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Maybe he just got lucky?

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Dr.Phlox and Klingon Scientist Antaak create a treatment which stops the virus from killing those infected during the second stage (the part where the ridges dissolve), this treatment makes the affected individual noncontagious. Those affected Klingons Worf encountered would have been either directly infected or descended from some one with virus and by virtue of the fact that they were alive(the augment virus is fatal) would have received this treatment and thus could not have been contagious.

For the same reason contemporary humans don't get measels, mumps or rubella

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