Related papers: Dynamical correlations in the escape strategy of I…
Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature…
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with…
The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune systems of infected populations get updated, chasing viruses…
Viruses like influenza have long coevolved with host immune systems, gradually shaping the evolutionary trajectory of these pathogens. Host immune systems develop immunity against circulating strains, which in turn avoid extinction by…
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between…
We introduce and discuss a minimal individual-based model for influenza dynamics. The model takes into account the effects of specific immunization against viral strains, but also infectivity randomness and the presence of a short-lived…
In this paper we study intra-host viral adaptation by antigenic cooperation - a mechanism of immune escape that serves as an alternative to the standard mechanism of escape by continuous genomic diversification and allows to explain a…
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…
The evolution of the hemagglutinin amino acids sequences of Influenza A virus is studied by a method based on an informational metrics, originally introduced by Rohlin for partitions in abstract probability spaces. This metrics does not…
Global mobility flow data are at the heart of spatial epidemiological models used to predict infectious disease behavior but this wealth of data on human mobility has been largely neglected by reconstructions of pathogen evolutionary…
We study an abstract model for the co-evolution between mutating viruses and the adaptive immune system. In sequence space, these two populations are localized around transiently dominant strains. Delocalization or error thresholds exhibit…
Since its emergence in 1968, influenza A (H3N2) has evolved extensively in genotype and antigenic phenotype. Antigenic evolution occurs in the context of a two-dimensional 'antigenic map', while genetic evolution shows a characteristic…
Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how…
Background: Influenza A/H3N2 has been circulating in humans since 1968, causing considerable morbidity and mortality. Although H3N2 incidence is highly seasonal, how such seasonality contributes to global phylogeographic migration dynamics…
Viral kinetics have been extensively studied in the past through the use of spatially homogeneous ordinary differential equations describing the time evolution of the diseased state. However, spatial characteristics such as localized…
One important feature of the mammalian immune system is the highly specific binding of antigens to antibodies. Antibodies generated in response to one infection may also provide some level of cross immunity to other infections. One model to…
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…
Antigenic escape constitutes the main mechanism allowing rapidly evolving viruses to achieve endemicity. Beyond granting immune escape, empirical evidence also suggests that mutations of viruses might increase their inter-host…
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…
The adaptive immune system engages in an arms race with evolving viruses, trying to generate new responses to viral strains that continually move away from the set of variants that have already elicited a functional immune response. In…