The federal government can do so, once the President has declared a state of emergency (which, he has).
I think people are also conflating what the Federal government can do, which is very little, and what local governments can do, which is considerably more. Broadly speaking, the Federal government operates in an "advise and support" role, the legal authority resides with the States and localities. This is an example of where State sovereignty becomes very obvious. But even with the States exercising their broader powers, they are still restricted from violating fundamental Constitutional rights like freedom of speech, assembly, travel, etc.
Until then, the President of the United States can make an order, and if it is enforced by local authorities, it's defacto legal for the duration.
This happens in many other contexts, there is no reason to believe it wouldn't happen here.
> or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
The interstate commerce clause is fundamentally restricted in scope such that it does not violate fundamental individual rights i.e. you cannot use the commerce clause to restrict free speech.
Freedom of travel -- what we are talking about with a "lockdown" -- is a thoroughly adjudicated fundamental right per the Supreme Court. Using the commerce clause to restrict travel in various ways has already been rejected by the Supreme Court, repeatedly.
But wait, haven't there been quarantines during past epidemics?