Publications

@article{Radvánszka2022,

title = {Sequential development of several RT-qPCR tests using LNA nucleotides and dual probe technology to differentiate SARS-CoV-2 from influenza A and B},

author = {M. Radvánszka and E. D. Paul and R. Hajdu and K. Boršová and V. Kováčová and P. Putaj and S. Bírová and I. Čirková and M. Čarnecký and K. Buranovská and A. Szobi and N. Vojtaššáková and D. Drobná and V. Čabanová and M. Sláviková and M. Ličková and V. Vaňová and S. Fumačová Havlíková and Ľ. Lukáčiková and I. Kajanová and J. Koči and D. Rusňáková and T. Sedláčková and K. E. A. Max and T. Tuschl and T. Szemes and B. Klempa and P. Čekan},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85126870587&doi=10.1111%2f1751-7915.14031&partnerID=40&md5=6bfbb30ff38aa6d088d9ffd526e1762f},

doi = {10.1111/1751-7915.14031},

issn = {17517907},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Microbial Biotechnology},

publisher = {John Wiley and Sons Ltd},

abstract = {Sensitive and accurate RT-qPCR tests are the primary diagnostic tools to identify SARS-CoV-2-infected patients. While many SARS-CoV-2 RT-qPCR tests are available, there are significant differences in test sensitivity, workflow (e.g. hands-on-time), gene targets and other functionalities that users must consider. Several publicly available protocols shared by reference labs and public health authorities provide useful tools for SARS-CoV-2 diagnosis, but many have shortcomings related to sensitivity and laborious workflows. Here, we describe a series of SARS-CoV-2 RT-qPCR tests that are originally based on the protocol targeting regions of the RNA-dependent RNA polymerase (RdRp) and envelope (E) coding genes developed by the Charité Berlin. We redesigned the primers/probes, utilized locked nucleic acid nucleotides, incorporated dual probe technology and conducted extensive optimizations of reaction conditions to enhance the sensitivity and specificity of these tests. By incorporating an RNase P internal control and developing multiplexed assays for distinguishing SARS-CoV-2 and influenza A and B, we streamlined the workflow to provide quicker results and reduced consumable costs. Some of these tests use modified enzymes enabling the formulation of a room temperature-stable master mix and lyophilized positive control, thus increasing the functionality of the test and eliminating cold chain shipping and storage. Moreover, a rapid, RNA extraction-free version enables high sensitivity detection of SARS-CoV-2 in about an hour using minimally invasive, self-collected gargle samples. These RT-qPCR assays can easily be implemented in any diagnostic laboratory and can provide a powerful tool to detect SARS-CoV-2 and the most common seasonal influenzas during the vaccination phase of the pandemic. © 2022 Multiplex DX, S.R.O. Microbial Biotechnology published by Society for Applied Microbiology and John Wiley & Sons Ltd.},

keywords = {Sars-cov-2, Viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Rusňáková2022,

title = {Systematic Genomic Surveillance of SARS-CoV-2 Virus on Illumina Sequencing Platforms in the Slovak Republic—One Year Experience},

author = {D. Rusňáková and T. Sedláčková and P. Radvák and M. Böhmer and P. Mišenko and J. Budiš and S. Bokorová and N. Lipková and M. Forgáčová-Jakúbková and T. Sládeček and J. Sitarčík and W. Krampl and M. Gažiová and A. Kaliňáková and E. Staroňová and E. Tichá and T. Vrábľová and L. Ševčíková and B. Kotvasová and L. Maďarová and S. Feiková and K. Beňová and L. Reizigová and Z. Onderková and D. Ondrušková and D. Loderer and M. Škereňová and Z. Danková and K. Janíková and E. Halašová and E. Nováková and J. Turňa and T. Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141590744&doi=10.3390%2fv14112432&partnerID=40&md5=ae8783f0d6a244a1eeea0fb3d17f7230},

doi = {10.3390/v14112432},

issn = {19994915},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Viruses},

volume = {14},

number = {11},

publisher = {MDPI},

abstract = {To explore a genomic pool of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the pandemic, the Ministry of Health of the Slovak Republic formed a genomics surveillance workgroup, and the Public Health Authority of the Slovak Republic launched a systematic national epidemiological surveillance using whole-genome sequencing (WGS). Six out of seven genomic centers implementing Illumina sequencing technology were involved in the national SARS-CoV-2 virus sequencing program. Here we analyze a total of 33,024 SARS-CoV-2 isolates collected from the Slovak population from 1 March 2021, to 31 March 2022, that were sequenced and analyzed in a consistent manner. Overall, 28,005 out of 30,793 successfully sequenced samples met the criteria to be deposited in the global GISAID database. During this period, we identified four variants of concern (VOC)—Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529). In detail, we observed 165 lineages in our dataset, with dominating Alpha, Delta and Omicron in three major consecutive incidence waves. This study aims to describe the results of a routine but high-level SARS-CoV-2 genomic surveillance program. Our study of SARS-CoV-2 genomes in collaboration with the Public Health Authority of the Slovak Republic also helped to inform the public about the epidemiological situation during the pandemic. © 2022 by the authors.},

keywords = {Sars-cov-2, Viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Smoľak2022,

title = {Analysis of RNA virome in rectal swabs of healthy and diarrheic pigs of different age},

author = {D. Smoľak and S. Šalamúnová and A. Jacková and M. Haršányová and J. Budiš and T. Szemes and Š. Vilček},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85140085232&doi=10.1016%2fj.cimid.2022.101892&partnerID=40&md5=e964d61275f2138aec68eafa8217a8a2},

doi = {10.1016/j.cimid.2022.101892},

issn = {01479571},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Comparative Immunology, Microbiology and Infectious Diseases},

volume = {90-91},

publisher = {Elsevier Ltd},

abstract = {The porcine enteric virome comprises a wide range of eukaryotic and prokaryotic viruses in healthy and diarrheic pigs. As RNA viruses are considered to be important agents responsible for diarrhoea in pigs, this work was focused on the RNA virome. To identify viruses, a next generation sequencing technique and bioinformatics analysis was employed. A wide spectrum of viral genera with RNA genomes, such as Kobuvirus, Picobirnavirus, Teschovirus, Posavirus, Mamastovirus, Enterovirus and Rotavirus were identified in both diarrheic and healthy pigs. No clear differences in the virome composition were found between healthy and diarrheic pigs. The data visualisation using Non-Metric Multidimensional Scaling as well as by the Analysis of Similarities test suggested that the virome depended on the age of animals and differed in piglets when compared to weaned and fattening pigs. © 2022 The Authors},

keywords = {Viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Šubr2020,

title = {Comparative transcriptome analysis of two cucumber cultivars with different sensitivity to cucumber mosaic virus infection},

author = {Z Šubr and L Predajňa and K Šoltys and B Bokor and J Budiš and M Glasa},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079843504&doi=10.3390%2fpathogens9020145&partnerID=40&md5=c92697bfc9481af2a87da1aae35966e1},

doi = {10.3390/pathogens9020145},

issn = {20760817},

year  = {2020},

date = {2020-01-01},

journal = {Pathogens},

volume = {9},

number = {2},

publisher = {MDPI AG},

abstract = {Cucumber mosaic virus (CMV), with extremely broad host range including both monocots and dicots around the world, belongs to most important viral crop threats. Either natural or genetically constructed sources of resistance are being intensively investigated; for this purpose, exhaustive knowledge of molecular virus-host interaction during compatible and incompatible infection is required. New technologies and computer-based “omics” on various levels contribute markedly to this topic. In this work, two cucumber cultivars with different response to CMV challenge were tested, i.e., sensitive cv. Vanda and resistant cv. Heliana. The transcriptomes were prepared from both cultivars at 18 days after CMV or mock inoculation. Subsequently, four independent comparative analyses of obtained data were performed, viz. mock-and CMV-inoculated samples within each cultivar, samples from mock-inoculated cultivars to each other and samples from virus-inoculated cultivars to each other. A detailed picture of CMV-influenced genes, as well as constitutive differences in cultivar-specific gene expression was obtained. The compatible CMV infection of cv. Vanda caused downregulation of genes involved in photosynthesis, and induction of genes connected with protein production and modification, as well as components of signaling pathways. CMV challenge caused practically no change in the transcription profile of the cv. Heliana. The main differences between constitutive transcription activity of the two cultivars relied in the expression of genes responsible for methylation, phosphorylation, cell wall organization and carbohydrate metabolism (prevailing in cv. Heliana), or chromosome condensation and glucan biosynthesis (prevailing in cv. Vanda). Involvement of several genes in the resistant cucumber phenotype was predicted; this can be after biological confirmation potentially applied in breeding programs for virus-resistant crops. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Plants, Transcriptomics, Viruses},

pubstate = {published},

tppubtype = {article}

}