Genetic variants of the chikungunya virus

Abstract

Chikungunya virus is a mosquito-borne human pathogen and therefore must develop strategies to replicate in these two different hosts. It achieves this because its RNA genome is very prone to incorporating changes. Recombination by mould change occurs with high frequency during the synthesis of the viral genome. In this process, the viral polymerase dissociates from the template and reassociates in a second molecule to continue the synthesis of the genome. This strategy allows the virus togenerate a collection of variants that make up the viral population.Using reverse genetics experiments, we demonstrated that there are opposing requirements for viral replication in mosquito and mammalian cells. As a consequence, different viral variants are selected in each host.To understand the mechanism of recombination, we sequenced the viral variants and identified the RNA motifs that promote template switching. This mechanism occurs most frequently in regions of the viral genome where repeated sequences and structured RNA elements are present.Based on these findings, we proposed a model in which RNA recombination allows the chikungunya virus to change its genome to overcome species-specific barriers and be transmitted in nature.