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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…
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…
Ecology and evolution under changing environments are important in many subfields of biology with implications for medicine. Here, we explore an example: the consequences of fluctuating environments on the emergence of antibiotic…
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.…
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…
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…
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…
RNA viruses exist in large intra-host populations which display great genotypic and phenotypic diversity. We analyze a model of viral competition between two different viral strains infecting a constantly replenished cell pool, in which we…
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,…
We study the competition and the evolution of nodes embedded in Euclidean restricted spaces. The population evolves by a branching process in which new nodes are generated when up to two new nodes are attached to the previous ones at each…
The emergence of mutant lineages within a viral species has become a public health problem, as the existing treatments and drugs are usually more effective on the original lineages than in the mutant ones. The following manuscript presents…
Different pathogens spreading in the same host population often generate complex co-circulation dynamics because of the many possible interactions between the pathogens and the host immune system, the host life cycle, and the space…
Competition within the immune system may degrade immune control of viral infections. We formalize the evolution that occurs in both HIV-1 and the immune system quasispecies. Inclusion of competition in the immune system leads to a novel…
Computer infections such as viruses and worms spread over networks of contacts between computers, with different types of networks being exploited by different types of infections. Here we analyze the structures of several of these…
The temporal dynamics of social interactions were shown to influence the spread of disease. Here, we model the conditions of progression and competition for several viral strains, exploring various levels of cross-immunity over temporal…
We propose a type-dependent branching model with mutation and competition for modeling phylogenies of a virus population. The competition kernel depends for any two virus particles on the particles' types, the total mass of the population…
This study investigates the role of spatial segregation, prompted by competition avoidance, as a key mechanism for emergent coexistence within microbial communities. Recognizing these communities as complex adaptive systems, we challenge…
We consider a discrete-time host-parasite model for a population of cells which are colonized by proliferating parasites. The cell population grows like an ordinary Galton-Watson process, but in reflection of real biological settings the…
We study the population dynamics of lytic viruses which replicate slowly in dividing host cells within an organism or cell culture, and find a range of viral replication rates that allows viruses to persist, avoiding extinction of host…
Spatially explicit models have been widely used in today's mathematical ecology and epidemiology to study persistence and extinction of populations as well as their spatial patterns. Here we extend the earlier work--static dispersal between…