Neem and oregano oil are antiviral, antibacterial and antifungal.
You can put drops of oregano oil in soup and get it in him that way. Oegano oil is powerful stuff. It should be a staple in your cabinet. You can also put it in capsules when he's old enough to swallow them. Neem capsules are a little big, I'd wait until he's old enough to swallow them. But I've used them to route out a stubborn virus in my throat that simply would not go away after a weeks and weeks. Since then, I keep neem capsules in my cabinet to dole out for colds.