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Zindović J, Čizmović M, Vučurović A, Margaria P, Škorić D. Increased Diversity of Citrus Tristeza Virus in Europe. PLANT DISEASE 2024; 108:1344-1352. [PMID: 37990525 DOI: 10.1094/pdis-09-23-1718-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
This study investigated the genetic diversity of Citrus tristeza virus (CTV) isolates from Montenegro and Croatia, European countries with the northernmost citrus-growing regions situated on the Eastern Adriatic coast. Fifteen complete or nearly complete CTV genomes were reconstructed by high-throughput sequencing of samples collected in distinct municipalities in Montenegro and Opuzen municipality in Croatia. Phylogenetic analyses assigned some of the sequences to VT and T30 strains, previously recorded in Europe, while remarkably other isolates were placed in S1 and RB groups, which have not been reported in Europe so far. In addition, a new phylogenetic lineage comprising only isolates from Montenegro was delineated and tentatively proposed as the MNE cluster. Recombination analysis revealed evidence of 11 recombination events in the sequences obtained in this study, between isolates of related strains, within isolates of the same strain, and between distant strains. These findings show that CTV diversity in Europe is higher than reported before and calls for the reevaluation of management strategies.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jelena Zindović
- Department for Plant Protection, Biotechnical Faculty, University of Montenegro, 81000 Podgorica, Montenegro
| | - Miroslav Čizmović
- Department for Plant Protection, Biotechnical Faculty, University of Montenegro, 81000 Podgorica, Montenegro
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Paolo Margaria
- Plant Virus Department, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
| | - Dijana Škorić
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
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Erkiş-Güngör G, Çevik B. Genetic Diversity and Phylogenetic Analysis of Citrus tristeza virus Isolates from Turkey. Adv Virol 2019; 2019:7163747. [PMID: 30906322 PMCID: PMC6393893 DOI: 10.1155/2019/7163747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/26/2018] [Indexed: 11/17/2022] Open
Abstract
The presence of Citrus tristeza virus (CTV) in Turkey has been known since the 1960s and the virus was detected in all citrus growing regions of the country. Even though serological and biological characteristics of CTV have been studied since the 1980s, molecular characteristics of CTV isolates have not been studied to date in Turkey. In this study, molecular characteristics of 15 CTV isolates collected from different citrus growing regions of Turkey were determined by amplification, cloning, and sequencing of their major coat protein (CP) genes. The sequence analysis showed that the CP genes were highly conserved among Turkish isolates. However, isolates from different regions showed more genetic variation than isolates from the same region. Turkish isolates were clustered into three phylogenetic groups showing no association with geographical origins, host, or symptoms induced in indicator plants. Phylogenetic analysis of Turkish isolates with isolates from different citrus growing regions of the world including well-characterized type isolates of previously established strain specific groups revealed that some Turkish isolates were closely related to severe quick decline or stem pitting isolates. The results demonstrated that although CTV isolates from Turkey are considered biologically mild, majority of them contain severe components potentially causing quick decline or stem pitting.
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Affiliation(s)
- Gözde Erkiş-Güngör
- Applied Sciences University of Isparta, Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, 32260 Isparta, Turkey
- Ministry of Food, Agriculture and Livestock, Antalya Agricultural Quarantine Office, Virology Laboratory, 07260 Antalya, Turkey
| | - Bayram Çevik
- Applied Sciences University of Isparta, Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, 32260 Isparta, Turkey
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Yokomi R, Selvaraj V, Maheshwari Y, Chiumenti M, Saponari M, Giampetruzzi A, Weng Z, Xiong Z, Hajeri S. Molecular and biological characterization of a novel mild strain of citrus tristeza virus in California. Arch Virol 2018; 163:1795-1804. [PMID: 29550931 DOI: 10.1007/s00705-018-3799-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
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.
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Affiliation(s)
- Raymond Yokomi
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA.
| | - Vijayanandraj Selvaraj
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA
| | - Yogita Maheshwari
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection, Italian National Research Council, Sezione di Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Maria Saponari
- Institute for Sustainable Plant Protection, Italian National Research Council, Sezione di Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Annalisa Giampetruzzi
- Department of Soil Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Ziming Weng
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, AZ, 85721-7186, USA
| | - Zhongguo Xiong
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, AZ, 85721-7186, USA
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA, 93274-9367, USA
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Xiao C, Yao RX, Li F, Dai SM, Licciardello G, Catara A, Gentile A, Deng ZN. Population structure and diversity of citrus tristeza virus (CTV) isolates in Hunan province, China. Arch Virol 2016; 162:409-423. [PMID: 27771790 DOI: 10.1007/s00705-016-3089-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/22/2016] [Indexed: 12/01/2022]
Abstract
Stem-pitting (SP) is the main type of citrus tristeza virus (CTV) that causes severe damage to citrus trees, especially those of sweet orange, in Hunan province, China. Understanding the local CTV population structure should provide clues for effective mild strain cross-protection (MSCP) of the SP strain of CTV. In this study, markers for the p23 gene, multiple molecular markers (MMMs), and sequence analysis of the three silencing suppressor genes (p20, p23 and p25) were employed to analyze the genetic diversity and genotype composition of the CTV population based on 51 CTV-positive samples collected from 14 citrus orchards scattered around six major citrus-growing areas of Hunan. The results indicated that the CTV population structure was extremely complex and that infection was highly mixed. In total, p23 gene markers resulted in six profiles, and MMMs demonstrated 25 profiles. The severe VT and T3 types appeared to be predominantly associated with SP, while the mild T30 and RB types were related to asymptomatic samples. Based on phylogenetic analysis of the amino acid sequences of p20, p23 and p25, 19 representative CTV samples were classified into seven recently established CTV groups and a potentially novel one. A high level of genetic diversity, as well as potential recombination, was revealed among different CTV isolates. Five pure SP severe and two pure mild strains were identified by genotype composition analysis. Taken together, the results update the genetic diversity of CTV in Hunan with the detection of one possible novel strain, and this information might be applicable for the selection of appropriate mild CTV strains for controlling citrus SP disease through cross-protection.
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Affiliation(s)
- Cui Xiao
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, 410128, China
| | - Run-Xian Yao
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, 410128, China
| | - Fang Li
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, 410128, China
| | - Su-Ming Dai
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, 410128, China.,Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Grazia Licciardello
- Parco Scientifico e Tecnologico della Sicilia, z.i., Stradale Lancia 57, 95121, Catania, Italy
| | - Antonino Catara
- Parco Scientifico e Tecnologico della Sicilia, z.i., Stradale Lancia 57, 95121, Catania, Italy
| | - Alessandra Gentile
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Piazza Università 2, 95131, Catania, Italy.
| | - Zi-Niu Deng
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, 410128, China. .,Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China.
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Wu GW, Tang M, Wang GP, Jin FY, Yang ZK, Cheng LJ, Hong N. Genetic diversity and evolution of two capsid protein genes of citrus tristeza virus isolates from China. Arch Virol 2014; 160:787-94. [PMID: 25387862 DOI: 10.1007/s00705-014-2281-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022]
Abstract
The genetic diversity and population structure of citrus tristeza virus (CTV) isolates from China were investigated based on partial sequences spanning the C-terminal end of p61 and the complete sequences of the CPm and CP genes. Phylogenetic analysis revealed five known groups (RB, T30, T36, HA and VT) and one new group (VI) consisting of only Chinese CTV isolates. Incongruent phylogenetic trees coupled with recombination analysis suggested several recombination events in the CPm gene. Positive selection was detected at codon 9 of CPm and codons 31, 41 and 68 of CP. The widespread CTV subpopulation AT-1 found in China has a unique amino acid insertion at the C-terminus of p61, which could increase CTV population complexity with implications for the evolutionary history of the virus. Our results suggest relevant roles for gene flow, purifying selection and recombination in shaping the CTV population in China.
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Affiliation(s)
- Guan-Wei Wu
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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Nchongboh CG, Wu GW, Hong N, Wang GP. Protein–protein interactions between proteins of Citrus tristeza virus isolates. Virus Genes 2014; 49:456-65. [DOI: 10.1007/s11262-014-1100-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/20/2014] [Indexed: 12/01/2022]
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Wu GW, Tang M, Wang GP, Wang CX, Liu Y, Yang F, Hong N. The epitope structure of Citrus tristeza virus coat protein mapped by recombinant proteins and monoclonal antibodies. Virology 2013; 448:238-46. [PMID: 24314654 DOI: 10.1016/j.virol.2013.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/03/2013] [Accepted: 10/14/2013] [Indexed: 11/24/2022]
Abstract
It has been known that there exists serological differentiation among Citrus tristeza virus (CTV) isolates. The present study reports three linear epitopes (aa 48-63, 97-104, and 114-125) identified by using bacterially expressed truncated coat proteins and ten monoclonal antibodies against the native virions of CTV-S4. Site-directed mutagenesis analysis demonstrated that the mutation D98G within the newly identified epitope (97)DDDSTGIT(104) abolished its reaction to MAbs 1, 4, and 10, and the presence of G98 in HB1-CP also resulted in its failure to recognize the three MAbs. Our results suggest that the conformational differences in the epitope I (48)LGTQQNAALNRDLFLT(63) between the CPs of isolates S4 and HB1 might contribute to the different reactions of two isolates to MAbs 5 and 6. This study provides new information for the antigenic structures of CTV, and will extend the understanding of the processes required for antibody binding and aid the development of epitope-based diagnostic tools.
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Affiliation(s)
- Guan-Wei Wu
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
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Rubio L, Guerri J, Moreno P. Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae. Front Microbiol 2013; 4:151. [PMID: 23805130 PMCID: PMC3693128 DOI: 10.3389/fmicb.2013.00151] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 05/29/2013] [Indexed: 11/15/2022] Open
Abstract
RNA viruses have a great potential for genetic variation, rapid evolution and adaptation. Characterization of the genetic variation of viral populations provides relevant information on the processes involved in virus evolution and epidemiology and it is crucial for designing reliable diagnostic tools and developing efficient and durable disease control strategies. Here we performed an updated analysis of sequences available in Genbank and reviewed present knowledge on the genetic variability and evolutionary processes of viruses of the family Closteroviridae. Several factors have shaped the genetic structure and diversity of closteroviruses. (I) A strong negative selection seems to be responsible for the high genetic stability in space and time for some viruses. (2) Long distance migration, probably by human transport of infected propagative plant material, have caused that genetically similar virus isolates are found in distant geographical regions. (3) Recombination between divergent sequence variants have generated new genotypes and plays an important role for the evolution of some viruses of the family Closteroviridae. (4) Interaction between virus strains or between different viruses in mixed infections may alter accumulation of certain strains. (5) Host change or virus transmission by insect vectors induced changes in the viral population structure due to positive selection of sequence variants with higher fitness for host-virus or vector-virus interaction (adaptation) or by genetic drift due to random selection of sequence variants during the population bottleneck associated to the transmission process.
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Affiliation(s)
- Luis Rubio
- Instituto Valenciano de Investigaciones AgrariasMoncada, Valencia, Spain
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Wu GW, Pan S, Wang GP, Tang M, Liu Y, Yang F, Hong N. The genotypes of citrus tristeza virus isolates from China revealed by sequence analysis of multiple molecular markers. Arch Virol 2012; 158:231-5. [PMID: 22987316 DOI: 10.1007/s00705-012-1475-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 07/31/2012] [Indexed: 11/28/2022]
Abstract
The genotypes of ten citrus tristeza virus (CTV) isolates from central China were determined by examining multiple molecular markers (MMMs) using 11 primer pairs. The results revealed that one isolate contained a single T30 genotype, two isolates contained a single VT genotype, and the other seven isolates were mixtures of two or more genotypes. Sequence analysis of amplified MMMs showed a high genetic diversity in Chinese CTV populations. The genotypes resembling T36, RB and B165 were identified from Chinese CTV isolates for the first time. Our results suggest that genotype assignment of CTV cannot be based solely on the amplification profiles of MMMs, and sequencing of MMMs is required.
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Affiliation(s)
- Guan-Wei Wu
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China
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