Cucumber mosaic virus variant with divergent RNA2 infecting solanaceous crops and their weeds in Java Island, Indonesia

Cucumber mosaic virus (CMV, Cucumovirus CMV ) is a significant plant pathogen with a wide host range, impacting agricultural productivity globally. This study investigated the genetic diversity, evolutionary dynamics, and recombination patterns of CMV in Java Island, Indonesia. A total of 52 leaf samples, including solanaceous crops (40) and their weeds (12), were collected based on viral symptoms. Twenty-nine samples (22 crops and 7 weeds) were tested positive for CMV by RT-PCR using specific primer pairs targeting partial RNA2 and RNA3, respectively, thus marking the first report of CMV infection in seven weed species in Indonesia. Phylogenetic analysis of partial RNA2 together with 41 isolates in NCBI GenBank identified the commonly reported subgroups IA, IB, and II, and positioned 3 new Indonesian isolates in the IB. However, the remaining 26 new isolates and 1 Indonesian isolates in GenBank (IA) were in a putative divergent lineage. According to analysis of partial RNA3, all 29 new Indonesian isolates belong to subgroup IB. Nucleotide identity ranged from 68.8% to 100% for RNA2 and 73.3% to 100% for RNA3. Recombination analysis detected no event in RNA2 but identified a significant recombination signal in RNA3 involving isolates from South Korea, Indonesia, and Hungary. The IA and IB populations are genetically variable with high S , η, k , and π values in both RNA2 and RNA3. Demographic analysis suggested population expansion, though results were not statistically significant. High genetic differentiation ( F ST > 0.33) between subgroups indicated limited gene flow and genetic isolation, including among the divergent lineage with others. • CMV was detected in 29 solanaceous crops and their weeds in Java Island, Indonesia. • Partial RNA2 of 26 and IA isolates formed a putative divergent lineage. • The putative divergent lineage was supported by genetic differentiation analysis.