Intra-host evolution of cell-fusing agent virus following acute infection in <i>Aedes aegypti</i> mosquito

While intra-host evolution of arboviruses in mosquitoes has been documented, studies of insect-specific viruses (ISVs) remain limited. This study examines evolutionary patterns [i.e. evolutionary process, mutational types (synonymous/nonsynonymous)] of the cell-fusing agent virus (CFAV), an ISV that infects adult <i>Aedes aegypti</i>, over a period of 21 days post-infection (dpi), with a focus on the relationship between viral population dynamics and genetic diversity. High-throughput sequencing of amplification products covering the entire viral genome revealed a significant positive correlation of CFAV genetic diversity with viral population size and natural selection ([Formula: see text]/[Formula: see text]). Notably, diversity for both synonymous and nonsynonymous single nucleotide variant (SNV) sites displayed a positive correlation with population size and natural selection suggesting that genetic drift and purifying selection contribute to the overall outcome of genetic diversity. Additionally, we confirmed that smaller viral population sizes lead to greater temporal changes in genetic structure, particularly evident between Day 1 dpi and Day 3 dpi when genetic drift was most pronounced. We found that non-structural (NS) genes accumulated a higher frequency of synonymous SNV sites than structural genes, likely due to reduced selection pressure acting on NS genes. In contrast, structural genes, particularly the E gene, are likely to exhibit strong selective pressure, as indicated by a significant frequency of nonsynonymous SNV sites. Overall, this study elucidated the evolutionary patterns of CFAV, highlighting the roles of reduced genetic drift as influenced by population size and purifying selection in shaping the overall genetic diversity-and possibly adaptive evolution within structural genes, such as the E gene.