Characterization of cucumber mosaic virus and its satellite RNAs associated with tomato lethal necrosis in Serbia

A four-year survey (2012–2015) was carried out to examine the genetic diversity of cucumber mosaic virus (CMV) isolates infecting tomato, as well as the presence and diversity of their satellite RNAs (satRNAs), collecting a total of 226 samples throughout the most important growing regions in Serbia. Besides CMV-like symptoms, the collected samples also exhibited more severe symptoms, such as systemic necrosis of leaves, branches and stems, accompanied by fruit malformation and necrosis. In a double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), the presence of CMV was detected in approximately one quarter of the tested samples. Identification of CMV was confirmed by conventional reverse transcription-polymerase chain reaction (RT-PCR) and sequencing of the coat protein (CP) gene of a group of 11 selected Serbian CMV isolates. Phylogenetic analysis of the CMV CP sequences of these selected isolates revealed their heterogeneity, as they fell into two different subgroups, IA and II. An additional RT-PCR analysis of CMV positive isolates using satellite RNAs specific primers detected the presence of satRNAs in eight samples. Sequence and phylogenetic analyses showed that Serbian CMV satRNAs variants were very heterogeneous, belonging to necrogenic and non-necrogenic variants. Necrogenic variants were divided into two groups, B and B1, containing a characteristic ‘necrogenic consensus’ sequence at the 3′ end of the RNA. A necrotic phenotype co-determined by satRNAs was expressed in inoculated tomato plants.