Related papers: Multiple possible patterns can emerge from virus-i…
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…
Pathogens drive changes in host immune systems that in turn exert pressure for pathogens to evolve. Quantifying and understanding this constant coevolutionary process has clear practical global health implications. Yet its relatively easier…
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 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…
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…
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…
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…
We present a novel model that describes the within-host evolutionary dynamics of parasites undergoing antigenic variation. The approach uses a multi-type branching process with two types of entities defined according to their relationship…
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…
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the…
A simple, but ``classical``, stochastic model for epidemic spread in a finite, but large, population is studied. The progress of the epidemic can be divided into three different phases that requires different tools to analyse. Initially the…
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation rates that allows viruses to thrive is…
We are interested in modeling some two-level population dynamics, resulting from the interplay of ecological interactions and phenotypic variation of individuals (or hosts) and the evolution of cells (or parasites) of two types living in…
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…
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…
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,…
The evolutionary dynamics of human Influenza A virus presents a challenging theoretical problem. An extremely high mutation rate allows the virus to escape, at each epidemic season, the host immune protection elicited by previous…
Population dynamics and evolutionary genetics underly the structure of ecosystems, changing on the same timescale for interacting species with rapid turnover, such as virus (e.g. HIV) and immune response. Thus, an important problem in…
We consider a stochastic model for a pathogen population in the presence of an immune response, in which pathogen types are partially ordered by ancestry and the immune system must eliminate ancestor types before it can eliminate their…