simplest method will be pcr which sensitive. If many viruses then go for multipex pcr which can detect more than 5 viruses/rexn. By this way u will b able to identify mother plants which are virus free
How will you find out that this virus is only active in that plants.You mean to say that I have to do simplest PCR reaction for a single virus.If I know about viruses then go for pultiplex PCR or RT PCR, which is best method.
It all depend on which virus(es) you are targeting. One can use ELISA, PCR or NASH depending on the availability of antibody, commercial kit, or specific primers for a particular virus. Off course sensitivity increases when we move from ELISA to PCR to NASH or even RT-PCR.