Complete genome sequence of a novel alternavirus infecting the fungus Ilyonectria crassa

A novel dsRNA mycovirus named Ilyonectria crassa alternavirus 1 (IcAV1) was found in Ilyonectria crassa isolate NW-FVA 1829. The fungus was isolated from an ash (Fraxinus excelsior L.) necrotic trunk disc infected with Hymenoscyphus fraxineus [(T. Kowalski) Baral, Queloz, Hosoya] causing ash dieback. The complete genome of IcAV1 is composed of three segments, each containing a single ORF on the positive-sense RNA. The extreme 5’ UTRs of dsRNA 1 (3604 bp), dsRNA 2 (2547 bp), and dsRNA 3 (2518 bp) share a conserved hexadecamer sequence (5’-GGCTGTGTGTTTAGTT-3’) and are capped. The 3’ UTRs are polyadenylated. In silico analysis showed that the viral RdRP is encoded on dsRNA 1 and the capsid-protein subunits are encoded on dsRNA 3. Maximum-likelihood analysis of the aa sequence of the viral RdRP showed that IcAV1 clusters with alternaviruses from Fusarium spp., while the type member of the proposed family "Alternaviridae", Alternaria alternata virus 1 (AaV1), formed a clade together with Stemphylium lycopersici mycovirus (SlV). The function of the protein encoded on segment 2 is unknown. Based on its genome organization and its phylogenetic position, IcAV1 is suggested to be a new member of the proposed family "Alternaviridae". This is the first report of a mycovirus infecting I. crassa. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00705-022-05652-y.