Enhanced Molecular Surveillance of Chikungunya Virus

Abstract

The life cycle of arboviruses relies on efficient infection of and transmission by arthropod vectors. Adaptation to new vectors can thus dramatically increase the geographic range of an arbovirus. Several adaptive mutations enhance chikungunya virus (CHIKV) transmissibility by different mosquito species. The appearance of those adaptive mutations has led to large-scale CHIKV outbreaks in Asia, Africa, and Europe. Molecular surveillance of circulating CHIKV strains for adaptive mutations contributes to precise risk assessments and efficient vector control and provides new insight into the evolution of vector adaptation. Existing assays for molecular CHIKV surveillance are limited by poor coverage of known adaptive mutations, low sensitivity, and cost-intensive deep sequencing approaches, preventing universal application. We developed two highly sensitive nested RT-PCR assays that cover hot spots of vector adaptation in CHIKV envelope domains. The new assays allow unprecedented molecular surveillance across all CHIKV genotypes and diagnostic use in resource-limited settings globally.