The complete genome of ScPV1 is comprised of two segments here named as dsRNA1 and dsRNA2, are 2352 bp and 2196 bp in length, respectively, with poly (A) tails at their 3’-termini. The 5’- untranslated region (UTR) and 3’- UTR of dsRNA1 were 84 bp and 210 bp long, respectively (Fig. 1A). Whereas 5’- and 3’- UTRs of dsRNA2 were 58 bp and 303 bp long, respectively (Fig. 1A). Alignment of the 5’- and 3’-UTR sequences of both ScPV1 dsRNAs showed that they were conservative each other (Fig. 1B). Sequence analysis revealed that both dsRNAs contain single ORF, ORF1 and ORF2 respectively.
ORF1 extends from nt position 85 to 2226, was predicted to encode a 713-aa protein with predicted molecular mass of 83 KDa (Fig. 1A). BLASTp search indicated that dsRNA1 product has the highest similarities with RdRps of Partitiviridae family members particularly with Plasmopara viticola associated Partitivirus 7 (GenBank accession number QHD64796.1; E value = 2e-142, 98% Query coverage and 47% Percent identity). A Conserved Domain Database (CDD) search showed that RdRp contains a conserved viral RdRp domain (RT_like super family, cl02808). Multiple sequence alignment of RdRps based amino acid sequences of ScPV1 and other related viruses indicated six conserved motifs (III-VIII) (Fig. 2A). ORF2 begins from 59 bp and ends at 1951 bp, encoding a 630-aa protein with calculated molecular mass of 71 KDa (Fig. 1A). A BLASTp search indicated that this protein was most closely related to the CP of Plasmopara viticola associated Partitivirus 7, with 33% aa sequence identity of (E value 1e-109; 96% Query coverage). In addition, multiple sequence alignment based on coat proteins of ScPV1 and other closely related members of Partitiviridae also showed conservation of few regions (Fig. S1A).
The phylogenetic analysis based on RdRp (Fig. 2B) and CP (Fig. S1B) sequences showed that ScPV1 grouped with members of genus Betapartitivirus. Selected members of family Partitiviridae were divided into four recognized genera (Alphapartitivirus, Betapartitivirus, Gammapartitivirus, and Deltapartitivirus) and two proposed genera (Epsilonpartitivirus and Zetapartitivirus) (Fig. 2B) (Fig. S1B). Therefore, ScpV1 can be considered a new member of the genus Betapartitivirus