Chikungunya virus from experimental passage

The 3’untranslated region (UTR) in alphavirus genomes functions in virus replication and plays a role in determining virus host range. Chikungunya virus (CHIKV) has the longest 3’UTR among the alphaviruses (500-700nt), and 3’UTR length and sequence structure vary substantially among different CHIKV lineages. Previous studies showed that genomic deletions and insertions are key drivers of CHIKV 3’UTR evolution. We used experimental evolution to examine CHIKV adaptation in response to a large 3’UTR deletion. We engineered a CHIKV mutant with a 258nt deletion in the 3’UTR (ΔDR1/2). This deletion reduced viral replication on mosquito cells, but did not reduce growth on mammalian cells. To examine how selective pressures from vertebrate and invertebrate hosts shape CHIKV evolution after a deletion in the 3’UTR, we passaged replicated ΔDR1/2 virus populations strictly on primate cells, strictly on mosquito cells, or with alternating primate/mosquito cell passages. We found that virus populations passaged on a single host increased in fitness relative to the ancestral deletion mutant on their selected host, and viruses that were alternately passaged improved on both hosts. Surprisingly, whole genome sequencing revealed few changes in the 3’UTR of evolved populations. Instead we identified highly convergent mutations in protein coding regions that were associated with specific hosts, but these mutations did not appear to be evolutionary responses to the 3’UTR deletion.