[quote=@Mao Mao]Does that mean ARGUS/S.H.I.E.L.D. was abolished, or did they never exist in the first place? Does that apply to the CIA as well, or is The Agency a separate government organization that works alongside other them and other organizations? 
[/quote]

ARGUS doesn't exist in this continuity, it was every real-world organization and SHIELD. The Agency would be the first other major fictional government outfit from the comics to come to fruition (apart from shadow organizations like Weapon X and the like). 

SHIELD exists, but its influence on the US government has been placed in an awkward position since Lord's election, much to Fury's chagrin.