The difference between an exosome and a virus is that you can put an exosome into the nose of a mouse and there will never happen anything. But you can prepare a virus in a way that it produces luciferase, and you can make a whole mouse glowing in the dark by putting such a virus into its nose. These glowing mice cannot get explained by any other mechanism.
To isolate a virus, you don't use a centrifuge, but a cell culture that can get infected by the virus. These cell cultures are handled for decades, so every single molecule is well known and can get filtered out, leaving only alien material. To make sure that no other material remains than the virus, the cell culture gets infected at one end and the virus gets extracted on the other end, after it made its way through the whole culture. The only way a virus can do that is by infecting one cell after another, there is no fluid stream it can use. The resulting virus gets sequenced, leaving an RNA sequence in a computer. There are machines that can create the RNA molecule out of the computer dataset, machines that can create the virus proteins out of the RNA molecule, and the resulting virus can infect an animal and can get isolated through a cell culture again.
Which study are you referring to about the luciferase?
Reporters are a huge toolbox used in biology, and luciferase is only one small set of tools that you can buy, for example here: https://reportergene.com/bioluminescent-imaging/
Learning to use these tools is basic knowledge for students and there are thousands of studies using these tools. This is just one example, they test how different medicine can make the mice less glowing after infection: https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC7162388/
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