Diversity and characterization of tomato viruses in Serbia

periodu od 2011. do 2015. godine, u okviru 22 administrativna okruga Srbije i 136 lokaliteta gajenja paradajza, utvrđeno je značajno prisustvo virusnih zaraza paradajza. Testiranjem 3486 sakupljenih uzoraka na prisustvo 10 virusa infektivnih za paradajz, primenom DAS-ELISA testa i/ili RT-PCR uz korišćenje virusno-specifičnih prajmera, detektovano je šest virusa paradajza: virus mozaika krastavca (Cucumber mosaic virus, CMV), virus crtičastog mozaika krompira (Potato virus Y, PVY), virus bronzavosti paradajza (Tomato spotted wilt orthotospovirus, TSWV), virus mozaika lucerke (Alfalfa mosaic virus, AMV), virus mozaika duvana (Tobacco mosaic virus, TMV) i virus mozaika paradajza (Tomato mosaic virus, ToMV). Testiranjem semena paradajza komercijalno dostupnih sorti i hibrida, koje je izvedeno 2012. godine DAS-ELISA metodom, na prisustvo četiri virusa koji se prenose semenom: AMV, ToMV, TMV i virusa mozaika pepina (Pepino mosaic virus, PepMV), nije utvrđeno prenošenje semenom paradajza ni jednog od ispitivanih virusa. Tokom petogodišnjeg perioda istraživanja utvrđeno je dominantno prisustvo CMV i PVY u različitim godinama istraživanja i lokalitetima gajenja paradajza. Pojedinačne infekcije su bile najznačajnije i njihova zastupljenost se kretala od 27,2% u 2014. godini do 60,7% tokom 2015. godine. Od mešanih infekcija najzastupljenije su bile dvostruke infekcije čija se zastupljenost kretala od 3% u 2014. godini do 33,7% tokom 2011. godine. Najzastupljeniju dvostruku infekciju činili su CMV i PVY čija se zastupljenost kretala od 5,8% tokom 2013. godine do 17,2% u 2011. godini. Trostruke i četvorostruke infekcije zabeležene su u manjem procentu i bile su značajne u pojedinim lokalitetima, a najviše su bile zastupljene sa 4,9% tokom 2011. godine. Detekcija i identifikacija svih šest prouzrokovača virusnih oboljenja na paradajzu u Srbiji potvrđena je RT-PCR metodom korišćenjem odgovarajućih specifičnih prajmera. Tokom istraživanja unapređena je molekularna dijagnostika svih šest virusa do nivoa vrste ili nižih taksonomskih kategorija. Determinisane su nukleotidne sekvence određenih delova genoma virusa i ustanovljen je stepen homologije dobijenih sekvenci sa sekvencama drugih izolata deponovanih u NCBI bazi podataka. Izolati CMV iz Srbije, na osnovu filogenetskih analiza sekvenci CP gena, grupisali su se u okviru podgrupa IA i II...In the period from 2011 to 2015, within the 22 administrative districts of Serbia and 136 localities of tomato cultivation, the significant presence of tomato virus infections was established. When testing 3486 collected samples for the presence of 10 viruses infectious to tomatoes by the DAS-ELISA test and/or RT-PCR using virus-specific primers, six tomato viruses were detected: Cucumber mosaic virus (CMV), Potato virus Y (PVY), Tomato spotted wilt orthotospovirus (TSWV), Alfalfa mosaic virus (AMV), Tobacco mosaic virus (TMV) and Tomato mosaic virus (ToMV). In 2012, tomato seeds of commercially available varieties and hybrids were tested using the DAS-ELISA method for the presence of four transmitted viruses (AMV, ToMV, TMV and PepMV) and the results show that no tomato seed transmissions of any of the tested viruses were detected. During the five-year research period, the dominant presence of CMV and PVY in different years of research and tomato cultivation sites was determined. Individual infections were most significant and their prevalence ranged from 27.2% in 2014 to 60.7% in 2015. Regarding the mixed infections, the most commonly reported cases were double infections with a prevalence ranging from 3% in 2014 to 33.7% in 2011. The most common double infection was made by CMV and PVY, whose presence ranged from 5.8% in 2013 to 17.2% in 2011. Triple and quadruple infections were minor and they were significant in certain localities, with the highest percentage of 4.9% in 2011. The detection and identification of all six viruses causing infections on tomatoes in Serbia were confirmed by the RT-PCR method using appropriate specific primers. During the study, the molecular diagnostics of all six viruses including the level of the species or lower taxonomic categories was improved. The nucleotide sequences of certain parts of the genome of the virus were determined and the degree of homology of the obtained sequences was verified determined with the sequences of other isolates deposited in the NCBI database. Isolates of CMV from Serbia, based on phylogenetic analysis of the CP gene sequences, were grouped in subgroups IA and II. Using phylogenetic analysis, based on the sequences of P1 gene, PVY isolates originating in Serbia were classified in the subclass N Europe within the clusters of necrotic strains..