Answer: I'm not convinced that your canna plants have a virus. The symptoms you describe sound more like a rhizome rot since the browning is at the base of the plant.
Canna mosaic virus causes chlorotic strips between the veins of the foliage. In severe cases, the disease causes stunting and plant death. The disease is vectored by aphids feeding on infected plant material so if you have lots of plant, you'll want to scout for and control aphids. Plants infected with a virus cannot be treated to eradicate the virus but under good growing conditions, viral symptoms may be less evident. However, the virus is still present and symptomatic plants should be removed and destroyed. Just FYI, fungicides will have no effect against viruses.
Since we're not sure what the problem is, why not take a sample of an affected plant to your local cooperative extension office for positive diagnosis and control strategies?
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