Molecular Identification and Phylogenetic Analysis of Tomato Mosaic Virus Infecting Tomato in Uzbekistan

Tomato mosaic virus (ToMV) is one of the most important viral pathogens affecting tomato production worldwide. This study investigated the occurrence, molecular characterization, and phylogenetic relationships of ToMV isolates infecting tomato plants in the Samarkand region of Uzbekistan. Field surveys conducted in May 2024 identified typical virus-like symptoms in tomato plants, including mosaic patterns, chlorosis, leaf deformation, and fruit malformations. Sixty symptomatic samples were collected and analyzed using reverse transcription–polymerase chain reaction (RT-PCR) with universal tobamovirus primers and ToMV-specific primers targeting the coat protein (CP) gene. RT-PCR screening revealed that 42 samples (70%) were infected with tobamoviruses, of which 29 (48.3% of all tested plants) were specifically positive for ToMV. Two representative isolates, Samarkand-1 and Samarkand-2, were sequenced and deposited in GenBank under accession numbers OR400153 and OR400155. Phylogenetic analysis based on CP gene sequences demonstrated that the two Uzbek isolates belong to distinct evolutionary lineages: Samarkand-2 clustered with East Asian isolates, whereas Samarkand-1 grouped with European and Middle Eastern isolates, suggesting independent introduction events likely associated with international seed trade. Amino acid comparison of the CP revealed two substitutions in the Samarkand-1 isolate, while Samarkand-2 was identical to the reference isolate DSMZ PV-0143 from the USA. The results indicate considerable genetic diversity of ToMV circulating in Uzbekistan and highlight the importance of molecular surveillance, the use of certified virus-free seeds, and strict phytosanitary measures to prevent the further spread of diverse ToMV lineages in Uzbekistan's tomato production systems.

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