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This is my first year trying out a small container garden on my back patio. My cucumber, tomato, and one of my sweet pepper plants seem to have a virus or something. I saw aphids on both the tomato and cucumber plants so I washed them and treated with neem oil. Are these plants done for?

It doesn't look like a virus. I do see what looks like thrip damage to the leaf and leaf miner damage. The cucumber looks like it may have some powdery mildew. Check the underside of the leaf for downy mildew.