Experimentally mimicking long term infections of Magallana gigas with the OsHV-1 virus reveals evolution through positive selection

This project was developed to investigate the genomic evolution and selection dynamics of OsHV-1 µVar during experimental infections in oyster populations. The accompanying R scripts implement a complete workflow from statistical analysis of mortality and viral load across generations, to de novo genome assembly, variant calling, and detailed intra-individual Single Nucleotide Variant (iSNV) analyses. The code enables reproducible reconstruction of viral consensus genomes, identification of genomic variability, analysis of substitution patterns, principal component analyses for population structure, detection of selection signatures, and visualization of genotype frequencies using Muller plots. This workflow is designed for large-scale genomic datasets and allows researchers to track viral evolution across host populations and generations. All raw sequencing data are publicly available in NCBI SRA under Bioproject PRJNA1216400, This framework can be applied to study evolutionary dynamics, viral adaptation, and population genomics in other pathogen-host systems.