Vol. 64 No. 1 (2025)
Articles

Molecular Detection and characterization of viruses infecting greenhouse-grown tomatoes in Albania

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  • Magdalena CARA,
  • Amani BEN SLIMEN,
  • Enea MITRI,
  • Orges CARA,
  • Dajana FRASHERI,
  • Jordan MERKURI,
  • Giuseppe PARRELLA,
  • Toufic ELBEAINO
Magdalena CARA
Agriculture University of Tirana, Rruga Paisi Vodica 1025, Tirana, Albania
Amani BEN SLIMEN
International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
Enea MITRI
International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
Orges CARA
International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
Dajana FRASHERI
International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Valenzano, Italy
Jordan MERKURI
Nanobalkan, Academy of Sciences of Albania, Murat Toptani Avenue, 1000 Tirana, Albania
Giuseppe PARRELLA
Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Portici, Italy
Toufic ELBEAINO
Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Portici, Italy
DOI: https://doi.org/10.36253/phyto-15811
Categories

Published 2025-05-14

Keywords

  • RT-PCR,
  • qPCR,
  • next-generation sequencing,
  • phylogenetic analysis,
  • emerging viruses

How to Cite

[1]
M. CARA, “Molecular Detection and characterization of viruses infecting greenhouse-grown tomatoes in Albania”, Phytopathol. Mediterr., vol. 64, no. 1, pp. 77–86, May 2025.

Copyright (c) 2025 Magdalena CARA, Amani BEN SLIMEN, Enea MITRI, Orges CARA, Dajana FRASHERI, Jordan MERKURI, Giuseppe PARRELLA, Toufic ELBEAINO

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This work is licensed under a Creative Commons Attribution 4.0 International License.

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Abstract

During the 2023–2024 growing season, a total of 45 tomato greenhouses were visited across five major production regions of Albania (Berat, Lushnje, Fier, Tirana, and Shkodra). A total of 196 greenhouse-grown tomato leaf samples, representing 31 varieties, were collected from plants showing virus-like symptoms. All samples were tested by RT-PCR and qPCR assays for the possible presence of significant tomato-infecting viruses and viroids, including alfalfa mosaic virus (AMV), cucumber mosaic virus (CMV), tomato brown rugose fruit virus (ToBRFV), tomato yellow leaf curl virus (TYLCV), tomato chlorosis virus (ToCV), tomato infectious chlorosis virus (TICV), tomato mottle mosaic virus (ToMMV), tomato spotted wilt virus (TSWV), tomato mild mottle virus (ToMMoV), tobacco mosaic virus (TMV), pepino mosaic virus (PepMV), potato viruses X and Y (PVX, PVY), potato leafroll virus (PLRV), tomato apical stunt viroid (TASVd), and potato spindle tuber viroid (PSTVd). In addition, Next-generation sequencing (NGS) using Illumina and MinION nanopore technologies were performed to characterize the complete genome of two Albanian ToBRFV isolates. RT-PCR and qPCR showed that ToCV, ToBRFV, AMV, and CMV were present in 25, 9.1, 4.1, and 4.1% of the samples, respectively, whereas all remaining viruses and viroids were absent. Illumina and MinION sequencing unveiled the complete genome sequences of ToBRFV (6,381 nucleotides) and of two additional viruses, i.e., Southern tomato virus, STV (3,437 nts) and tobacco vein clearing virus, TVCV (7,596 nts), both of which were not included in our initial screening. The two latter viruses were afterward diagnosed by PCR and found to be present in 2 and 3% of the tested samples, respectively. ToCV was most prevalent in Lushnje and Fier regions, while ToBRFV in Berat and Fier. The phylogenetic analyses predominantly clustered together the different Albanian viruses isolate, suggesting a local or regional origin. This study reports for the first time the presence of STV and TVCV in Albania and highlights the emergence of ToCV and ToBRFV in the country.

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