I worked on the faba bean necrotic stunt virus (FBNSV), a multipartite plant virus (nanovirus) composed of eight genomic segments, each of them containing one gene, and being encapsidated independently. Multipartite viruses are fascinating since nobody really understand how such organism can survive and be maintained. A central question is: what is the selective advantage for these viruses, of spliting their genomes and pack their genes in independant capsids? Previous to my arrival, the team has observed that the relative frequencies of FBNSV genomic segments vary from one host species to another, and that this pattern is consistent across replicates. This phenomenon was called: the genomic formula. One of my input in this project was to show that such a genomic structure provides a high level of genomic plasticity, allowing the regulation of gene expression by the modulation of the gene copy number within the host. Thus, FBNSV can adapt to various host environments without any point mutations (submitted article). This step involved the deep sequencing of 20 parallel viral populations, before and after transmission. In order to make evaluate the size of the viral populations we were sequencing, we also developed a technique estimating the number of molecules that were sequenced. During this project, I also measured the bottleneck undergone by the virus during a plant-to-plant transmission, which was surprisingly small.

Overall, the functioning of FBNSV and more specifically the plasticity of its genome composition modulated by the genomic formula question the nature of this organism. Should we consider that the eight genomic segments constitute a single viral species, or should we consider that each capsid containing one FBNSV gene is a very specialized virus, and that all capsids compose a viral microbiota. More investigations are required to answer this fascinating question.