Related papers: A minimal stochastic model for influenza evolution
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…
We introduce a two-strain model with asymmetric temporary immunity periods and partial cross-immunity. We derive explicit conditions for competitive exclusion and coexistence of the strains depending on the strain-specific basic…
From footpaths to flight routes, human mobility networks facilitate the spread of communicable diseases. Control and elimination efforts depend on characterizing these networks in terms of connections and flux rates of individuals between…
In this work we analyze the evolution of voluntary vaccination in networked populations by entangling the spreading dynamics of an influenza-like disease with an evolutionary framework taking place at the end of each influenza season so…
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…
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…
We investigate how a population's natural and vaccine immunity affects the competitive balance between two strains of an infectious disease with different epidemiological characteristics. Specifically, we consider the case where one strain…
We consider a model for an influenza-like disease, in which, between seasons, the virus makes a random genetic drift $\delta$, (reducing immunity by the factor $\delta$) and obtains a new random transmissibility $\tau$ (closely related to…
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…
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…
We develop a multiple compartment Susceptible-Infected-Recovered (SIR) model to analyze the spread of several infectious diseases through different geographic areas. Additionally, we propose a data-quality sensitive optimization framework…
Determining phenotype from genetic data is a fundamental challenge. Influenza A viruses undergo rapid antigenic drift and identification of emerging antigenic variants is critical to the vaccine selection process. Using former seasonal…
Modelling the transmission dynamics of an infectious disease is a complex task. Not only it is difficult to accurately model the inherent non-stationarity and heterogeneity of transmission, but it is nearly impossible to describe,…
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…
The propagation of model epidemics on a small-world network under the action of immunization is studied. Although the connectivity in this kind of networks is rather uniform, a vaccination strategy focused on the best connected individuals…
When analysing in vitro data, growth kinetics of influenza strains are often compared by computing their growth rates, which are sometimes used as proxies for fitness. However, analogous to mechanistic epidemic models, the growth rate can…
Epidemiological data on seasonal influenza show that the growth rate of the number of infected individuals can increase passing from one exponential growth rate to another one with a larger exponent. Such behavior is not described by…
Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…
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.…
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…