I don't think you are familiar with the commerce clause [1].
It gives the federal government control to regulate anything that would effect interstate commerce which would obviously include spread of a novel infectious virus.
Obviously State issued mandatory lock-downs effect interstate commerce and that where there federal government can begin regulating.
[1] https://en.wikipedia.org/wiki/Commerce_Clause
Edit:
In 1902, the Supreme Court directly addressed a state’s power to quarantine an entire geographical area. In Compagnie Francaise de Navigation a Vapeur v. Louisiana State Board of Health, the justices upheld a Louisiana Supreme Court decision that the state could enact and enforce quarantine laws unless Congress had decided to preempt them.