Related papers: Multi-scale phylodynamic modelling of rapid punctu…
It is a fundamental question in epidemiology to estimate, model and predict the growth rate of a pandemic. Analogously, analysing the diffusion of innovation, (fake) news, memes, and rumours is of key importance in the social sciences. The…
This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and…
The SARS-CoV-2 virus and COVID-19 disease have posed unprecedented and overwhelming demand, challenges and opportunities to domain, model and data driven modeling. This paper provides a comprehensive review of the challenges, tasks,…
In the recent COVID-19 pandemic we assisted at a sequence of epidemic waves intertwined by anomalous fade-outs with periods of low but persistent epidemic prevalence. These long-living epidemic states complicate epidemic control and…
This paper presents a compact pairwise model that describes the spread of multi-stage epidemics on networks. The multi-stage model corresponds to a gamma-distributed infectious period which interpolates between the classical Markovian…
Genomic surveillance of SARS-CoV-2 has been instrumental in tracking the spread and evolution of the virus during the pandemic. The availability of SARS-CoV-2 molecular sequences isolated from infected individuals, coupled with phylodynamic…
Networks of contacts capable of spreading infectious diseases are often observed to be highly heterogeneous, with the majority of individuals having fewer contacts than the mean, and a significant minority having relatively very many…
Between pandemics, the influenza virus exhibits periods of incremental evolution via a process known as antigenic drift. This process gives rise to a sequence of strains of the pathogen that are continuously replaced by newer strains,…
A significant proportion of the infections driving the current {SARS-CoV-2} pandemic are transmitted asymptomatically. Here we introduce and study a simple epidemic model with separate compartments comprising asymptomatic and symptomatic…
A central feature of an emerging infectious disease in a pandemic scenario is the spread through geographical scales and the impacts on different locations according to the adopted mitigation protocols. We investigated a stochastic epidemic…
This paper investigates the dynamics of infectious diseases with a non-exponentially distributed infectious period. This is achieved by considering a multi-stage infection model on networks. Using pairwise approximation with a standard…
Longitudinal molecular data of rapidly evolving viruses and pathogens provide information about disease spread and complement traditional surveillance approaches based on case count data. The coalescent is used to model the genealogy that…
We introduce and analyze a within-host dynamical model of the coevolution between rapidly mutating pathogens and the adaptive immune response. Pathogen mutation and a homeostatic constraint on lymphocytes both play a role in allowing the…
A pipeline to evaluate the evolution of viral dynamics based on a new model-driven approach has been developed in the present study. The proposed methods exploit real data and the multiscale structure of the infection dynamics to provide…
Modern Bayesian approaches and workflows emphasize in how simulation is important in the context of model developing. Simulation can help researchers understand how the model behaves in a controlled setting and can be used to stress the…
Pandemics, in addition to affecting the health of populations, can have huge impacts on their social and economic behavior. These factors, on the other hand, have the potential to feed back to and influence the disease spreading. It is…
Breaking a complex bio-social phenomenon (epidemic) into its components, considering the processes that determine its dynamics, formalizing the accepted hypotheses in mathematical equations, selecting appropriate experimental and…
A central pillar of the UK's response to the SARS-CoV-2 pandemic was the provision of up-to-the moment nowcasts and short term projections to monitor current trends in transmission and associated healthcare burden. Here we present a…
We investigate the Susceptible-Infectious-Recovered contagion dynamics in a system of self-propelled particles with polar alignment. Using agent-based simulations, we analyze the outbreak process for different combinations of the spatial…
We here propose to model active and cumulative cases data from COVID-19 by a continuous effective model based on a modified diffusion equation under Lifshitz scaling with a dynamic diffusion coefficient. The proposed model is rich enough to…