Plus if Krauser did indeed have a modified control plaga, then why doesn't he just go straight back to Wesker if he is carrying in his body what Wesker and The Organisation are seeking in the first place?
He couldn't have been implanted with a subordinate plaga as he wouldn't be in control of his own actions, let alone control his own mutation. Saddler always had a mis-trust of him so if anything he would want Krauser to have a sub-ordinate plaga, so he could keep him in check.
There's nothing to suggest she hasn't seen his arm before if say it was Wesker who did something to him.
His Plaga bears traits of the modified subordinate Plagas (he can control his mutation, but can't control other Plagas). Until someone can outright prove that he has a virus, I'm sticking to this since its the most plausible explanation with a fair amount of evidence. Randomly stating he has a virus with no real way of telling is grasping for straws.
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