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Volume 17
Issue 5
10.3390/v17050650
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

High-Throughput Sequencing Reveals Apple Virome Diversity and Novel Viruses in the Czech Republic

by
Karima Ben Mansour
1,*,
Igor Koloniuk
2,*,
Jana Brožová
1,
Marcela Komínková
1,
Jaroslava Přibylová
2,
Tatiana Sarkisova
2,
Jiří Sedlák
3,
Josef Špak
2 and
Petr Komínek
1
1
Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Czech Agrifood Research Center, Drnovská 507, 161 00 Prague, Czech Republic
2
Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
3
Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 50801 Holovousy, Czech Republic
*
Authors to whom correspondence should be addressed.
Viruses 2025, 17(5), 650; https://doi.org/10.3390/v17050650 (registering DOI)
Submission received: 5 February 2025 / Revised: 26 April 2025 / Accepted: 29 April 2025 / Published: 29 April 2025
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses, 3rd Edition)
Versions Notes

Abstract

Apple viruses pose significant threat to global apple production. In this study, HTS technology was used to investigate the apple virome in the Czech Republic. Previously reported viruses, including ACLSV, ASPV, ASGV, ApMV, AGCaV, and CCGaV, were confirmed, and near-complete genomes were assembled. Additionally, two novel viruses, ARWV1 and ARWV2 were identified for the first time in the Czech Republic. Phylogenetic analyses showed low genetic variability among ARWV2 isolates, suggesting a possible recent introduction or limited diversification. In contrast, ARWV1 isolates displayed distinct clustering in the coat protein coding region, separating symptomatic and asymptomatic samples, indicating a potential involvement of genetic determinants in symptom expression. Mixed infections were prevalent, with multiple molecular variants of ACLSV, ASPV, and AGCaV detected within individual samples, along with co-infections involving viruses from different families. Recombination analysis identified frequent recombination events in ACLSV and ASPV, often involving non-apple parental sequences, suggesting their potential for cross-host infections. Additionally, an interspecific recombination event was detected in an almond ApMV isolate, with PNRSV as a minor parent. These findings highlight the impact of agricultural practices on viral evolution and host adaptation. This study demonstrates the utility of HTS as a powerful tool for uncovering viral diversity, recombination events, and evolutionary dynamics.
Keywords: apple; HTS; molecular variants; coinfection; ARWV1; ARWV2; recombination apple; HTS; molecular variants; coinfection; ARWV1; ARWV2; recombination

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MDPI and ACS Style

Ben Mansour, K.; Koloniuk, I.; Brožová, J.; Komínková, M.; Přibylová, J.; Sarkisova, T.; Sedlák, J.; Špak, J.; Komínek, P. High-Throughput Sequencing Reveals Apple Virome Diversity and Novel Viruses in the Czech Republic. Viruses 2025, 17, 650. https://doi.org/10.3390/v17050650

AMA Style

Ben Mansour K, Koloniuk I, Brožová J, Komínková M, Přibylová J, Sarkisova T, Sedlák J, Špak J, Komínek P. High-Throughput Sequencing Reveals Apple Virome Diversity and Novel Viruses in the Czech Republic. Viruses. 2025; 17(5):650. https://doi.org/10.3390/v17050650

Chicago/Turabian Style

Ben Mansour, Karima, Igor Koloniuk, Jana Brožová, Marcela Komínková, Jaroslava Přibylová, Tatiana Sarkisova, Jiří Sedlák, Josef Špak, and Petr Komínek. 2025. "High-Throughput Sequencing Reveals Apple Virome Diversity and Novel Viruses in the Czech Republic" Viruses 17, no. 5: 650. https://doi.org/10.3390/v17050650

APA Style

Ben Mansour, K., Koloniuk, I., Brožová, J., Komínková, M., Přibylová, J., Sarkisova, T., Sedlák, J., Špak, J., & Komínek, P. (2025). High-Throughput Sequencing Reveals Apple Virome Diversity and Novel Viruses in the Czech Republic. Viruses, 17(5), 650. https://doi.org/10.3390/v17050650

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