RNA recombination allows chikungunya virus to overcome barriers imposed during mosquito transmission

MERWAISS, FERNANDO; FILOMATORI CLAUDIA V.; SALEH, MARÍA CARLA; BARDOSSY, EUGENIA S.; ALVAREZ, DIEGO E.

Killarney

Simposio; Keystone Symposia conference on positive-strand RNA viruses; 2019

Chikungunya virus is a mosquito-borne alphavirus. The emerging lineages of chikungunya virus that have caused the recent epidemicsin the Indian Ocean and the Americas have originated from ancient African and Asian isolates. Notably, these new lineages have fixed mutations in the coding sequence and large variations in the 3´UTR. As a result, these chikungunya lineages feature 3´UTRs carrying different copy numbers of conserved sequence blocks referred to as direct repeats. Using co-transfections of recombinant marked genomes in mammalian and mosquito cell lines, we showed that virus passaging results in the generation of new 3´UTR variants of chikungunya virus through copy-choice RNA recombination by template switching. In addition, we found a positive correlation between the number of direct repeats and virus fitness in mosquito cells. To study the relevance of this mechanism in vivo, we infected laboratory mosquito colonies with wild type chikungunya virus and a deletion mutant that exhibits a markedly delayed replication in cultured mosquito cells. Virus fitness was assessed by virus titration and sequencing of virus RNAs isolated from infected mosquitoes. We observed that recombination occurs in vivo giving raise to new 3´UTR variants of chikungunya virus. Indeed, in mosquitoes infected with the mutant virus, we isolated variants that had introduced duplications of the direct repeats at the 3´UTR. These variants displayed higher fitness and were selected in mosquitoes, highlighting the relevance of recombination for host adaptation. Altogether, our data show for the first time the ability of chikungunya virus to recombine in vivo and provide insight into the mechanisms that originated the re-emergent variants of the epidemic virus. We propose a model for chikungunya virus transmission where RNA recombination accounts for the ability of the virus to rapidly adapt after population bottlenecks imposed during host switch.