The Church teaches that neither holy water nor even the consecrated wine / blood of Christ prevent contagion. I think many people don't realize that, though.
The Catholic Church learned its lesson with Galileo. It stays out of science only things. For example, the evolution vs. creationism battle is not typically fought by Catholics; that is a protestant fight. (Although Francis has been dabbling a bit lately with his climate talk, I don't expect his views to be treated as anything other than that...his views.)
Sure, you can pray for deliverance from a pandemic...but the prayer would typically be answered with spiritual grace, not with physical immunity or a physical cure. Physical effects like that would be classified as an outright miracle, which is to say, totally unpredicted/unexpected.
(Sorry if I ruined a joke. TTTK's response was far better than mine.)