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At some point, the virus in use was no longer cowpox, but vaccinia.
en.wikipedia.org
The most common notion is that vaccinia virus, cowpox virus, and variola virus (the causative agent of smallpox) were all derived from a common ancestral virus.
en.wikipedia.org
Four orthopoxviruses cause infection in humans: variola, vaccinia, cowpox, and monkeypox.
en.wikipedia.org
Scientists have not determined exactly when the change or mutation occurred, but the effects of vaccinia and cowpox virus as vaccine are nearly the same.
en.wikipedia.org

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