observed log-odds ratios of pathogen positivit...

Declining vaccine coverage across the United States has increased the risk of outbreaks of vaccine-preventable diseases. Even when vaccines have low primary failure rates, conventional epidemic theory predicts a strongly nonlinear, positive relationship between vaccine coverage and the fraction of breakthrough infections in vaccinated individuals. These breakthrough infections may generate misconceptions that vaccines are not working and accelerate declines in confidence and coverage. Here, we s...

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...

Nosocomial transmission of respiratory infections poses a major threat to patient safety, while also affecting healthcare workers (HCW) health, generating substantial costs for hospitals. These infections spread through both close-proximity interactions at short distances, and via aerosols that remain suspended in the air, enabling long-range transmission. The relative contribution of each transmission route is pathogen-dependent, and evidence to distinguish them remains scarce. Here, we propose...

In this research, we create a new fractional-order SEIHRD framework to examine how the Nipah virus moves from one species to another (zoonotic spillover) and how it later spreads throughout a community (via contact with one another) or in a hospital or isolation situation (via entering into a hospital or being placed under quarantine). We used the fractional-derivative formulation of the SEIHRD model to demonstrate memory-based effects related to the progression of an infection and also reflect ...

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...

Lassa fever is classically defined as a rural zoonosis constrained by the agricultural niche of its reservoir, Mastomys natalensis. However, current risk models rely on historical sampling heavily biased toward rural settings (>67%). Here, I reconstruct the realised niche of M. natalensis using an Integrated Multi-Species Occupancy Model (IMSOM) accounting for biotic interactions with invasive rodents. Contrary to climatic predictions of urban exclusion, I identify a cryptic reservoir niche in W...

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...