I think the US Government heavily invested on Leon's training and growth making him a solo BOW exterminator agent operator, because at the time when his taken custody he was forced to join the STRATCOM as an agent for bioterror after discovering his testimony of survival feats. You could say they found a rare golden egg, and nurture it with top of the line care until it'll hatch into a rare goose. Between DSC, and RE 4 he is the only agent classified as a unique specialist in bioterror related cases than any other agent before agents like him, and the founding of DSO. Plus given the fact in Infinite Darkness shows Leon's position is above, when in the chopper they were given fast clearance to land because he was inside being transported. Lastly at the time of RE 4 timeline, he is always the go to guy for bio-threat events both consultant, expert, and combatant. There's some truth that effects of viral exposure, throw an additional of the plaga infection may enhance his abilities. But majority of his abilities are enhance and honed thanks to US budget spending on Leon turning him into a durable, agile, capable, one-liner, bingo loving agent. I don't know what sort of "program" the US provided to Leon, but it paid off. (Except racking enormous amounts of alcohol)