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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #341385

Title: Molecular and biological characterization of a novel mild strain of citrus tristeza virus in California

item Yokomi, Raymond - Ray
item SELVARAJ, VIJAY ANAND RAJ - Foreign Agricultural Service (FAS, USDA)
item MAHESHWARI, YOGITA - Foreign Agricultural Service (FAS, USDA)
item CHIUMENTI, MICHELA - Consiglio Per La Ricerca In Agricoltura E L'Analisi Dell'economia Agraria, Unita Di Ricerca Per I S
item SAPONARI, MARIA - Consiglio Per La Ricerca In Agricoltura E L'Analisi Dell'economia Agraria, Unita Di Ricerca Per I S
item GIAMPETRUZZI, ANNALISA - Bari University
item WENG, ZIMING - University Of Arizona
item XIONG, ZHONGGUO - University Of Arizona
item HAJERI, SUBAS - Central California Tristeza Eradication Agency

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/8/2018
Publication Date: 3/17/2018
Citation: Yokomi, R.K., Selvaraj, V., Maheshwari, Y., Chiumenti, M., Saponari, M., Giampetruzzi, A., Weng, Z., Xiong, Z., Hajeri, S. 2018. Molecular and biological characterization of a novel mild strain of citrus tristeza virus in California. Archives of Virology. 163(7):1795-1804.

Interpretive Summary: Citrus tristeza virus (CTV) is the most important virus affecting citrus. Infection of citrus grown on sour orange rootstock by certain strains of CTV is lethal. Citrus industries in many regions (e.g., Brazil, Peru, Venezuela, Australia, Spain, Southern California) were decimated by CTV in the early to mid-1900’s. In addition to viral strains, susceptibility to CTV is affected by the citrus scion cultivar. The most virulent CTV strains cause stem pitting (regardless of rootstock) and react with the monoclonal antibody, MCA13. Recently, an MCA13-positive CTV strain (S1) isolated in California was shown to cause mild disease. A unique portion of the genome was used to develop a marker assay to rapidly identify S1 genotype isolates. Analysis of the worldwide database of CTV isolates revealed that that putative S1-like CTV isolates occur in many countries. This new information is important for regulatory programs using MCA13 to screen for virulent strains of CTV. The use of the S1 marker probe can be used to rapidly characterize MCA13-reative isolates that are mild and, therefore, of lower priority for eradication.

Technical Abstract: Strain differentiating marker profiles of Citrus tristeza virus (CTV) isolates from California indicated presence of genetic variation and bioindexing showed at least two phenotypes: mild and seedling yellows (SY)/stem pitting (SP). To define the genetic diversity involved, full-length genome sequences from one severe and three mild isolates were determined by small RNA sequencing. Phylogenetic analyses and nucleotide percent identities differentiated these isolates into the following genotypes: VT (CA-VT-AT39), T30 (CA-T30-AT4), and a new genotype called S1 (CA-S1-L and CA-S1-L65). Recombination analysis of the S1 genotype revealed a major event between nucleotide positions 14,534 and 16,745 similar to T36. CA-VT-AT39, CA-S1-L, and CA-S1-L65 reacted to monoconal antibody MCA13, whereas CA-T30-AT4 did not. Detection of the S1 genotype was developed for both RT-PCR and RT-qPCR and used to screen MCA13-reactive isolates from 557 accessions in the in planta CTV collection from Central California collected by the CCTEA from 1968 to 2011. Forty-two isolates were found that had the S1 genotype either alone or in combinations with other genotypes. BLAST and phylogenetic analysis of the S1 p25 gene region gene with other extant CTV sequences from the NCBI Database suggested putative S1-like isolates occur elsewhere (e.g., China, So. Korea, Turkey, Bosnia, and Croatia). This information is useful for the CTV control program in California which is based on screening potential severe CTV isolates by MCA13.