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In this paper we study intra-host viral adaptation by antigenic cooperation -a mechanism of immune escape that serves as an alternative to the standardmechanism of escape by continuous genomic diversification and allows to explaina number of experimental observations associated with the establishment ofchronic infections by highly mutable viruses. Within this mechanism, thetopology of a cross-immunoreactivity network forces intra-host viral variantsto specialize for complementary roles and adapt to host's immune response as aquasi-social ecosystem. Here we study dynamical changes in immune adaptationcaused by evolutionary and epidemiological events. First, we show that theemergence of a viral variant with altered antigenic features may result in arapid re-arrangement of the viral ecosystem and a change in the roles played byexisting viral variants. In particular, it may push the population under immuneescape by genomic diversification towards the stable state of adaptation byantigenic cooperation. Next, we study the effect of a viral transmissionbetween two chronically infected hosts, which results in merging of twointra-host viral populations in the state of stable immune-adapted equilibrium.In this case, we also describe how the newly formed viral population adapts tothe host's environment by changing the functions of its members. The resultsare obtained analytically for minimal cross-immunoreactivity networks andnumerically for larger populations.

Antigenic cooperation in Viral Populations: Transformation of Functions of Intra-Host Viral Variants