"There are no Iranian nuclear scientists in Syria," said Deputy Foreign Minister Hassan Ghashghavi, quoted by state news agency IRNA.
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The Syrian Observatory for Human Rights, a Britain-based monitoring group, said five nuclear engineers, including an Iranian, were killed Sunday as unknown assailants attacked their bus just north of Damascus, near the research centre where they worked.
Iran backs Syrian President Bashar al-Assad who has since March 2011 faced an armed revolt aimed at toppling his regime, but it denies providing his forces with military support.
It is in talks with world powers concerned over Iran's nuclear programme, although Tehran insists it is for purely civilian use and not aimed at building a bomb.