Population structure and genetic variation of cucumber mosaic virus isolates in Serbia: evidence for high diversity and the occurrence of natural recombinant and reassortant isolates

Cucumber mosaic virus (CMV) causes significant economic losses and threatens the sustainable production of many important crops. This study represents the first analysis of CMV genetic diversity and population structure in Serbia, based on all five ORFs from nineteen isolates collected across various hosts and regions. Results of molecular and population genetic investigations revealed high genetic diversity and the presence of numerous genetic variants. Phylogenetic analyses showed that isolates from all three subgroups exist in Serbia, with IA being the most prevalent and IB occurring at the 1a gene only. Although findings indicate that majority of the observed variation arises from differences between subgroups, intra-subgroup fixed polymorphisms were also identified. Notably, both recombinants and reassortants were detected, indicating dynamic genetic exchange within the population. Recombination between subgroups IA and II was confirmed in both RNA 2 (II-IA,II-II,II and IB-IA,II-IA,IA) and RNA 3 segments (IA-IA,IA-IA,II), with recombination in the RNA 2 segment being predominant. Additionally, both types of reassortment, including IA/IB (IB-IA,IA-IA,IA) and IA/II (II-IA,IA-II,II) reassortants, were recorded. Moreover, we uncover a novel reassortant/recombinant variant (IB-IA,II-IA,IA) in the natural CMV population. Finally, results of a neutrality test across all five loci suggest demographic effects consistent with population size expansion following bottleneck events during host plant infection. This study provides the first molecular insight into CMV population structure in Serbia, offering new insights into the regional diversity and evolution of the virus. By identifying recombinant and reassortant CMV isolates circulating in Serbia, this work reveals previously unrecognized evolutionary processes shaping CMV populations in the region. These findings fill a significant geographic gap in CMV research in Western Balkans and contribute to a broader understanding of CMV evolution, diversification, and population dynamics globally.