Lukáš Predajňa

Biomedical Research Center of the Slovak Academy of Sciences

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Miroslav Glasa

Institute of Virology of the Slovak Academy of Sciences

KŠ

Katarína Šoltýs

Comenius University Bratislava

Z Subr

Institute of Virology of the Slovak Academy of Sciences

Thierry Candresse

Biologie du Fruit et Pathologie

Nina Sihelská

Biomedical Research Center of the Slovak Academy of Sciences

Michaela Mrkvová

University of Ss. Cyril and Methodius in Trnava

Daniel Mihálik

National Agricultural and Food Centre

A. NAGYOVÁ

Institute of Virology of the Slovak Academy of Sciences

Ján Kraic

University of Ss. Cyril and Methodius in Trnava

Sead Sabanadzovic

Mississippi State University

Cooperative Institutions

National Agricultural and Food Centre

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Gembloux Agro-Bio Tech

University of Ss. Cyril and Methodius in Trnava

University of Liège

Slovak Academy of Sciences

Biomedical Research Center of the Slovak Academy of Sciences

Institute of Virology of the Slovak Academy of Sciences

Comenius University Bratislava

Biologie du Fruit et Pathologie

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Competitiveness of different Plum pox virus isolates in experimental mixed infection reveals rather isolate- than strain-specific behaviour.

Journal of Plant Pathology (2010)

Miroslav Glasa Lukáš Predajňa Z Subr

Strain (injury)

Pox virus

Genetic Variability

10.4454/jpp.v92i1.42

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Citations (6)

A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies

Frontiers in Microbiology (2017)

Sébastien Massart Thierry Candresse J. Gil Christophe Lacomme Lukáš Predajňa

Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time is also faced with substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.

Biosecurity

10.3389/fmicb.2017.00045

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Citations (159)

Clematis vitalba Is a Natural Host of the Novel Ilarvirus, Prunus Virus I

Viruses (2023)

P. Salamon Zsuzsanna Nagyne-Galbacs Emese Demián Adam Achs Peter Alaxin

Clematis vitalba L. is a climbing shrub and a pioneer plant in abandoned orchards or vineyards that are widespread in temperate climate zones. In past years, several viruses infecting the Clematis species have been identified, including different ilarviruses. Prunus virus I (PrVI) is a recently described ilarvirus, which has been shown to infect sweet cherries and peaches in Greece. Moreover, its presence has been detected in ornamental Clematis in Russia. In the present work, we analyzed the virome of wildly growing C. vitalba plants from Hungary, Slovakia and Croatia showing different kinds of symptoms using high-throughput sequencing (HTS) of small RNAs or ribodepleted RNAs. Applying HTS enabled us to identify the presence of PrVI in C. vitalba, and the bioinformatic analyses were further validated with RT-PCR using PrVI-specific primers and Sanger dideoxy sequencing. Nearly full genome sequences of all three viral RNAs of one Hungarian, two Slovak and one Croatian isolate were determined. Their phylogenetic analysis showed high similarity to each other and to other PrVI isolates described from Central Europe. As the sampled plants were co-infected with other viruses, it is not possible to determine a direct correlation between the infection with PrVI and the observed symptoms. Analyses of different Prunus species in stock collection showed infection of several peach and sweet cherry varieties in Hungary. Our results expand the knowledge on the natural host range of PrVI and highlight the necessity to evaluate alternative plant hosts (even non-Prunus) of PrVI and the role of the virus in the etiology of the potential diseases.

10.3390/v15091964

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Citations (1)

Cloning of the complete infectious cDNA of the plum pox virus strain PPV-Rec

Acta Virologica (2012)

Lukáš Predajňa A. NAGYOVÁ Miroslav Glasa Z Subr

Plum pox virus (PPV) is the causal agent of Sharka, considered to be the most detrimental viral disease of Prunus spp. worldwide. So far, several PPV strains have been recognized, three of them (PPV-D, PPV-M, and PPV-Rec) having shown serious economic impact in the European area. Infectious cDNA clones of plant RNA viruses are excellent tools for functional studies of viral genomes. Preparation and use of PPV-D and PPV-M infectious clones have been previously reported. Here we describe the construction of an infectious cDNA clone of the strain PPV-Rec (isolate BOR-3) by the strategy involving the subsequent exchanges of homologous BOR-3 genome parts in the backbone of the previously prepared PPV-D infectious construct. The infectivity of each intermediate chimeric cDNA as well as that of the final construct (pIC-PPV-Rec) was confirmed by biolistic transfection of Nicotiana benthamiana plants. Complete sequence of the cloned viral BOR-3 cDNA revealed 0.14% of difference at the nucleotide level compared to original BOR-3 sequence, resulting in four amino acid changes. This slight inequality was related to the population heterogeneity of the initial BOR-3 isolate; no difference in the amino acid sequence resulted from the cloning steps performed.inter-strain chimera; biolistics; genome sequence.

10.4149/av_2012_02_129

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Citations (9)

Characterization of Sour Cherry Isolates of Plum pox virus from the Volga Basin in Russia Reveals a New Cherry Strain of the Virus

Phytopathology (2013)

Miroslav Glasa Yuri Prikhodko Lukáš Predajňa A. NAGYOVÁ Y. Shneyder

Plum pox virus (PPV) is the causal agent of sharka, the most detrimental virus disease of stone fruit trees worldwide. PPV isolates have been assigned into seven distinct strains, of which PPV-C regroups the genetically distinct isolates detected in several European countries on cherry hosts. Here, three complete and several partial genomic sequences of PPV isolates from sour cherry trees in the Volga River basin of Russia have been determined. The comparison of complete genome sequences has shown that the nucleotide identity values with other PPV isolates reached only 77.5 to 83.5%. Phylogenetic analyses clearly assigned the RU-17sc, RU-18sc, and RU-30sc isolates from cherry to a distinct cluster, most closely related to PPV-C and, to a lesser extent, PPV-W. Based on their natural infection of sour cherry trees and genomic characterization, the PPV isolates reported here represent a new strain of PPV, for which the name PPV-CR (Cherry Russia) is proposed. The unique amino acids conserved among PPV-CR and PPV-C cherry-infecting isolates (75 in total) are mostly distributed within the central part of P1, NIa, and the N terminus of the coat protein (CP), making them potential candidates for genetic determinants of the ability to infect cherry species or of adaptation to these hosts. The variability observed within 14 PPV-CR isolates analyzed in this study (0 to 2.6% nucleotide divergence in partial CP sequences) and the identification of these isolates in different localities and cultivation conditions suggest the efficient establishment and competitiveness of the PPV-CR in the environment. A specific primer pair has been developed, allowing the specific reverse-transcription polymerase chain reaction detection of PPV-CR isolates.

Strain (injury)

Pox virus

Potyviridae

10.1094/phyto-11-12-0285-r

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Citations (52)

Partial sequence analysis of a Grapevine leafroll-associated virus 3 isolate from Slovakia.

Journal of Plant Pathology (2012)

Miroslav Glasa Lukáš Predajňa

Genetic Variability

Slovak

10.4454/jpp.fa.2012.067

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Citations (3)

Experimental Infection of Different Tomato Genotypes with Tomato mosaic virus Led to a Low Viral Population Heterogeneity in the Capsid Protein Encoding Region

The Plant Pathology Journal (2017)

Nina Sihelská Z. Vozárová Lukáš Predajňa Katarína Šoltýs Martina Hudcovicová

The complete genome sequence of a Slovak SL-1 isolate of Tomato mosaic virus (ToMV) was determined from the next generation sequencing (NGS) data, further confirming a limited sequence divergence in this tobamovirus species. Tomato genotypes Monalbo, Mobaci and Moperou, respectively carrying the susceptible tm-2 allele or the Tm-1 and Tm-2 resistant alleles, were tested for their susceptibility to ToMV SL-1. Although the three tomato genotypes accumulated ToMV SL-1 to similar amounts as judged by semi-quantitative DAS-ELISA, they showed variations in the rate of infection and symptomatology. Possible differences in the intra-isolate variability and polymorphism between viral populations propagating in these tomato genotypes were evaluated by analysis of the capsid protein (CP) encoding region. Irrespective of genotype infected, the intra-isolate haplotype structure showed the presence of the same highly dominant CP sequence and the low level of population diversity (0.08-0.19%). Our results suggest that ToMV CP encoding sequence is relatively stable in the viral population during its replication in vivo and provides further demonstration that RNA viruses may show high sequence stability, probably as a result of purifying selection. Keywords: tobamovirus, diversity, haplotype, resistance gene

Tobamovirus

Potyviridae

10.5423/ppj.nt.04.2017.0082

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Citations (5)

Complete and partial genome sequences of the unusual Plum pox virus (PPV) isolates from sour cherry in Russia suggest their classification to a new PPV strain

Miroslav Glasa Y. Prichodko Т.С. Живаева Y. Schneider Lukáš Predajňa

Pox virus

Strain (injury)

Source

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Citations (0)

First Report of Grapevine Rupestris Vein Feathering Virus in Grapevine in Slovakia

Plant Disease (2018)

Miroslav Glasa Lukáš Predajňa Thierry Wetzel Katarína Šoltýs Sead Sabanadzovic

10.1094/pdis-06-18-1112-pdn

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Citations (12)

Detection and molecular characterization of Slovak tomato isolates belonging to two recombinant strains of potato virus Y

Acta Virologica (2016)

Nina Sihelská Lukáš Predajňa A. NAGYOVÁ Katarína Šoltýs Jaroslav Budiš

Total RNAs from a symptomless tomato plant were subjected to next-generation sequencing (NGS) analysis, revealing the presence of a single viral agent -potato virus Y (PVY).The analysis of determined full-length genome sequence assigned the PVY SL16 isolate to the recombinant PVY-N-Wi strain group.A series of primers targeting the four main recombinant junction (RJ) sites were used for characterization of additional 5 tomato PVY isolates recovered in Western Slovakia.Based on the partial sequences, the isolates could be classified as belonging to PVY-N-Wi and PVY-NTNa strain groups.Interestingly, both these distinct recombinant PVY types were identified in mixed infection in one tomato sample (SL31).Our results further reinforce the data on the complexity of PVY infection and confirm the recombination as a significant evolutionary process shaping the PVY diversity.

Potato virus Y

Strain (injury)

10.4149/av_2016_04_347

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Citations (10)