Multipartite BNYVV regulates its genome formula differentially during host infection and vector transmission

Beet necrotic yellow vein virus (BNYVV) is a soil-borne virus, transmitted by Polymyxa betae. BNYVV is a multipartite virus containing four or five genomic RNAs depending on the isolates, which are encapsidated in separate viral particles. The relative frequencies of all genomic segments of a multipartite virus pooled to an equilibrium value in a given environment is termed the set-point genome formula (SGF). Multipartite viruses can regulate the expression level of viral genes in different environments, and the gene expression may depend on SGF. Here, we investigate the relative frequency of the four genomic RNAs of BNYVV (B type) in leaves and roots of four different host plants and in two stages of the vector P. betae by a validated protocol of two-step reverse transcriptase droplet digital PCR (RT-ddPCR). Our results show that BNYVV genome formula reaches a different setpoint in distinct host plant species and organs with some viral genomic segments accumulate at low frequency, whereas others dominate. Moreover, the vector P. betae has a limited effect on the accumulation of BNYVV genomic RNAs in the host. We characterized as well the BNYVV SGF within zoospores and resting spores of P. betae taking into account contamination issued from infected Beta vulgaris roots. Results show the virus reaches a dedicated SGF also in each of the two stages of P. betae life cycle. Furthermore, the viral load in zoospores was significantly higher than in resting spores.