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I have a shiny legendary that I got from the GTS, and recently learned that it is hacked. But, it already infected the event shiny Zeraora from the Sword and Shield games. Is the Zeraora now (at least a bit) illegitimate?

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All in the eye of the beholder. Does it bother you? Does it bother Timmy who lives next door?

The game does not store enough information about where Pokerus originated that a person (or the game itself) without knowledge of the events could look at the "victim" Pokemon and retell your story. So, as far as tournament legitimacy is concerned, the Pokemon is all clear (and if it weren't, then we'd be rewriting a lot of history of competitive players spreading hacked Pokerus).

However, if you really wanted to forensicate this, then you might look into the strain of Pokerus shared between the two Pokemon. If the hacked Pokemon and the Zeraora share the same strain of Pokerus (of which there are 14 possible), then a person using a tool like PKHeX might conclude that beyond a reasonable doubt, one of those Pokemon spread Pokerus to the other -- and we all know which one had it first.

But nobody except you is going to put your save through PKHeX, and Pokemon's hack checks need to be less speculative than that. In most people's book, you'd be welcome not to care.

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