I mean, that's the whole point with isolation, isn't it? To tell the difference between something new and something not new, yes?
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The problem is much much older than you think. It dates back to the dawn of Germ Theory and Virology. No one has ever isolated a virus in the history of virology.
What virologists call "isolation", is the process of growing a cell culture, damaging it, and then viewing the dead cell debris under an electron microscope, which they then consider "the isolated virus", even though nothing was ever isolated by the process. Identical dead cell debris is common organic matter which is observed in nature by scientists in other biology fields.
The biochemical make up of the "isolated" particles is never analyzed. There is also never any control, because the only times a sterilized control has been included in a study, it resulted in identical debris particles without ever being contaminated with a virus.
There only times that animal tests are done, no control is included, even though a control would be the only way to rule out the environment and handling of the animals being the cause of the observed outcomes.