First Report and Nearly Complete Genome Sequence of Paris deltapartitivirus 1 in Paris yunnanensis

Purpose To clarify the taxonomic status and occurrence of the new members of genus Deltapartitivirus in family Partitivridae discovered on Paris yunnanensis.

Methods High-throughput sequencing (HTS) was used to detect the P. yunnanensis leaf samples with virus-disease-like symptoms collected in 2020 from Lijiang City, Yunnan Province, obtaining the nearly complete genome sequence of a novel deltapartitivirus-like in genus Deltapartitivirus and temporarily designated as Paris deltapartitivirus 1 (ParDPV1). RT-PCR technology was used to amplify ParDPV1, and its classification was validated based on nucleotide and amino acid sequence identity, as well as phylogenetic analyses of CP and RdRp. By testing 798 samples collected in 2020, 2023 and 2024, the occurrence of ParDPV1 in the field was assessed.

Results The nearly complete genome sequences of ParDPV1, comprising 1570 bp (dsRNA1) and 1522 bp (dsRNA2), were obtained from P. yunnanensis leaves exhibiting mild mottling symptoms. Sequence analysis showed that these two segments encoded the RdRp and CP of the virus, and the amino acid identities of RdRp and CP with members of the genus Deltapartitivirus were 34.80%-62.18% and 17.51%-29.19%, respectively, which were significantly lower than the taxonomic thresholds for this genus (≤90% of RdRp, and ≤80% of CP). The phylogenetic tree constructed based on RdRp and CP amino acid sequences showed that ParDPV1 was clustered with members of the genus Deltapartitivirus. RT-PCR screening of 798 samples revealed that ParDPV1 was detected only in three plants exhibited no obvious symptoms or mild mottling.

Conclusion ParDPV1 is an new member in genus Deltapartitivirus, occurring only sporadically in the field and causing no or only mild symptoms in infected plants. It is proposed that “Paris deltapartitivirus 1” (ParDPV1) as its generic name, and Deltapartivirus paris of its species name.