When a plant virus was inoculated into its host and established a infection, the virus will move up to the meristem where the virus replicates and then spread into the newly developed leaves and show symptom. The newly replicated viruses are accumulated in these leaves first and will be detected easily. In your case, you detect the virus using PCR which is very sensitive, if you analyse the inoculated leaves, you can detect the inoculated virus even they did not establish  an infection. This is another reason you need to detect the newly emerged leaves where any detected virus are newly replicated virus from your inoculation.

When a plant virus was inoculated into its host and established a infection, the virus will move up to the meristem where the virus replicates and then spread into the newly developed leaves and show symptom. The newly replicated viruses are accumulated in these leaves first and will be detected easily. In your case, you detect the virus using PCR which is very sensitive, if you analyse the inoculated leaves, you can detect the inoculated virus even they did not establish  an infection. This is another reason you need to detect the newly emerged leaves where any detected virus are newly replicated virus from your inoculation.

my view would be that viruses cannot enter the meristem and thus this tissue is used as explant for micropropagation...

during DNA extraction from tomato leaves it is usually advised in the articles to pick up young leaves as they are easy to use for extraction procedure and they contain comparatively less amounts of secondary metabolites, which cause hindrance in DNA extraction final steps and later purification of DNA for end use.