Genetic testing. The viral genome is sequenced and edits between specimens are catalogued.

There are a shitload of mutations between most specimens. Many of these might be single amino acid flips which might not do anything at all. But the viral genome has certain core regions essential to its function. For instance, with Covid, one of these regions codes for the spike protein necessary for infecting host cells.

We can then count up the major core mutations and get an idea of how different one specimen is from another. And indeed, because this science has advanced so much, we can even make predictions about how certain mutations will affect the viral proteins, and how those changes might affect transmissibility and immune evasion.