Genomic sequence of a novel endornavirus from Phaseolus vulgaris and occurrence in mixed infections with two other endornaviruses

The Endornaviridae family includes viruses with ssRNA genome that infect plants, fungi, and oomycetes. Plant endornaviruses do not cause visible symptoms and are transmitted only vertically. Many common bean (Phaseolus vulgaris) genotypes have been reported to be infected by Phaseolus vulgaris endornavirus 1 and Phaseolus vulgaris endornavirus 2. Using next-generation sequencing, we obtained the RNA sequence of a third common bean endornavirus, which we named Phaseolus vulgaris endornavirus 3 (PvEV3). The complete sequence consisted of 15,205nt in length with a single open reading frame (ORF) coding for a polyprotein of 4932 aa, and untranslated regions of 344ont and 628ont at the 5' and 3' ends respectively. The polyprotein contained conserved protein domains including viral helicase 1, peptidase C97, glycosyltransferases of the GTB-type, and RdRp 2. The polyprotein shared 31% amino acid identity with the counterpart encoded by Hordeum vulgare endornavirus. A phylogenetic tree constructed with the RdRp sequences of PvEV3 and other endornaviruses placed PvEV3 in a Glade with members of the genus Alphaendornavirus. PvEV3 was detected in cultivated and wild P. vulgaris genotypes as single and mixed infections with two other common bean endornaviruses. The natural occurrence of three distinct endornaviruses in a single plant species is unique and has not been reported in other plant-endornavirus systems.