Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster

This collection contains the data underlying Chapter 2 of the PhD thesis “On the fly: Host Determinants of RNA Virus Evolution” and the associated publication “Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster” (Virus Evolution, 2023). The study investigated how modulation of the antiviral RNA interference (RNAi) pathway influences RNA virus evolution in Drosophila melanogaster. Drosophila C virus (DCV) was serially passaged for ten generations (P1 to P10) in wild-type flies (WT), Dicer-2 knockout flies (KO), and flies overexpressing Dicer-2 (OE). Viral populations were propagated in five independent replicate lineages and analyzed to characterize adaptation to different host immune backgrounds. The collection contains the raw experimental measurements and processed datasets used to generate the figures and supplementary figures presented in the manuscript. These include measurements of viral titers obtained during the experimental evolution study, mortality data from survival assays, RT-qPCR data used to quantify viral RNA accumulation in flies and cell culture, and next-generation sequencing data used to characterize genetic diversity in evolving virus populations. The collection further contains processed datasets describing single-nucleotide variant frequencies, deletion frequencies in homopolymeric regions, and structural analyses of adaptive mutations in the viral capsid protein VP3. The data were collected to investigate the role of antiviral RNAi in shaping RNA virus evolution and adaptation. The datasets document the phenotypic and genetic changes that occurred during serial virus passage in hosts with differing RNAi activity and can be used to reproduce the analyses reported in the manuscript. Raw sequencing data associated with this study have been deposited in NCBI BioProject PRJNA993483. The files deposited here contain the experimental measurements and processed data underlying the results, statistical analyses, tables, and graphical representations reported in Chapter 2.