High prevalence and low genetic diversity of grapevine yellow speckle viroid 1 in Slovakia: down the rabbit hole of RNA secondary structure and phylogeny
Grapevine yellow speckle viroid 1 (GYSVd-1) is a widespread subviral pathogen affecting grapevine (Vitis vinifera L.), with potential implications for viticulture. This study investigates the prevalence, genetic variability, intrahost population polymorphism and secondary RNA structure of GYSVd-1 in...
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Frontiers Media S.A.
2025-04-01
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| Series: | Acta Virologica |
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| Online Access: | https://www.frontierspartnerships.org/articles/10.3389/av.2025.14361/full |
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| author | Jana Kemenczeiová Jana Kemenczeiová Peter Alaxin Peter Alaxin Lukáš Predajňa Zdeno Šubr Miroslav Glasa Miroslav Glasa Adam Achs |
| author_facet | Jana Kemenczeiová Jana Kemenczeiová Peter Alaxin Peter Alaxin Lukáš Predajňa Zdeno Šubr Miroslav Glasa Miroslav Glasa Adam Achs |
| author_sort | Jana Kemenczeiová |
| collection | DOAJ |
| description | Grapevine yellow speckle viroid 1 (GYSVd-1) is a widespread subviral pathogen affecting grapevine (Vitis vinifera L.), with potential implications for viticulture. This study investigates the prevalence, genetic variability, intrahost population polymorphism and secondary RNA structure of GYSVd-1 in Slovakia, where its molecular characteristics have been largely unexplored. Leaf samples from 49 grapevine plants across western and southern Slovakia were analyzed using RT-PCR, followed by sequencing and phylogenetic analyses. GYSVd-1 was detected in 73% of the samples, demonstrating high prevalence rates across vineyards in Slovakia. Sequence analysis revealed a high degree of genetic similarity among Slovak isolates, with nucleotide identity ranging from 96.2% to 100%, consistent with low variability reported globally. Phylogenetic analyses showed no specific grouping of Slovak isolates. Intrahost variability, assessed via subcloning of RT-PCR products, demonstrated the presence of random mutations among viroid clones, consistent with quasispecies nature of viroids in their hosts. These findings suggest that both interhost and intrahost viroid populations evolve under similar pressures to maintain structural stability essential for viroid function. Secondary RNA structure analysis of Slovak GYSVd-1 isolates revealed that all unambiguous sequences exhibited the characteristic rod-like conformation. In contrast, a significant proportion of sequences from mixed populations failed to form proper rod-like structures, suggesting that these variants may lack biological viability. Overall, this study unveils the prevalence of GYSVd-1 in Slovak vineyards and provides valuable insights to guide future phylogenetic studies and structural analyses of viroids. |
| format | Article |
| id | doaj-art-28980880ed874ae9b5308fd314e8a6b3 |
| institution | DOAJ |
| issn | 1336-2305 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Frontiers Media S.A. |
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| series | Acta Virologica |
| spelling | doaj-art-28980880ed874ae9b5308fd314e8a6b32025-08-20T03:17:44ZengFrontiers Media S.A.Acta Virologica1336-23052025-04-016910.3389/av.2025.1436114361High prevalence and low genetic diversity of grapevine yellow speckle viroid 1 in Slovakia: down the rabbit hole of RNA secondary structure and phylogenyJana Kemenczeiová0Jana Kemenczeiová1Peter Alaxin2Peter Alaxin3Lukáš Predajňa4Zdeno Šubr5Miroslav Glasa6Miroslav Glasa7Adam Achs8Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, SlovakiaFaculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, SlovakiaInstitute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, SlovakiaFaculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, SlovakiaInstitute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, SlovakiaInstitute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, SlovakiaInstitute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, SlovakiaFaculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, SlovakiaInstitute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, SlovakiaGrapevine yellow speckle viroid 1 (GYSVd-1) is a widespread subviral pathogen affecting grapevine (Vitis vinifera L.), with potential implications for viticulture. This study investigates the prevalence, genetic variability, intrahost population polymorphism and secondary RNA structure of GYSVd-1 in Slovakia, where its molecular characteristics have been largely unexplored. Leaf samples from 49 grapevine plants across western and southern Slovakia were analyzed using RT-PCR, followed by sequencing and phylogenetic analyses. GYSVd-1 was detected in 73% of the samples, demonstrating high prevalence rates across vineyards in Slovakia. Sequence analysis revealed a high degree of genetic similarity among Slovak isolates, with nucleotide identity ranging from 96.2% to 100%, consistent with low variability reported globally. Phylogenetic analyses showed no specific grouping of Slovak isolates. Intrahost variability, assessed via subcloning of RT-PCR products, demonstrated the presence of random mutations among viroid clones, consistent with quasispecies nature of viroids in their hosts. These findings suggest that both interhost and intrahost viroid populations evolve under similar pressures to maintain structural stability essential for viroid function. Secondary RNA structure analysis of Slovak GYSVd-1 isolates revealed that all unambiguous sequences exhibited the characteristic rod-like conformation. In contrast, a significant proportion of sequences from mixed populations failed to form proper rod-like structures, suggesting that these variants may lack biological viability. Overall, this study unveils the prevalence of GYSVd-1 in Slovak vineyards and provides valuable insights to guide future phylogenetic studies and structural analyses of viroids.https://www.frontierspartnerships.org/articles/10.3389/av.2025.14361/fullApscaviroid alphaflavivitisdetectionepidemiologymolecular diversityVitis vinifera |
| spellingShingle | Jana Kemenczeiová Jana Kemenczeiová Peter Alaxin Peter Alaxin Lukáš Predajňa Zdeno Šubr Miroslav Glasa Miroslav Glasa Adam Achs High prevalence and low genetic diversity of grapevine yellow speckle viroid 1 in Slovakia: down the rabbit hole of RNA secondary structure and phylogeny Acta Virologica Apscaviroid alphaflavivitis detection epidemiology molecular diversity Vitis vinifera |
| title | High prevalence and low genetic diversity of grapevine yellow speckle viroid 1 in Slovakia: down the rabbit hole of RNA secondary structure and phylogeny |
| title_full | High prevalence and low genetic diversity of grapevine yellow speckle viroid 1 in Slovakia: down the rabbit hole of RNA secondary structure and phylogeny |
| title_fullStr | High prevalence and low genetic diversity of grapevine yellow speckle viroid 1 in Slovakia: down the rabbit hole of RNA secondary structure and phylogeny |
| title_full_unstemmed | High prevalence and low genetic diversity of grapevine yellow speckle viroid 1 in Slovakia: down the rabbit hole of RNA secondary structure and phylogeny |
| title_short | High prevalence and low genetic diversity of grapevine yellow speckle viroid 1 in Slovakia: down the rabbit hole of RNA secondary structure and phylogeny |
| title_sort | high prevalence and low genetic diversity of grapevine yellow speckle viroid 1 in slovakia down the rabbit hole of rna secondary structure and phylogeny |
| topic | Apscaviroid alphaflavivitis detection epidemiology molecular diversity Vitis vinifera |
| url | https://www.frontierspartnerships.org/articles/10.3389/av.2025.14361/full |
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