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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » National Germplasm Resources Laboratory » Research » Publications at this Location » Publication #357599

Research Project: Characterizing and Detecting Pathogens to Ensure Safe Exchange of Plant Germplasm

Location: National Germplasm Resources Laboratory

Title: Molecular characterization of a novel citrivirus infecting citrus using next-generation sequencing

Author
item Cao, Mengji - Southwest University
item Li, Ping - Southwest University
item Zhang, Song - Southwest University
item Yang, Fanyun - Southwest University
item Zhou, Yan - Southwest University
item Wang, Xuefeng - Southwest University
item Li, Ruhui

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/1/2018
Publication Date: 9/17/2018
Citation: Cao, M., Li, P., Zhang, S., Yang, F., Zhou, Y., Wang, X., Li, R. 2018. Molecular characterization of a novel citrivirus infecting citrus using next-generation sequencing. Archives of Virology. https://doi.org/10.1007/s00705-018-4039-8.
DOI: https://doi.org/10.1007/s00705-018-4039-8

Interpretive Summary: Citrus is one of the most economically important fruit crops worldwide. Many viruses and virus-like pathogens infect citrus, causing various diseases that reduce yields and market value of the fruit. In this study, a new virus was identified from a citrus tree in China with leaf chlorosis and blotching symptoms by using a sensitive sequencing technology. The complete genomic sequence of the virus was determined. Analyses of the genetic information show that it is a new virus that is closely related to a known citrus virus, citrus leaf blotch virus, in the citivirus group. The new virus, named citrus leaf blotch virus-2, was detected in two popular citrus cultivars in China. The study provides the information necessary to classify the virus and to help develop detection methods for quarantine and certification programs.

Technical Abstract: A novel positive-strand RNA virus infecting citrus with the tentative name “citrus leaf blotch virus 2” (CLBV-2), was identified in the present work. The complete genome sequence of CLBV-2 comprises 8,697 nucleotides (nt) excluding a poly(A) tail and three open reading frames (ORFs), showing the highest nucleotide sequence identity with the Actinidia strain (JN983456) of citrus leaf blotch virus (CLBV). The putative movement protein (ORF2), coat protein (ORF3), and 3' untranslated region (UTR) shared high sequence similarity with those of the extant CLBV isolates. In contrast, only low sequence similarity was observed in the 5' UTR and putative replicase polyprotein (ORF1) regions. The distant phylogenetic relationship between CLBV-2 and CLBV was deduced based on whole-genome nucleotide and whole-ORF1 amino acid sequence comparisons. Sequence comparisons suggest that CLBV-2 acquired an ORF2-ORF3-3' UTR region homologous to CLBV by recombination with of an unknown citrivirus. In view of the fact that this genomic recombination event appears to have occurred between members of different species in the genus Citrivirus, we propose that CLBV-2 should be considered a member of a distinct species.