In order to understand the ecology of viruses, it is necessary to obtain comprehensive information on virus-virus and virus-host interactions in natural systems. In this study, it is found that RNA-Seq enabled this analysis without prior assumptions about infectious viruses, virus symptoms, or host genes. New generation sequencing allows identifying potential facilitators of multiple infections. Host antiviral responses occur naturally under RNA silencing. Because research into plant viruses has focused primarily on crop diseases, little is known about these viruses in the wild. RNA sequencing in plants belonging to a natural population is used to determine the simultaneous presence or absence of all viruses whose sequence has been reported, to identify new viruses, and to quantify host transcriptomes. By introducing the criteria for the number of readings and coverage of the genome, virus-induced infections and intrinsic and latent plant-virus interactions can have important applications in controlling these pathogens.