Complete genome sequence analysis of Paris alphapartitivirus 1: a novel member of the genus Alphapartitivirus infecting Paris polyphylla var. yunnanensis

A novel double-stranded RNA (dsRNA) virus, tentatively named “Paris alphapartitivirus 1” (ParAPV1, OL960006-OL960007), was detected in Paris polyphylla var. yunnanensis plants exhibiting leaf chlorosis and shrinkage symptoms in Yunnan. Its complete genome sequence was determined using Illumina and Sanger sequencing. ParAPV1 has a bipartite genome that consists of dsRNA1 (1,917 bp) encoding the viral RNA-dependent RNA polymerase (RdRp), and dsRNA2 (1,818 bp) encoding the putative coat protein (CP). Sequence comparisons showed that the RdRp and CP of ParAPV1 are most similar to those of pear alphapartitivirus (PpPV2), with 69.97% and 54.21% amino acid sequence identities respectively. Phylogenetic analysis of the RdRp amino acid sequences of ParAPV1 and other partitiviruses showed that ParAPV1 cluster with viruses in a clade containing alphapartitiviruses, and that its closest known relatives are PpPV2 (BBA66577) and rose partitivirus (RoPV, ANQ45203S). Taken together, these results suggest that ParAPV1 should be regarded as a new member of genus Alphapartitivirus in the family Partitiviridae. This is the first report of a partitivirus infecting P. polyphylla var. yunnanensis.