Pulse Virome Profiling in India: Incidence, Diversity, and Mixed Infection Dynamics

Although India leads global food legume production, productivity remains low largely due to viral diseases. Despite the known diversity of legume-infecting viruses, comprehensive studies integrating disease incidence, severity, virome composition, co-infection dynamics, and spatial genetic variability across major pulse-growing regions of northern and central India remain limited. To address these gaps, the present study employed an integrated approach involving field surveys across 117 pulse fields in six Indian states, high-throughput sequencing, RT-PCR validation, phylogeny and MAPI-based genetic diversity analysis to characterize the pulse virome and its association with viral diseases. Yellow mosaic was the most dominant symptom, followed by leaf crinkle, with average disease severities exceeding 70% and 22%, respectively, in several districts surveyed. Among symptomatic plant samples, MYMIV was the most frequently detected virus (94.02%), followed by MYMV (70.94%) and GBNV (48.72%). Analyses of PCR-based detection of individual symptomatic samples revealed frequent mixed infections, with MYMIV+MYMV+GBNV representing the predominant co-infection combination. Satellite molecules including PaLCuB and ChiLCA were also detected in mungbean. Phylogenetic analysis revealed moderate intermixing of viral isolates across host crops and geographic regions without clear host-specific clustering. Spatial genetic analysis identified regional nucleotide divergence for MYMV and MYMIV, whereas GBNV populations showed comparatively lower nucleotide variability. Correlation analysis suggested MYMIV as the principal contributor to yellow mosaic severity, while GBNV, SYMMV and CPMMV showed stronger association with necrosis symptom. Overall, the study revealed a complex and regionally heterogeneous pulse virome dominated by begomoviruses and orthotospoviruses, highlighting the importance of continuous viral surveillance and integrated resistance breeding strategies targeting prevalent mixed infections.