If the vaccines were made for eugenic reasons, then to make mankind stronger - eugenicists and transhumanists believe that mankind can only survive and colonize the universe if the strongest individuals survive. So they would never have targeted the strong right, but the scared people on the left.
But I think they haven't targeted people at all, they just made huge medical trials to advance the technology (they want to use DNA manipulation for their own bodies), and they collected DNA samples.
They can do targeted killing with viruses too, they have collected enough DNA material to create viruses that release their payload only when they detect the DNA of the targeted group. This will be much more hidden than a vaccination campaign, a virus can spread without causing symptoms.
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