Related papers: From viral evolution to spatial contagion: a biolo…
Containing the recent West African outbreak of Ebola virus (EBOV) required the deployment of substantial global resources. Operationally, health workers and surveillance teams treated cases, collected genetic samples, and tracked case…
Cooperation and competition between pathogens can alter the amount of individuals affected by a co-infection. Nonetheless, the evolution of the pathogens' behavior has been overlooked. Here, we consider a co-evolutionary model where the…
The 2014 epidemic of the Ebola virus is governed by a genetically diverse viral population. In the early Sierra Leone outbreak, a recent study has identified new mutations that generate genetically distinct sequence clades. Here we find…
In 2014, a major epidemic of human Ebola virus disease emerged in West Africa, where human-to-human transmission has now been been sustained for greater than 10 months. In the summer of 2014, there was great uncertainty about the answers to…
Motivated by the recent outbreak of coronavirus (COVID-19), we propose a stochastic model of epidemic temporal growth and mitigation based on a time-modulated Hawkes process. The model is sufficiently rich to incorporate specific…
Self-exciting spatiotemporal Hawkes processes have found increasing use in the study of large-scale public health threats ranging from gun violence and earthquakes to wildfires and viral contagion. Whereas many such applications feature…
The Ebola virus in West Africa has infected almost 30,000 and killed over 11,000 people. Recent models of Ebola Virus Disease (EVD) have often made assumptions about how the disease spreads, such as uniform transmissibility and homogeneous…
Infectious diseases outbreaks are often characterized by a spatial component induced by hosts' distribution, mobility, and interactions. Spatial models that incorporate hosts' movements are being used to describe these processes, to…
This paper investigates the dynamics of Ebola virus transmission in West Africa during 2014. The reproduction numbers for the total period of epidemic and for different consequent time intervals are estimated based on a newly suggested…
The transmission dynamics of an epidemic are rarely homogeneous. Super-spreading events and super-spreading individuals are two types of heterogeneous transmissibility. Inference of super-spreading is commonly carried out on secondary case…
The increase in the connectivity between hosts in recent times has facilitated the emergence of more aggressive mutant viral strains, making their containment and eradication significantly more challenging compared to the original variants.…
Coalescent models are used to study the transmission dynamics of rapidly evolving pathogens from molecular sequence data obtained from infected individuals. However coalescent parameters, such as effective population size, offer limited…
Infectious disease spread is a multi-scale process composed of within-host (biological) and between-host (social) drivers and disentangling them from each other is a central challenge in epidemiology. Here, we introduce VIBES, a multi-scale…
Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed…
The fundamental models of epidemiology describe the progression of an infectious disease through a population using compartmentalized differential equations, but do not incorporate population-level heterogeneity in infection susceptibility.…
The temporal dynamics of social interactions were shown to influence the spread of disease. Here, we model the conditions of progression and competition for several viral strains, exploring various levels of cross-immunity over temporal…
The spread of infectious disease and the evolution of antigenically distinct strains are often modeled separately, despite strong feedbacks mediated by host immune memory and heterogeneous contacts. To tackle this challenging problem, we…
Throughout the course of an epidemic, the rate at which disease spreads varies with behavioral changes, the emergence of new disease variants, and the introduction of mitigation policies. Estimating such changes in transmission rates can…
Epidemic models study the spread of an undesired agent through a population, be it infectious diseases through a country, misinformation in online social media, or pests infesting a region. In combating these epidemics, we rely neither on…
Mathematical models of infectious disease transmission typically neglect within-host dynamics. Yet within-host dynamics - including pathogen replication, host immune responses, and interactions with microbiota - are crucial not only for…