Phenotypic symptom development in plants due to viral infection is believed to be a result of developmental defects caused by regulation of gene expression by viral suppressors. Since viral suppressors of viruses differentially regulate small RNAs (siRNA and miRNA), viral pathogenicity and symptom development in the host cannot apply universally. In present study, we demonstrated the differential effects of presence of two viruses (Tomato leaf curl virus and Cucumber mosaic virus) in organogenesis of two separate hosts (tomato and tobacco). Presence of ToLCV in the tomato explants severely affected the tomato organogenesis leading to sharp decrease in the survival percentage and severe developmental defects. On the other hand presence of CMV in the tobacco explants had not shown much effect in tobacco organogenesis as well as survival percentage. This study has not only highlighted our basic understanding of host-virus interactions in terms of viral suppressors and symptom development, but also provide an alternative way of maintaining and reviving viral cultures in vitro.