Maturation, selection and response in immune repertoires

One of the feats of adaptive immunity is its ability to recognize foreign pathogens while sparing the self. During maturation in the thymus, T cells are selected through the binding properties of their antigen-specific T-cell receptor (TCR), through the elimination of both weakly (positive selection) and strongly (negative selection) self-reactive receptors. I will present the results of a search for eliminated motifs and how they can be interpreted from a quorum sensing perspective. At the population scales, the repertoires of many hosts drive the evolution of viruses. I will present a framework of coevolution between immune systems and viruses in a finite-dimensional antigenic space, which describes the cross-reactivity of viral strains and immune systems primed by previous infections. I will show the emergence of an antigenic wave that is pushed forward and canalized by cross-reactivity. I will discuss the results in the context of the observed antigenic turnover of influenza strains, and we discuss how the dimensionality of antigenic space impacts the predictability of the evolutionary dynamics.