Related papers: How host mobility patterns shape antigenic escape …
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…
The dynamics of infectious diseases propagating in populations depends both on human interaction patterns, the contagion process and the pathogenesis within hosts. The immune system follows a circadian rhythm and, consequently, the chance…
Viral kinetics have been extensively studied in the past through the use of spatially well-mixed ordinary differential equations describing the time evolution of the diseased state. However, emerging spatial structures such as localized…
In this work we have investigated the evolutionary dynamics of a generalist pathogen, e.g. a virus population, that evolves towards specialisation in an environment with multiple host types. We have particularly explored under which…
The dynamics of epidemic spreading is often reduced to the single control parameter $R_0$, whose value, above or below unity, determines the state of the contagion. If, however, the pathogen evolves as it spreads, $R_0$ may change over…
The twin processes of viral evolutionary escape and reversion in response to host immune pressure, in particular the cytotoxic T-lymphocyte (CTL) response, shape Human Immunodeficiency Virus-1 sequence evolution in infected host…
In early HIV infection, the virus population escapes from multiple CD8+ cell responses. The later an escape mutation emerges, the slower it outgrows its competition, i. e. the escape rate is lower. This pattern could indicate that the…
RNA viruses exist as genetically diverse populations displaying different phenotypes, including diverse degrees of virulence. The evolution of virulence in viral populations is, however, poorly understood. Based on the experimental…
We investigate a stochastic individual-based model for the population dynamics of host-virus systems where the microbial hosts may transition into a dormant state upon contact with virions, thus evading infection. Such a contact-mediated…
The flux of visitors through popular places undoubtedly influences viral spreading -- from H1N1 and Zika viruses spreading through physical spaces such as airports, to rumors and ideas spreading though online spaces such as chatrooms and…
Population expansions trigger many biomedical and ecological transitions, from tumor growth to invasions of non-native species. Although population spreading often selects for more invasive phenotypes, we show that this outcome is far from…
Viruses display striking diversity in structure, transmission mode, immune interaction, and evolutionary behavior. Despite this diversity, viral strategies are not unconstrained. Here we present a unifying framework that treats viral…
Infectious diseases often spread faster near their peak than would be predicted given early data on transmission. Despite the commonality of this phenomena, there are no known general mechanisms able to cause an exponentially spreading dis-…
The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected for by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a…
In this paper, we study into the impact of the preference of an individual for public transport on the spread of infectious disease, through a quantity known as the public mobility. Our theoretical and numerical results based on a…
Mathematical disease modelling has long operated under the assumption that any one infectious disease is caused by one transmissible pathogen spreading among a population. This paradigm has been useful in simplifying the biological reality…
Chronic viral infections can persist in an infected person for decades. From the perspective of the virus, a single infection can span thousands of generations, leading to a highly diverse population of viruses with its own complex…
Human mobility is a key factor in spatial disease dynamics and related phenomena. In computational models host mobility is typically modelled by diffusion in space or on metapolulation networks. Alternatively, an effective force of…
Numerous experimental studies have demonstrated that the microenvironment is a key regulator influencing the proliferative and migrative potentials of species. Spatial and temporal disturbances lead to adverse and hazardous…
RNA viruses are a widely used tool to study evolution experimentally. Many standard protocols of virus propagation and competition are done at nominally low multiplicity of infection (m.o.i.), but lead during one passage to two or more…