What is the timing of the Hidden Pocket effect?
This card is definitely ambiguous, which is strange, as all the other virulent strain Epidemic cards are quite clear about when they take effect. However, Tom Lehmann, the game's designer, has actually answered this specific question on BoardGameGeek:


  Hidden Pocket is resolved after Infect (and before Intensify).
  
  So, if the Virulent Strain disease has been eradicated and a city of
  that disease is drawn during the Infect step, you don't place 3 cubes
  on it (as per the normal eradication rules).
  
  However, that card then goes into the Infection Discard Pile (see page
  6 of the Pandemic rules), and therefore will end up with 1 cube on it
  when Hidden Pocket is applied, before resetting the Infection Discard
  Pile.


So yeah, it's pretty nasty!