Related papers: The context-specificity of virulence evolution rev…
We introduce a minimal multiscale framework that links within-host virus dynamics to population-level SIRS epidemiology through explicit, bidirectional coupling. At the microscopic layer, a two variant quasispecies (master and mutant…
Epidemiological models describe the spread of an infectious disease within a population. They capture microscopic details on how the disease is passed on among individuals in various different ways, while making predictions about the state…
The recent pandemic emphasized the need to consider the role of human behavior in shaping epidemic dynamics. In particular, it is necessary to extend beyond the classical epidemiological structures to fully capture the interplay between the…
Metapopulation models are commonly used in ecology, evolution, and epidemiology. These models usually entail homogeneity assumptions within patches and study networks of migration between patches to generate insights into conservation of…
Sensitivity Analysis (SA) is a useful tool to measure the impact of changes in model parameters on the infection dynamics, particularly to quantify the expected efficacy of disease control strategies. SA has only been applied to epidemic…
Airborne infection risk analysis is usually performed for enclosed spaces where susceptible individuals are exposed to infectious airborne respiratory droplets by inhalation. It is usually based on exponential, dose-response models of which…
We study the problem of estimating the origin of an epidemic outbreak -- given a contact network and a snapshot of epidemic spread at a certain time, determine the infection source. Finding the source is important in different contexts of…
With the exponential growth in the world population and the constant increase in human mobility, the danger of outbreaks of epidemics is rising. Especially in high density urban areas such as public transport and transfer points, where…
With the unprecedented global vaccination campaign against SARS-CoV-2 attention has now turned to the potential impact of this large-scale intervention on the evolution of the virus. In this perspective we summarize what is currently known…
The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge,…
We consider the spread of infectious disease through contact networks of Configuration Model type. We assume that the disease spreads through contacts and infected individuals recover into an immune state. We discuss a number of existing…
Human mobility forms the backbone of contact patterns through which infectious diseases propagate, fundamentally shaping the spatio-temporal dynamics of epidemics and pandemics. While traditional models are often based on the assumption…
Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…
Rapidly mutating pathogens may be able to persist in the population and reach an endemic equilibrium by escaping hosts' acquired immunity. For such diseases, multiple biological, environmental and population-level mechanisms determine the…
The global impact of the COVID-19 pandemic on the livelihoods of people worldwide prompted the implementation of a range of preventive measures at local, national, and international levels. Early in the outbreak, before the vaccine became…
Uncertainty can be classified as either aleatoric (intrinsic randomness) or epistemic (imperfect knowledge of parameters). The majority of frameworks assessing infectious disease risk consider only epistemic uncertainty. We only ever…
Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the…
We consider a flexible Bayesian evidence synthesis approach to model the age-specific transmission dynamics of COVID-19 based on daily mortality counts. The temporal evolution of transmission rates in populations containing multiple types…
The COVID-19 pandemic has given rise to numerous articles from different scientific fields (epidemiology, virology, immunology, airflow physics...) without any effort to link these different insights. In this review, we aim to establish…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…