Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants

Abstract

Many viruses, including human norovirus and influenza, cause self-limiting diseases of short duration. However, infection by the same viruses in an immunocompromised host can result in prolonged illness in the absence of effective treatment. Such persistent infections are often characterized by increased genetic diversity with potentially elevated rates of evolution compared to acute infections, leading to suggestions that immunocompromised hosts represent an important reservoir for the emergence of novel viral variants. Here, we develop a mathematical model that combines epidemiological dynamics with within-host evolution to quantify the relative contribution of immunocompromised hosts to t..