Molecular and biological characterization of infectious full- length cDNA clones of two viruses in Paris yunnanensis, including a novel potyvirus

Abstract Paris yunnanensis, also named as Rhizoma Paridis in the Chinese Pharmacopeia, is a perennial Chinese medicinal herb commonly grown in Southwest China. In recent years, this plant has been found to be infected with many viruses. Using high-throughput sequencing (HTS) and Sanger sequencing, we obtained the complete genome sequences of three capillovirus isolates and one potyvirus isolate. Genomic and phylogenetic analysis results revealed that these three capillovirus isolates and the Paris polyphylla chlorotic mottle virus, a newly reported capillovirus, are the same virus belonging to the genus Capillovirus. The newly found potyvirus isolate shares 52.4-68.9% nucleotide sequence identity with other known potyviruses and thus, is grouped into the bean common mosaic virus subgroup. Based on the nucleotide sequence identity, we consider this virus is a novel potyvirus species and name Paris potyvirus 5 (ParPV-5) as its common virus name, Potyvirus shilinense as its species name. To characterize their biological features, two infectious clones, representing the two viruses, have been constructed through homologous recombination or yeast homologous recombination, respectively. Agrobacterium-mediated inoculation assay results showed that the Paris polyphylla chlorotic mottle virus (PpCMV) can infect P. yunnanensis, Nicotiana benthamiana, N. tabacum var. Xanthi nc, Cucurbita moschata, and Capsicum annuum, while the potyvirus can infect N. benthamiana, Cucumis sativus L., and Bidens pilosa L. A total of 179 field P. yunnanensis leave samples from four counties were detected using RT-PCR, the result showed that ParPV-1 is uncommon in Paris yunnanensis but PpCMV is an preponderant species in some surveyed regions.