Archives of Virology

, Volume 163, Issue 7, pp 1795–1804 | Cite as

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

  • Raymond Yokomi
  • Vijayanandraj Selvaraj
  • Yogita Maheshwari
  • Michela Chiumenti
  • Maria Saponari
  • Annalisa Giampetruzzi
  • Ziming Weng
  • Zhongguo Xiong
  • Subhas Hajeri
Original Article


Strain differentiating marker profiles of citrus tristeza virus (CTV) isolates from California have shown the presence of multiple genotypes. To better define the genetic diversity involved, full-length genome sequences from four California CTV isolates were determined by small-interfering RNA sequencing. Phylogenetic analysis and nucleotide sequence comparisons differentiated these isolates into the genotypes VT (CA-VT-AT39), T30 (CA-T30-AT4), and a new strain called S1 (CA-S1-L and CA-S1-L65). S1 isolates had three common recombination events within portions of genes from VT, T36 and RB strains and were transmissible by Aphis gossypii. Virus indexing showed that CA-VT-AT39 could be classified as a severe strain, whereas CA-T30-AT4, CA-S1-L and CA-S1-L65 were mild. CA-VT-AT39, CA-S1-L, and CA-S1-L65 reacted with monoclonal antibody MCA13, whereas CA-T30-AT4 did not. RT-PCR and RT-qPCR detection assays for the S1 strain were developed and used to screen MCA13-reactive isolates in a CTV collection from central California collected from 1968 to 2011. Forty-two isolates were found to contain the S1 strain, alone or in combinations with other genotypes. BLAST and phylogenetic analysis of the S1 p25 gene region with other extant CTV sequences from the NCBI database suggested that putative S1-like isolates might occur elsewhere (e.g., China, South Korea, Turkey, Bosnia and Croatia). This information is important for CTV evolution, detection of specific strains, and cross-protection.



This work was supported in part by grants from the Citrus Research Board and Tulare County Pest Control District. We thank Robert DeBorde and Casey Crockett, United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, for technical assistance. Mention of trade names or commercial products in this publication is solely for providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

Author contributions

RKY, VS, YM, MS, and SH conceived and designed the experiments; RKY, VS, YM, MS, and AG performed the experiments; RKY, VS, YM, MS, and MC analyzed the data; RKY, MS, SH, ZX, and ZW contributed reagents/materials/analysis tools; RKY, VS, YM, and SH wrote the paper.


This study was funded in part by Citrus Research Board Grants 5300-138 and 5300-166 and Tulare County Pest Control District Agreement 58-2034-5-026 to Raymond Yokomi.

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest. The funding sponsors had no role in the design of the study, in the collection, analysis, or interpretation of data, in the writing of the manuscript, or in the decision to publish the results.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

705_2018_3799_MOESM1_ESM.docx (567 kb)
Supplementary material 1 (DOCX 566 kb)


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Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2018

Authors and Affiliations

  • Raymond Yokomi
    • 1
  • Vijayanandraj Selvaraj
    • 1
  • Yogita Maheshwari
    • 1
  • Michela Chiumenti
    • 2
  • Maria Saponari
    • 2
  • Annalisa Giampetruzzi
    • 3
  • Ziming Weng
    • 4
  • Zhongguo Xiong
    • 4
  • Subhas Hajeri
    • 5
  1. 1.United States Department of Agriculture-Agricultural Research ServiceSan Joaquin Valley Agricultural Sciences CenterParlierUSA
  2. 2.Institute for Sustainable Plant Protection, Italian National Research Council, Sezione di BariBariItaly
  3. 3.Department of Soil Plant and Food ScienceUniversity of Bari Aldo MoroBariItaly
  4. 4.School of Plant Sciences and BIO5 InstituteUniversity of ArizonaTucsonUSA
  5. 5.Citrus Pest Detection ProgramCentral California Tristeza Eradication AgencyTulareUSA

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