Molecular characterization of two positive-strand RNA viruses co-infecting a hypovirulent strain of Sclerotinia sclerotiorum

•Two novel positive-strand RNA viruses co-infect the hypovirulent strain SX247.•The full-length of two positive-strand RNA viruses are determined.•SsDRV/SX247 is a new strain of the Sclerodarnavirus SsDRV.•SsHV2/SX247 is related to hypoviruses of genus Alphahypovirus.•SsHV2/SX247 is a hypovirus that belongs to the newly proposed genus Gammahypovirus.

Two dsRNA segments, the replicative forms of two ssRNA viruses of SsHV2/SX247 (Sclerotinia sclerotiorum hypovirus 2) and SsDRV/SX247 (Sclerotinia sclerotiorum debilitation-associated RNA virus), were isolated from the hypovirulent strain SX247 of Sclerotinia sclerotiorum. SsDRV/SX247 has the highest similarities (81% aa identity) with the previously reported virus SsDRV/Ep-1PN. The genome of SsHV2/SX247 is 15,219 bp in length with a poly-A tail, and it has only one large putative open reading frame (ORF) that encodes a polyprotein containing RNA-dependent RNA polymerase (RdRp) and viral RNA helicase domains. The RdRp domain shares amino acid similarity with that of CHV1 (23%). However, the genome organization of SsHV2/SX247 is significantly different from that of CHV1 on genomic size and ORFs. We conclude that SsDRV/SX247 is a novel strain in species SsDRV of genus Sclerodarnavirus, whereas SsHV2/SX247 is a representative member of new proposed lineage Gammahypovirus in the family Hypoviridae and confers hypovirulence in its host.