Complete genome sequence of Valeriana jatamansi cryptic virus 1: a novel member of the genus Alphapartitivirus infecting Valeriana jatamansi Jones

A new double-stranded RNA (dsRNA) virus, tentatively named "Valeriana jatamansi cryptic virus 1" (VJCV1, GenBank accession nos. PP482519 and PP482520), was isolated from diseased Valeriana jatamansi Jones plants exhibiting vein-banding in Yunnan. Its complete genome sequence was determined using metatranscriptomic and Sanger sequencing. The genome of VJCV1 consists of two dsRNA of different size, namely dsRNA1 (2,026 bp) and dsRNA2 (1,754 bp), which are predicted to encode an RNA-dependent RNA polymerase (RdRp, 616 aa) with molecular weight of 72.6 kDa and coat protein (CP, 491 aa) with molecular weight of 55.8 kDa, respectively. The non-coding region of dsRNA in VJCV1 is predicted to have a stem-loop structure and a poly(A) tail that are unique to the members of the genus Alphapartitivirus. Multiple sequence alignments showed that the RdRp and CP of VJCV1 shared the highest amino acid sequence identity (86.2% and 56.1%, respectively) with red clover cryptic virus 1 (RCCV1). These values are below the threshold for creating new species within the genus Alphapartitivirus. Phylogenetic analysis based on RdRp and CP sequences showed that VJCV1 clustered independently from members of the genus Alphapartitivirus, with RCCV1 being the closest relative. It is therefore suggested that VJCV1 should be considered a member of a new species of the genus Alphapartitivirus in the family Partitiviridae. This is the first report of a member of the genus Alphapartitivirus infecting a plant of the genus Valeriana.