On his first official visit abroad, the new senator from Illinois, Barack Obama, was taken to a facility in Ukraine where the U.S. helped scientists working with dangerous biological materials. But rather than produce weapons, U.S. officials in that ramshackle building were trying to prevent lethal pathogens from falling into the hands of terrorists.


“I removed a tray of glass vials containing Bacillus anthracis, which is the bacterium that causes the anthrax,” recalls Andrew Weber, the Pentagon official who was in charge of the U.S.-funded program that worked with the Ukrainian government. Mr. Weber said he showed the tray “to a very concerned-looking young senator.”


Mr. Obama himself recalled seeing in his 2005 trip to Ukraine “test tubes filled with anthrax and the plague lying virtually unlocked and unguarded.”


A decades-old Pentagon program that was used to secure biological weapons across the former Soviet Union—and to build trust between Washington and Moscow after the Cold War—has instead become a new flashpoint in an information war between the two countries in the wake of Russia’s invasion of Ukraine.


Moscow has accused the Pentagon of funding weapons work in Ukraine’s biological laboratories. “These were not peaceful experiments,” Russian Foreign Minister Sergei Lavrov said earlier this month.


China, whose leader Xi Jinping has cultivated a close relationship with Russian President Vladimir Putin, has echoed those allegations. “Russia has found during its military operations that the U.S. uses these facilities to conduct bio-military plans,” the Chinese Foreign Ministry spokesman told reporters.


U.S. officials have flatly denied those claims and warned that Moscow could use its allegations to justify its own use of weapons of mass destruction in Ukraine.


“They’re outrageous claims,” said Robert Pope, the head of the Defense Threat Reduction Agency, or DTRA, the arm of the Pentagon in charge of running the program. “We were created 30 years ago to eliminate weapons of mass destruction, and Russia knows well we eliminate weapons of mass destruction.”


The program, which dates back to 1991 and continues today, stretches across the former Soviet Union. Since the program started, the Pentagon has spent approximately $12 billion on securing material used in weapons of mass destruction in post-Soviet republics, according to a DTRA spokeswoman. Of those funds, about $200 million has been spent on the biological work in Ukraine since 2005. The funds have supported dozens of labs, health facilities and diagnostic sites around the country, the DTRA spokeswoman said.


Mr. Weber, who was in charge of negotiating the initial agreement with Kyiv to work on securing the country’s biological materials and facilities, said that work expanded to Ukraine after the 9/11 attacks, when al Qaeda terrorists hijacked aircraft and crashed them into the World Trade Center towers and the Pentagon.


U.S. policy makers grew worried about the potential for terrorists to steal biological materials—fears that were heightened after letters containing anthrax were sent in the U.S. mail to congressional offices and media outlets. The FBI eventually concluded that an American scientist employed at a military lab sent the letters.


The president of Ukraine at the time, Leonid Kuchma, concerned about the threat of terrorism in his own country, asked the U.S. for help. Since the collapse of the Soviet Union a decade earlier, Ukraine had been starved of the funds needed to secure its biological facilities.


Mr. Weber put together a team that visited Ukraine’s biological and chemical facilities, which ranged from large laboratories to small veterinary research centers. “We found that a number of them had dangerous pathogen collections left over from Soviet days,” he said. “They were in pretty bad shape.”


Ukraine’s laboratories—unlike some in other former Soviet republics—weren’t directly involved in the Cold War biological-weapons program, but they did have pathogens that fed into offensive work, according to Mr. Weber.


Those pathogens, like anthrax, could pose a threat if released, whether accidentally or on purpose. The focus of U.S. work in Ukraine was to consolidate that biological material, much of it related to agriculture, into secure facilities, which the U.S. would pay to build or upgrade.


Paul McNelly, who from 1995 to 2003 directed the U.S. chemical and biological elimination programs in Russia, Kazakhstan and Uzbekistan, said he was stunned with what he saw inside the former Soviet facilities.


“You would walk into these places and the refrigerators that stored these dangerous pathogens, they had no locks on them at all,” Mr. McNelly said. “There would be vials that were labeled tularemia, plague, different things like that. And these people, most of them, weren’t masked. Their gowns were antiquated. It was horrible.”


As part of the program, the Pentagon spent $1 billion to build the Russians a facility in Shchuchye, Siberia, to demilitarize some two million chemical weapons. By the time it was done in 2009, ties with Moscow were growing tense. The price of oil was going up, giving Russia more revenue to wean itself off foreign assistance.


As a result, the Russian government became a less-willing partner to the Pentagon’s drive to secure the deadly materials, according to James Tegnelia, who served as the head of DTRA from 2005 to 2009. “They wanted our money, but they didn’t want to admit that we built the facility,” Mr. Tegnelia said. “You could see that they were getting ready to pull back.”


Russia’s Foreign Ministry had in the past praised the program. But by 2012, Moscow declined to renew cooperation, saying it could pay for the work on its own. A spokesman for the Russian Embassy in Washington, D.C., didn’t respond to a request for comment on the Pentagon program.

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