Characterization of a divergent isolate of rice stripe virus from volunteer durum wheat in France

A highly divergent isolate of rice stripe virus (RSV, Tenuivirus oryzaclavatae) was identified by high-throughput sequencing (HTS) of volunteer durum wheat (Triticum turgidum subsp. durum (Desf.) Husn.) plants collected in summer 2023 in Loir-et-Cher (France). The complete sequence of all four genomic RNAs was obtained from a single plant, showing a genomic organization similar to that of known RSV isolates but with significant indel polymorphism in non-coding regions. Genomic RNAs showed between 81.6% (RNA4) and 88.3% (RNA3) nucleotide identity with RSV reference isolates, while encoded proteins showed between 86.3% (NSvc2) and 97.4% (L and NSvc4 (movement protein)) with those of the reference RSV isolate. The 97.4% identity in the L protein should be compared with the average pairwise identity of 99.0% +/- 0.1% among all RSV isolates present in GenBank, as well as with the ICTV species demarcation threshold of 5% divergence. This demonstrates that the French wheat variant is indeed an RSV isolate but a highly divergent one, which questions our current understanding of RSV geographic distribution, diversity and evolution history.