The potential of RNA viruses to adapt to new environments relies on their ability to introduce changes in their genomes, which has resulted in the recent expansion of re-emergent viruses. Chikungunya virus is an important human pathogen transmitted by mosquitoes that, after 60 years of exclusive circulation in Asia and Africa, has rapidly spread in Europe and the Americas. Here, we examined the evolution of CHIKV in different hosts and uncovered host-specific requirements of the CHIKV 3’UTR. Sequence repeats are conserved at the CHIKV 3’UTR but vary in copy number among viral lineages. We found that these blocks of repeated sequences favor RNA recombination processes through copy-choice mechanism that acts concertedly with viral selection, determining the emergence of new viral variants. Functional analyses using a panel of mutant viruses indicated that opposite selective pressures in mosquito and mammalian cells impose a fitness cost during transmission that is alleviated by recombination guided by sequence repeats. Indeed, drastic changes in the frequency of viral variants with different numbers of repeats were detected during host switch. We propose that RNA recombination accelerates CHIKV adaptability, allowing the virus to overcome genetic bottlenecks within the mosquito host. These studies highlight the role of 3’UTR plasticity on CHIKV evolution, providing a new paradigm to explain the significance of sequence repetitions.

Chikungunya virus (CHIKV) is a reemerging and rapidly spreading pathogen transmitted by mosquitoes. The emergence of new epidemic variants of the virus is associated with genetic evolutionary traits, including duplication of repeated RNA elements in the 3′UTR that seemingly favor transmission by mosquitoes. The transmission potential of a given variant results from a complex interplay between virus populations and anatomical tissue barriers in the mosquito. Here, we used the wild type CHIKV Caribbean strain and an engineered mutant harboring a deletion in the 3′UTR to dissect the interactions of virus variants with the anatomical barriers that impede transmission during the replication cycle of the virus in Aedes mosquitos. Compared to the 3′UTR mutant, we observed that the wild type virus had a shorter extrinsic incubation period after an infectious blood meal and was expectorated into mosquito saliva much more efficiently. We found that high viral titers in the midgut are not sufficient to escape the midgut escape barrier. Rather, viral replication kinetics play a crucial role in determining midgut escape and transmission ability of CHIKV. Finally, competition tests in mosquitoes co-infected with wild type and mutant viruses revealed that both viruses successfully colonized the midgut, but wild type viruses effectively displaced mutant viruses during systemic infection due to their greater efficiency of escaping from the midgut into secondary tissues. Overall, our results uncover a link between CHIKV replication kinetics and the effect of bottlenecks on population diversity, as slow replicating variants are less able to overcome the midgut escape barrier. Importance It is well established that selective pressures in mosquito vectors impose population bottlenecks for arboviruses. Here, we used a CHIKV Caribbean lineage mutant carrying a deletion in the 3′UTR to study host-virus interactions in vivo in the epidemic mosquito vector, Aedes aegypti. We found that the mutant virus had a delayed replication rate in mosquitoes, which lengthened the extrinsic incubation period (EIP), and reduced fitness relative to the wild type virus. As a result, the mutant virus displayed a reduced capacity to cross anatomical barriers during the infection cycle in mosquitoes, thus reducing the virus transmission rate. Our findings show how selective pressures act on CHIKV non-coding regions to select variants with shorter EIPs that are preferentially transmitted by the mosquito vector.

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RNA viral genomes compact information into functional RNA structures. Here, using chikungunya virus as a model, we investigated the structural requirements of conserved RNA elements in the 3’ untranslated region (3’UTR) for viral replication in mosquito and mammalian cells. Using structural predictions and co-variation analysis, we identified a highly stable and conserved Y-shaped structure (SLY) at the end of the 3’UTR that is duplicated in the Asian lineage. Functional studies with mutant viruses showed that the SLY has host-specific functions during viral replication and evolution. The SLY positively modulates viral replication in mosquito cells but has the opposite effect in mammalian cells. Additional structural/functional analyses showed that maintaining the Y-shaped fold and specific nucleotides in the loop are critical for full SLY functionality and optimal viral replication in mosquito cells. Experimental adaptation of viruses with duplicated SLYs to mammalian cells resulted in the generation of heterogeneous viral populations comprising variants with diverse 3’UTRs, contrasting with the homogeneous populations from viruses without SLY copies. Altogether, our findings constitute the first evidence of an RNA secondary structure in the 3’UTR of chikungunya virus genome that plays host-dependent functions.