It's worse than that.
If they can't isolate the virus from the body - how do they sequence its RNA?
When I brought up this argument with a virologist, I got a bit of a scoff because "that is outdated and no one does that anymore." Effectively. That is - no one has actually gotten a vial of just water and the virus (or blood plasma and the virus - or some similar known background and the virus with no cells or other contaminants).
If you can't isolate the virus, then how do you sequence it?
The answer is that you test for the presence of certain peptide sequences in samples and use statistics to conjure up a virus from the data.
They haven't actually taken a bunch of these viruses and then busted them apart to read their code. They have just looked at the smear of RNA in tissue samples and then crafted an idea of what the virus code might be based on reactions and theories/observations about how viruses mutate.