Interpreting pathogen genetic diversity during measles epidemics

While measles remains endemic in parts of the world, efforts to eliminate measles transmission continue, and viral sequence data may shed light on progress towards these goals. Genetic diversity has been used as a proxy for disease prevalence; however, seasonally-driven disease dynamics are typically characterized by deep population bottlenecks between epidemics, which severely disrupt the genetic signal. Here, we simulate measles metapopulation dynamics, and show that it is the population bottleneck, rather than epidemic size, which plays the largest role in observed pathogen diversity. While high levels of vaccination greatly reduces measles diversity, paradoxically, diversity increases with intermediate levels of vaccination, despite reducing incidence. We examined diversity and incidence using published data to compare our simulated outcomes with real observations, finding a significant relationship between harmonic mean incidence and genetic diversity. Our study demonstrates that caution should be taken when interpreting pathogen diversity, particularly for short-term, local dynamics.