The actual destruction should be fairly easy, biosecurity consultant Erik Heegaard told Popular Science in July. (See more of his, and other experts', insights into deadly, forgotten samples).) Smallpox can killed by autoclaving, then incinerating it. However, officials from the World Health Organization are supposed to witness the destruction of the forgotten U.S. vials and the WHO is a bit busy right now with Ebola. Nature News reports:
The CDC promised to destroy the NIH samples immediately, with WHO officials present. But that has proved more difficult than anticipated. . . . no WHO employee is certified to enter the CDC's high-security smallpox lab. This means that a WHO official must fly to Atlanta to witness the destruction of the virus on closed-circuit television. Arranging the trip has been made more difficult by the Ebola crisis, says Alejandro Costa, head of the WHO team in Geneva, Switzerland, that monitors smallpox issues.
Meanwhile, the vials are being kept in a U.S. Centers for Disease Control and Prevention facility in Atlanta, Georgia, which is one of the two places in the world authorized to store smallpox, according to international agreement.
Check out Nature for more on the fate of not just the forgotten vials, but smallpox samples that officials are deliberately storing in the U.S. and Russia.