Deciphering the intra-host genetic diversity of Barley yellow dwarf virus (BYDV)

High-throughput sequencing (HTS) technologies allow researchers to gain access to the complexity of the within-host virus population with an unprecedented resolution. While de novo consensus sequences have been extensively used to describe the virus population, more accurate methods, which identify the different viral molecules infecting the host, could be used to better understand the actual variability of viral genomes. In this study, we propose and apply a framework allowing a robust characterization of the within-host virus population. We performed an experimental evolution of Barley yellow dwarf virus (BYDV) to study its adaptation to four Poaceae species (wheat, oat, two-row and six-row barleys). An initial inoculum composed of a mix of BYDV-PAV and BYDV-PAS species infecting wheat was used. After four months of evolution (4 passages from plant to plant), the fitness of the final viral populations was estimated and the complete viral genomes were sequenced through HTS in the different populations.