If you were really concerned about it, you can rinse off the intake with some of the filtered water. However, in general, it's not a problem. Just use basic common sense. It's not like a tiny amount of untreated water is going to hurt you. After all, people go boating on lakes and get very wet from the untreated lake water without getting sick.

If you are traveling in the third world where you need to protect yourself from viruses, perhaps it would be a different story, but most water purifiers do not have tight enough filtration to trap viruses. fortunately, in the US/Canada, viruses are not a significant concern in ground water. It's bacteria that are the main problem.