My 2yr old has had a runny nose x3days... The drainage is clear. Doctor says viral. Now he has fever/sore throat/vomiting/lethargy. Is it bacterial?

Probably not. Clear mucus is not a typical finding in bacterial infection. The symptoms are more suggestive of a viral illness. If the fever persists see your doctor.
Maybe. There is always the day before the appendicitis, ear infection, pneumonia, etc. If you went in for an exam and the kid had no treatable illness, it doesn't mean it won't happen the next day.Kids who drain can develop other issues overnight, and if the symptoms have increased and the kid is feeling worse, it may be something treatable. It might also just be the natural course of a virus.

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