Coevolutionary dynamics in the immune system

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 engaging in a coevolutionary arms race with the adaptive immune system: The B-cell receptors in the adaptive immune system diversify to neutralize the virus and HIV evolves to evade the immune response. While it is clear that HIV exerts strong selection on the adaptive immune system, the modes of immune response are still unknown. Here I introduce a non-equilibrium framework to characterize the rapid coevolution of immune cells and pathogens. By tracing the immune repertoire of HIV patients over time and reconstructing the history of the accumulated mutations within patients, I show evidence for strong co-adaptation of the immune repertoire and HIV. I argue that rapid affinity maturation of the immune system upon viral expansion and a quasi-stationary response during chronic infection characterize the B-cell response to HIV.