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Many viruses and bacteria are known to evolve rapidly over the course of an infection. However, epidemiological studies generally assume that within-host evolution is an instantaneous process. We argue that the dynamics of within-host evolution has implications at the within-host and at the between-host levels. We first show that epidemiologists should consider within-host evolution, notably because...
Over the course of infection, the coreceptor usage of the HIV virus changes from a preference for CCR5 to a preference for CXCR4 in ∼50% of infected individuals. The change in coreceptor usage is the result of the complex interaction of the viral population with various cell populations of the immune system. Although many of the molecular processes involved in viral attachment and entry have been...
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