Identification of a novel phenuivirus with an unusual ambisense genome from the ascomycete fungus Fusarium fujikuroi

Abstract

A novel virus, tentatively named “Fusarium fujikuroi negative-strand RNA virus 1” (FfNSRV1), was identified in a Fusarium fujikuroi strain isolated from a small brown planthopper. The FfNSRV1 genome consists of three negative-sense, single-stranded RNA segments (RNA1-3) with lengths of 6649, 1609, and 1380 nt, respectively. The viral complementary (vc) strand (positive sense) of RNA1 encodes a large protein (∼252 kDa) containing a conserved domain of the bunyavirus RNA-dependent RNA polymerase (RdRP) superfamily, with the highest sequence similarity (40-44% identity) to the RdRPs encoded by established members of the genus Coguvirus in the family Phenuiviridae. The RNA2 vc strand encodes a protein (∼54 kDa) showing sequence similarity (38-40% identity) to the movement protein-like (MP-L) proteins of coguviruses. The RNA3 vc strand encodes a protein (∼44 kDa) with a conserved domain of the phenuivirid nucleocapsid protein superfamily. Interestingly, the RNA2 and RNA3 segments (negative sense) each also contain an open reading frame (ORF) that overlaps with the ORF in the vc strand. The protein encoded by the RNA2 negative-strand ORF shows a low degree of sequence similarity (23-30% identity) to the MP-L proteins of unassigned phenuiviruses, and the protein encoded by the RNA3 negative-strand ORF shows a low degree of similarity (26-29% identity) to the nucleocapsid proteins of established members of the genus Bocivirus in the family Phenuiviridae. Phylogenetic analysis based on RdRP sequences showed that FfNSRV1 clustered with coguviruses, but in a separate monophyletic clade. Our results suggest that FfNSRV1 should be placed in a new genus within the family Phenuiviridae due to its unusual tripartite ambisense genome organization.