# Complete genome sequence and characterisation of a novel flexivirus infecting the necrotrophic conifer pathogen Diplodia sapinea

## TL;DR

Scientists discovered a new virus infecting a conifer pathogen fungus in Finland and characterized its genome.

## Contribution

This is the first report of a positive-sense RNA virus infecting Diplodia sapinea, expanding viral diversity in fungal pathogens.

## Key findings

- DsFLV1 has a 7,494-nucleotide RNA genome with replication-associated polyprotein domains.
- Phylogenetic analysis placed DsFLV1 in the Deltaflexiviridae family, close to Erysiphe necator-associated flexivirus 2.
- The virus encodes a capsid protein and three putative proteins with unknown functions.

## Abstract

Using total RNA sequencing, we detected a novel RNA virus infecting a Finnish isolate of the fungal conifer pathogen Diplodia sapinea, and its genome sequence was verified by Sanger sequencing. This virus, which we have named "Diplodia sapinea flexi-like virus 1" (DsFLV1), has a 7,494-nucleotide-long positive-sense single-stranded RNA genome, excluding the poly(A) tail. The largest open reading frame (ORF1) encodes a replication-associated polyprotein (RP) that contains conserved domains characteristic of members of the order Tymovirales, including viral methyltransferase (Mtr), viral helicase (Hel), and RNA-dependent RNA polymerase (RdRP) domains. Four smaller ORFs were also identified. ORF2 potentially encodes a capsid protein, while the other three ORFs, initiated by alternative start codons, encode putative proteins with unknown functions. Phylogenetic analysis placed DsFLV1 in a distinct clade within the family Deltaflexiviridae, close to Erysiphe necator-associated flexivirus 2. This is the first report of a positive-sense single-stranded RNA virus infecting D. sapinea.

The online version contains supplementary material available at 10.1007/s00705-025-06313-6.