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Marpaung DSS, Sinaga AOY, Damayanti D, Taharuddin T. Bridging biological samples to functional nucleic acid biosensor applications: current enzymatic-based strategies for single-stranded DNA generation. ANAL SCI 2024; 40:1225-1237. [PMID: 38607600 DOI: 10.1007/s44211-024-00566-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
The escalating threat of emerging diseases, often stemming from contaminants and lethal pathogens, has precipitated a heightened demand for sophisticated diagnostic tools. Within this landscape, the functional nucleic acid (FNA) biosensor, harnessing the power of single-stranded DNA (ssDNA), has emerged as a preeminent choice for target analyte detection. However, the dependence on ssDNA has raised difficulties in realizing it in biological samples. Therefore, the production of high-quality ssDNA from biological samples is critical. This review aims to discuss strategies for generating ssDNA from biological samples for integration into biosensors. Several innovative strategies for ssDNA generation have been deployed, encompassing techniques, such as asymmetric PCR, Exonuclease-PCR, isothermal amplification, biotin-streptavidin PCR, transcription-reverse transcription, ssDNA overhang generation, and urea denaturation PAGE. These approaches have been seamlessly integrated with biosensors for biological sample analysis, ushering in a new era of disease detection and monitoring. This amalgamation of ssDNA generation techniques with biosensing applications holds significant promise, not only in improving the speed and accuracy of diagnostic processes but also in fortifying the global response to deadly diseases, thereby underlining the pivotal role of cutting-edge biotechnology in public health and disease prevention.
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Affiliation(s)
- David Septian Sumanto Marpaung
- Department of Biosystems Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia.
| | - Ayu Oshin Yap Sinaga
- Department of Biology, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Damayanti Damayanti
- Department of Chemical Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Taharuddin Taharuddin
- Department of Chemical Engineering, University of Lampung, Jl. Prof. Dr. Ir. Sumantri Brojonegoro No.1, Gedong Meneng, Kec. Rajabasa, Kota Bandar Lampung, Lampung, 35141, Indonesia
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Tennant P, Rampersad S, Alleyne A, Johnson L, Tai D, Amarakoon I, Roye M, Pitter P, Chang PG, Myers Morgan L. Viral Threats to Fruit and Vegetable Crops in the Caribbean. Viruses 2024; 16:603. [PMID: 38675944 PMCID: PMC11053604 DOI: 10.3390/v16040603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Viruses pose major global challenges to crop production as infections reduce the yield and quality of harvested products, hinder germplasm exchange, increase financial inputs, and threaten food security. Small island or archipelago habitat conditions such as those in the Caribbean are particularly susceptible as the region is characterized by high rainfall and uniform, warm temperatures throughout the year. Moreover, Caribbean islands are continuously exposed to disease risks because of their location at the intersection of transcontinental trade between North and South America and their role as central hubs for regional and global agricultural commodity trade. This review provides a summary of virus disease epidemics that originated in the Caribbean and those that were introduced and spread throughout the islands. Epidemic-associated factors that impact disease development are also discussed. Understanding virus disease epidemiology, adoption of new diagnostic technologies, implementation of biosafety protocols, and widespread acceptance of biotechnology solutions to counter the effects of cultivar susceptibility remain important challenges to the region. Effective integrated disease management requires a comprehensive approach that should include upgraded phytosanitary measures and continuous surveillance with rapid and appropriate responses.
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Affiliation(s)
- Paula Tennant
- Department of Life Sciences, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica;
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
| | - Sephra Rampersad
- Department of Life Sciences, The University of the West Indies, St. Augustine 999183, Trinidad and Tobago;
| | - Angela Alleyne
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill, Bridgetown BB11000, Barbados;
| | - Lloyd Johnson
- Department of Life Sciences, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica;
| | - Deiondra Tai
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
| | - Icolyn Amarakoon
- Department of Basic Medical Sciences, Biochemistry Section, Faculty of Medical Sciences Teaching and Research Complex, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica;
| | - Marcia Roye
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
| | - Patrice Pitter
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
- Ministry of Agriculture, Bodles Research Station, Old Harbour, St. Catherine JMACE18, Jamaica; (P.-G.C.); (L.M.M.)
| | - Peta-Gaye Chang
- Ministry of Agriculture, Bodles Research Station, Old Harbour, St. Catherine JMACE18, Jamaica; (P.-G.C.); (L.M.M.)
| | - Lisa Myers Morgan
- Ministry of Agriculture, Bodles Research Station, Old Harbour, St. Catherine JMACE18, Jamaica; (P.-G.C.); (L.M.M.)
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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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5
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Shokri E, Hosseini M, Faridbod F, Rahaie M. Rapid pre-symptomatic recognition of tristeza viral RNA by a novel fluorescent self-dimerized DNA–silver nanocluster probe. RSC Adv 2016. [DOI: 10.1039/c6ra15199j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Citrus tristeza virus (CTV), a positive-strand RNA virus within the family of Closteroviridae, is distributed worldwide and causes one of the most economically important diseases of citrus.
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Affiliation(s)
- Ehsan Shokri
- Department of Life Science Engineering
- Faculty of New Sciences & Technologies
- University of Tehran
- Tehran
- Iran
| | - Morteza Hosseini
- Department of Life Science Engineering
- Faculty of New Sciences & Technologies
- University of Tehran
- Tehran
- Iran
| | - Farnoush Faridbod
- Center of Excellence in Electrochemistry
- Faculty of Chemistry
- University of Tehran
- Tehran
- Iran
| | - Mahdi Rahaie
- Department of Life Science Engineering
- Faculty of New Sciences & Technologies
- University of Tehran
- Tehran
- Iran
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6
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Benítez-Galeano MJ, Rubio L, Bertalmío A, Maeso D, Rivas F, Colina R. Phylogenetic Studies of the Three RNA Silencing Suppressor Genes of South American CTV Isolates Reveal the Circulation of a Novel Genetic Lineage. Viruses 2015; 7:4152-68. [PMID: 26205407 PMCID: PMC4517143 DOI: 10.3390/v7072814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/04/2015] [Accepted: 07/17/2015] [Indexed: 11/16/2022] Open
Abstract
Citrus Tristeza Virus (CTV) is the most economically important virus of citrus worldwide. Genetic diversity and population structure of CTV isolates from all citrus growing areas from Uruguay were analyzed by RT-PCR and cloning of the three RNA silencing suppressor genes (p25, p20 and p23). Bayesian phylogenetic analysis revealed the circulation of three known genotypes (VT, T3, T36) in the country, and the presence of a new genetic lineage composed by isolates from around the world, mainly from South America. Nucleotide and amino acid identity values for this new genetic lineage were both higher than 97% for the three analyzed regions. Due to incongruent phylogenetic relationships, recombination analysis was performed using Genetic Algorithms for Recombination Detection (GARD) and SimPlot software. Recombination events between previously described CTV isolates were detected. High intra-sample variation was found, confirming the co-existence of different genotypes into the same plant. This is the first report describing: (1) the genetic diversity of Uruguayan CTV isolates circulating in the country and (2) the circulation of a novel CTV genetic lineage, highly present in the South American region. This information may provide assistance to develop an effective cross-protection program.
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Affiliation(s)
- María José Benítez-Galeano
- Laboratorio de Virología Molecular, Centro Universitario Regional Noroeste (CENUR Noroeste), Universidad de la Republica (UdelaR), Rivera 1350, 50000 Salto, Uruguay.
| | - Leticia Rubio
- Programa Nacional de Investigación en Producción Citrícola, Instituto Nacional de Investigación Agropecuaria (INIA), Urguay.
| | - Ana Bertalmío
- Programa Nacional de Investigación en Producción Citrícola, Instituto Nacional de Investigación Agropecuaria (INIA), Urguay.
| | - Diego Maeso
- Programa Nacional de Investigación en Producción Citrícola, Instituto Nacional de Investigación Agropecuaria (INIA), Urguay.
| | - Fernando Rivas
- Programa Nacional de Investigación en Producción Citrícola, Instituto Nacional de Investigación Agropecuaria (INIA), Urguay.
| | - Rodney Colina
- Laboratorio de Virología Molecular, Centro Universitario Regional Noroeste (CENUR Noroeste), Universidad de la Republica (UdelaR), Rivera 1350, 50000 Salto, Uruguay.
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8
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Sue MJ, Yeap SK, Omar AR, Tan SW. Application of PCR-ELISA in molecular diagnosis. BIOMED RESEARCH INTERNATIONAL 2014; 2014:653014. [PMID: 24971343 PMCID: PMC4058250 DOI: 10.1155/2014/653014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/12/2014] [Indexed: 12/27/2022]
Abstract
Polymerase chain reaction-enzyme linked immunosorbent assay (PCR-ELISA) is an immunodetection method that can quantify PCR product directly after immobilization of biotinylated DNA on a microplate. This method, which detects nucleic acid instead of protein, is a much more sensitive method compared to conventional PCR method, with shorter analytical time and lower detection limit. Its high specificity and sensitivity, together with its semiquantitative ability, give it a huge potential to serve as a powerful detection tool in various industries such as medical, veterinary, and agricultural industries. With the recent advances in PCR-ELISA, it is envisaged that the assay is more widely recognized for its fast and sensitive detection limit which could improve overall diagnostic time and quality.
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Affiliation(s)
- Mei Jean Sue
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia
| | - Swee Keong Yeap
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia
| | - Abdul Rahman Omar
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia
| | - Sheau Wei Tan
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400 Serdang, Selangor, Malaysia
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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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Harper SJ. Citrus tristeza virus: Evolution of Complex and Varied Genotypic Groups. Front Microbiol 2013; 4:93. [PMID: 23630519 PMCID: PMC3632782 DOI: 10.3389/fmicb.2013.00093] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/03/2013] [Indexed: 12/22/2022] Open
Abstract
Amongst the Closteroviridae, Citrus tristeza virus (CTV) is almost unique in possessing a number of distinct and characterized strains, isolates of which produce a wide range of phenotype combinations among its different hosts. There is little understanding to connect genotypes to phenotypes, and to complicate matters more, these genotypes are found throughout the world as members of mixed populations within a single host plant. There is essentially no understanding of how combinations of genotypes affect symptom expression and disease severity. We know little about the evolution of the genotypes that have been characterized to date, little about the biological role of their diversity and particularly, about the effects of recombination. Additionally, genotype grouping has not been standardized. In this study we utilized an extensive array of CTV genomic information to classify the major genotypes, and to determine the major evolutionary processes that led to their formation and subsequent retention. Our analyses suggest that three major processes act on these genotypes: (1) ancestral diversification of the major CTV lineages, followed by (2) conservation and co-evolution of the major functional domains within, though not between CTV genotypes, and (3) extensive recombination between lineages that have given rise to new genotypes that have subsequently been retained within the global population. The effects of genotype diversity and host-interaction are discussed, as is a proposal for standardizing the classification of existing and novel CTV genotypes.
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Affiliation(s)
- S J Harper
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida Lake Alfred, FL, USA
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11
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Generic and sequence-variant specific molecular assays for the detection of the highly variable Grapevine leafroll-associated virus 3. J Virol Methods 2013; 189:20-9. [DOI: 10.1016/j.jviromet.2012.12.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 11/19/2022]
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Silva G, Marques N, Nolasco G. The evolutionary rate of citrus tristeza virus ranks among the rates of the slowest RNA viruses. J Gen Virol 2011; 93:419-429. [PMID: 22071513 DOI: 10.1099/vir.0.036574-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Citrus tristeza virus (CTV) has been studied intensively at the molecular level. However, knowledge regarding the dynamics of its evolution is practically non-existent. In the past, diverse authors have referred to CTV as a highly variable virus, implying rapid evolution. Others have, in recent times, referred to CTV as an exceptionally slowly evolving virus. In this work, we used the capsid protein (CP) gene to estimate the rate of evolution. This was obtained from a large set of heterochronous CP gene sequences using a bayesian coalescent approach. The best-fitting evolutionary and population models pointed to an evolutionary rate of 1.58×10(-4) nt per site year(-1) (95 % highest posterior density, 1.73×10(-5)-3.16×10(-4) nt per site year(-1)). For an unbiased comparison with other plant and animal viruses, the evolutionary rate of synonymous substitutions was considered. In a series of 88 synonymous evolutionary rates, ranging from 5.2×10(-6) to 6.2×10(-2) nt per site year(-1), CTV ranks in the 10th percentile, embedded among the slowest animal RNA viruses. At the time of citrus dissemination to Europe and the New World, the major clades that led to the current phylogenetic groups were already defined, which may explain the absence nowadays of geographical speciation.
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Affiliation(s)
- Gonçalo Silva
- Plant Virology Laboratory, Center for Biodiversity, Functional and Integrative Genomics (BioFig), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Natália Marques
- Plant Virology Laboratory, Center for Biodiversity, Functional and Integrative Genomics (BioFig), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Gustavo Nolasco
- Plant Virology Laboratory, Center for Biodiversity, Functional and Integrative Genomics (BioFig), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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Li J, Wan Y, Wang L, Zhu X, Su Y, Li D, Zhao Y, Huang Q, Song S, Fan C. Universal optical assays based on multi-component nanoprobes for genomic deoxyribonucleic acid and proteins. Anal Chim Acta 2011; 702:114-9. [PMID: 21819868 DOI: 10.1016/j.aca.2011.06.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 06/09/2011] [Accepted: 06/21/2011] [Indexed: 11/18/2022]
Abstract
In this report, we developed a universal assay method for both genomic DNA and proteins by using enzyme-based multi-component optical nanoprobes. The nanoprobes are gold nanoparticles assembled with bio-recognizing and signaling elements. We firstly demonstrated that the nanoprobes could detect unpurified asymmetric polymerase chain reaction (PCR) product from genomic DNA of Escherichia coli, with the sensitivity approximately 10 times higher than that of quantitative real-time PCR assay. The limit of detection (LOD) of our nanoprobe-based method is less than 10 pg template DNA (target DNA). Using DNA aptamers as recognition elements, we also showed that as few as 0.1 nM thrombin could be colorimetrically detected with high specificity. These results indicated that the enzyme-based multi-component nanoprobes have the capability to work with real biological samples, and have the potential in various biological and clinical applications.
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Affiliation(s)
- Jiang Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, PR China
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14
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Gouveia P, Santos MT, Eiras-Dias JE, Nolasco G. Five phylogenetic groups identified in the coat protein gene of grapevine leafroll-associated virus 3 obtained from Portuguese grapevine varieties. Arch Virol 2010; 156:413-20. [DOI: 10.1007/s00705-010-0878-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 11/25/2010] [Indexed: 10/18/2022]
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Roy A, Ananthakrishnan G, Hartung JS, Brlansky RH. Development and application of a multiplex reverse-transcription polymerase chain reaction assay for screening a global collection of Citrus tristeza virus isolates. PHYTOPATHOLOGY 2010; 100:1077-88. [PMID: 20839943 DOI: 10.1094/phyto-04-10-0102] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The emerging diversity of Citrus tristeza virus (CTV) genotypes has complicated detection and diagnostic measures and prompted the search for new differentiation methods. To simplify the identification and differentiation of CTV genotypes, a multiplex reverse-transcription polymerase chain reaction (RT-PCR) technique for the screening of CTV isolates was developed. Variable regions within the open reading frame (ORF)-1a of diverse CTV genotypes were identified to develop first a simplex (S) and then a hexaplex (H) RT-PCR. CTV isolates have been grouped previously into five genotypes (namely, T3, T30, T36, VT, and B165) based on the nucleotide sequence comparisons and phylogenetic analyses. Nucleotide sequences from GenBank were used to design species and genotype-specific primers (GSPs). The GSPs were initially used for reliable detection of all CTV genotypes using S-RT-PCR. Furthermore, detection of all five recognized CTV genotypes was established using the H-RT-PCR. Six amplicons, one generic to all CTV isolates and one for each of the five recognized genotypes, were identified on the basis of their size and were confirmed by sequence analysis. In all, 175 CTV isolates from 29 citrus-growing countries were successfully analyzed by S- and H-RT-PCR. Of these, 97 isolates contained T36 genotypes, 95 contained T3 genotypes, 76 contained T30 genotypes, 71 contained VT genotypes, and 24 contained B165 genotype isolates. In total, 126 isolates contained mixed infections of 2 to 5 of the known CTV genotypes. Two of the CTV isolates could not be assigned to a known genotype. H-RT-PCR provides a sensitive, specific, reliable, and rapid way to screen for CTV genotypes compared with other methods for CTV genotype detection. Efficient identification of CTV genotypes will facilitate a better understanding of CTV isolates, including the possible interaction of different genotypes in causing or preventing diseases. The methods described can also be used in virus-free citrus propagation programs and in the development of CTV-resistant cultivars.
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Affiliation(s)
- Avijit Roy
- University of Florida, IFAS, Citrus Research and Education Center, Lake Alfred, FL 33850-2299, USA
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