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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…
Multipartite viruses replicate through a puzzling evolutionary strategy. Their genome is segmented into two or more parts, and encapsidated in separate particles that appear to propagate independently. Completing the replication cycle,…
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…
Mutations sometimes increase contagiousness for evolving pathogens. During an epidemic, scientists use viral genome data to infer a shared evolutionary history and connect this history to geographic spread. We propose a model that directly…
Models are often employed to integrate knowledge about epidemics across scales and simulate disease dynamics. While these approaches have played a central role in studying the mechanics underlying epidemics, we lack ways to reliably predict…
Rapidly evolving viruses use antigenic drift as a key mechanism to evade host immunity and persist in real populations. While traditional models of antigenic drift and epidemic spread rely on low-dimensional antigenic spaces, genomic…
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…
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…
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 introduce a minimal multiscale framework that links within-host virus dynamics to population-level SIRS epidemiology through explicit, bidirectional coupling. At the microscopic layer, a two variant quasispecies (master and mutant…
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…
Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a…
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…
Despite being similar in structure, functioning, and size viral pathogens enjoy very different mostly well-defined ways of life. They occupy their hosts for a few days (influenza), for a few weeks (measles), or even lifelong (HCV), which…
Intrapatient HIV-1 evolution is dominated by selection on the protein level in the arms race with the adaptive immune system. When cytotoxic CD8+ T-cells or neutralizing antibodies target a new epitope, the virus often escapes via…
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…
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…
Recent studies reveal even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce…
Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an…