Changes in intra-host mycovirus population diversity after vertical and horizontal transmission

The remarkable speed at which viral populations mutate allows them to evolve quickly, so that the viral diversity can change, especially when the virus is transmitted, i.e. its population goes through a bottleneck. Our experiments assessed the diversity of the intra-host populations of a mycovirus Cryphonectria hypovirus 1 (CHV1), a natural biocontrol agent of chestnut blight disease, using PacBio long-read HiFi sequencing. The intra-host viral population diversity before and after either vertical or horizontal transmission was estimated using two metrics-nucleotide (mutational) diversity measured as π, and viral variant diversity measured as Nei's H. A significant bottleneck effect, demonstrated by the decline of the mutational diversity (π), was observed after vertical transmission of prototypical viral populations into conidia, in both investigated viral subtypes, French 1 (F1) and Italian (I). In contrast, the number of viral variants was significantly reduced after the vertical transmission of subtype I but increased for the subtype F1. In newly isolated fungal strains infected with CHV1 subtype I, fewer viral variants were vertically transferred into conidia, relative to the prototypical laboratory isolates, i.e. the average number of transmitted viral variants was smaller. In the horizontal viral transmission assays, the number of transmitted viral variants was closely linked to the genotype of the fungal host at the vegetative compatibility loci. Specifically, recipient viral populations' diversity was greater when the alleles at loci vic2 and vic3 were the same in the donor and recipient fungal isolate, relative to when they were different. Heteroallelism at the vic4 locus had no impact on viral populations' diversity. Despite the strong bottlenecks, purifying selection shaped the diversity of intra-host CHV1 populations. In both transmission experiments on average, synonymous mutational diversity was higher than non-synonymous, across all replicates. Signs of positive selection or mutation accumulations, inferred by a surplus of nonsynonymous mutations, were less common and mostly observed during vertical transmission experiments, i.e. in new viral populations arising from conidia.