Chikungunya virus (CHIKV) is a re-emerging global health threat that produces debilitating arthritis in people. Like other RNA viruses with high mutation rates, CHIKV produces populations of genetically diverse genomes within a host. While several known CHIKV mutations influence disease severity in vertebrates and transmission by mosquitoes, the role of intrahost diversity in chikungunya arthritic disease is not studied. In this study, high and low fidelity CHIKV variants, previously characterized by altered in vitro population mutation frequencies, were used to evaluate how intrahost diversity influences clinical disease, CHIKV replication, and antibody neutralization in immunocompetent adult mice inoculated in the rear footpads. Both high and low fidelity mutations were hypothesized to attenuate CHIKV arthritic disease, replication, and neutralizing antibody levels compared to wildtype (WT) CHIKV. Unexpectedly, high fidelity mutants elicited more severe arthritic disease than WT despite comparable CHIKV replication, whereas a low fidelity mutant produces attenuated disease and replication. Serum antibody developed against both high and low fidelity CHIKV exhibited reduced neutralization of WT CHIKV. Using next-generation sequencing NGS), the high fidelity mutations were demonstrated to be genetically stable, but produce more genetically diverse populations than WT CHIKV in mice. This enhanced diversification was subsequently reproduced after serial in vitro passage. The NGS results contrast with previously reported population diversities for fidelity variants, which focused mainly on part of the E1 gene, and highlight the need for direct measurements of mutation rates to clarify CHIKV fidelity phenotypes. [ABSTRACT FROM AUTHOR]