Intrahost population dynamics of chikungunya virus in humans and naturally infected Aedes mosquitoes

RNA viruses are characterized by high mutation rates due to the lack of proofreading activity in their RNA polymerases, a feature that drives genetic diversity. Arboviruses, which alternate between vertebrate and invertebrate hosts, are subjected to host specific selective pressures and population bottlenecks, particularly within mosquito vectors. Although experimental studies have elucidated aspects of their evolutionary dynamics, data from naturally infected vectors remain limited. Here, we investigated the intrahost genetic diversity of chikungunya virus through whole genome sequencing of 19 human and 19 mosquito derived genomes from 2023 and 2024 outbreak in Sao Jose do Rio Preto, Brazil.