Tomato spotted wilt virus in tomato from Croatia, Montenegro and Slovenia: genetic diversity and evolution

Dijana Skoric¹Jelena Zindovic²Dorotea Grbin¹Patrik Pul¹Vladan Božović³Paolo Margaria⁴Nataša Mehle^5,6Anja Pecman⁵Zala Kogej Zwitter^5,7Denis Kutnjak⁵Ana Vučurović^5*

• ¹Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
• ²Department of Plant Protection, Biotechnical Faculty, University of Montenegro, Podgorica, Montenegro
• ³Faculty for Food Technology, Food Safety and Ecology, University of Donja Gorica, Podgorica, Montenegro
• ⁴Plant Virus Department, Leibniz Institute DSMZ GmbH, Braunschweig, Germany
• ⁵Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana, Slovenia
• ⁶School for Viticulture and Enology, University of Nova Gorica, Nova Gorica, Slovenia
• ⁷Jožef Stefan International Postgraduate School, Ljubljana, Slovenia

Tomato spotted wilt orthotospovirus (TSWV) is a major plant pathogen causing significant economic losses in tomato production worldwide. Understanding its genetic diversity and evolutionary mechanisms is crucial for effective disease management. This study analysed TSWV isolates from symptomatic tomato plants collected across Croatia, Montenegro and Slovenia between 2020 and 2024. High-throughput sequencing (HTS) was employed to obtain whole-genome sequences, followed by phylogenetic analyses to assess genetic variability and relationships among isolates from these three countries and other isolates of worldwide geographic origin. Phylogenetic analyses placed all studied isolates within the L1-M3-S3 genotype, commonly associated with solanaceous crops in Europe. While Croatian and Slovenian isolates exhibited high genetic similarity, Montenegrin isolates clustered in a distinct subgroup, showing closer relationships to Asian and Mediterranean accessions. Despite the severe disease symptoms observed, no substitutions in the NSm protein associated with resistancebreaking (RB) phenotypes were detected. These findings suggest that additional virome components, environmental factors or so far unknown mechanism(s) may contribute to infection and disease severity in tomato and strongly support the need of continuous surveillance of TSWV genetic diversity in order to inform breeding programs and develop sustainable management strategies to mitigate future outbreaks.