How/how often to clean watering fountain when cat has herpes flare up?

Robin saw the vet again, got new meds. Vet believes his herpesvirus is in his eye in the conjunctiva, and that dust and allergies in the environment are causing his eye to water more than normal, causing the watering eye he's had for the past 2 months.

It's occurred to me that his water bowls might be contributing to this, if the virus happens to get in the water.

I've no issue with his one bowl as I can use hot soapy water every day. But how can I disinfect his CatMate waterering fountain? Its plastic. I'm sure the plastic parts can take hot water but what about the pump? Might the filter be harboring germs? How can I clean these? Would straight white vinegar be ok or would that hurt the fountain? Can I add a few drops of vinegar to the water every day? Would that discourage herpes virus from surviving in the water?

You can use vinegar to clean the fountain, but don't put it in the water. The filters should be replaceable, and there are small brush kits to clean the pump.

Thank you.