PokéBase - Pokémon Q&A
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I also have many Pokémon with pokerus this includes Groudon and kyogre. I can't get rid of it and now my suicune has it! it is starting to spread when I rest my Pokémon! I DO have the orbs and put them on the Pokémon.

EDIT: I got them from qr codes.

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Pokerus is only beneficial, it would not be the cause.

To see more information on pokerus see here

To activate Primal Reversion you must have the appropriate orb (red on groudon, blue on kyogre) and it will activate upon being sent out in battle. It will loose the effect afterwoods. If this does not solve it, blame it on glitches :D

EDIT: Red and blue orbs or primal reversion does not exist in x or y only in omega ruby and alpha saphire.

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Pokérus has nothing to do with this. To activate the Primal Reversion of Kyogre or Groudon, you must have them hold the Blue Orb (Kyogre) or Red Orb (Groudon). When put into battle, they will automatically transform.

The coding for the orbs and their Primal Reversions does not exist in Pokémon X & Y

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but I doesn't on mine. remember though, I have x.
The coding for the Red/Blue Orbs did not exist in XY, so you cannot activate Primal Reversion.
Astro answered it.