Sequence properties
The complete genome of NsFV2 is 6,156 nt long, excluding the polyA tail, with a G + C content of 54%. The genome contains two ORFs (ORF1 and 2), the lengths of the 5’ and 3’ untranslated regions (UTRs) are 83 nt and 87 nt, respectively (Fig. 1a). The NsFV2 genome schematic diagram is shown in Fig. 1a. The ORF1 encodes a large polypeptide of 1,509 aa with a molecular mass of 169.73 KDa, and ORF2 encodes a small ploypeptide of 483 aa with a molecular mass of 52.84 KDa, respectively (Fig. 1a). A conserved domain search of the NCBI database revealed an RdRp domain from aa position 470 to 702 (accession, cl40470; E-value, 1.35e− 23) and a helicase domain at aa positions 1026–1306 (accession, cl34083; E-value, 1.46e− 07) were identified in the ORF1-encoded ploypeptide, as described in the RdRps of other fusariviruses [21,22]. In addition, a chromosome segregation protein SMC domain at aa position 67–230 (accession, cl37069; E-value, 7.11e− 04) was identified in the ORF2-encoded polypeptide. BLASTp results showed that the ORF1-encoded polyprotein of NsFV2 had the highest similarity to those of Nigrospora sphaerica fusarivirus 1 (100% query cover; 68.48% identity), Gaeumannomyces tritici fusarivirus 1 (96% query cover; 49.01% identity) and Plasmopara viticola lesion associated fusarivirus 2 (95% query cover; 40.37% identity), respectively. However, a BLASTp search of ORF2-encoded polypetide revealed only three similar proteins, all of which were fusarivirus proteins (Table 1). It is noteworthy that the NsFV2 and NsFV1 isolates were from different host, i.e.,Nigrospora sphaerica strains isolated from tea plants and peper plant, respectively[18].
Table 1
Comparison of the ORF1 and ORF2 sequences of NsFV2 with those of other fusariviruses with BLASTp search
| Virus name | query cover(%) | E- value | Identity(%) | Accession number |
ORF1 | Nigrospora sphaerica fusarivirus 1 | 100 | 0.0 | 68.48 | UBK24763.1 |
Gaeumannomyces tritici fusarivirus 1 | 96 | 0.0 | 49.01 | AZT88652.1 |
Plasmopara viticola lesion associated fusarivirus 2 | 95 | 0.0 | 40.37 | YP_010800287.1 |
Penicillium aurantiogriseum fusarivirus 1 | 97 | 0.0 | 38.56 | YP_009182154.1 |
Zymoseptoria tritici fusarivirus 1 | 85 | 0.0 | 39.65 | YP_010799569.1 |
Monilinia fructicola fusarivirus 3 | 89 | 0.0 | 36.44 | UTQ48847.1 |
Sclerotinia sclerotiorum fusarivirus 2 | 99 | 0.0 | 35.19 | QUE49153.1 |
Botrytis cinerea fusarivirus 6 | 85 | 0.0 | 37.94 | QJT73721.1 |
ORF2 | Nigrospora sphaerica fusarivirus 1 | 84 | 9e−98 | 44.26 | UBK24764.1 |
Phomopsis asparagi Fusarivirus 1 | 80 | 1e−65 | 38.78 | WQB68776.1 |
Gaeumannomyces tritici fusarivirus 1 | 88 | 8e−35 | 29.16 | AZT88653.1 |
A multiple aa sequence alignment of the RdRp domains of NsFV2 and six other fusariviruses showed that eight conserved motifs were found in the conserved RdRp domains (Fig. 1b). Furthermore, a GDD tripeptide (the hallmark of most viral RdRps) was found within the RdRp domain of NsFV2, similar to other fusariviruses (Fig. 1b). Phylogenetic analysis based on the ORF1-encoded polyprotein containing the RdRp and RNA helicase (Hel) domains indicated that NsFV2 clustered closely with NsFV1 in a separate branch within the genus Alphafusarivirus of the family Fusariviridae. In conclusion, NsFV2 has the typical characteristics of a fusarivirus.
According to a report by the International Committee on Taxonomy of Viruses (ICTV, https://talk.ictvonline.org/), the species demarcation threshold for fusariviruses is less than 80% identity in the ORF1-encoded protein. Therefore, based on the sequence similarity, genome organization, and phylogenetic analysis, we suggest that NsFV2 should be considered as a member of a new species in the genus Alphafusarivirus, family Fusariviridae.