Which city is the one being searched for the virologist?
Frankly, I don't see how you could entertain the second interpretation at all! From this picture: https://boardgamegeek.com/article/20687079#20687079


  ADVANCE 3 SPACES IF YOU DISCARD THE CARD MATCHING YOUR CITY


There is clearly a distinction between the [city listed on the] discarded card and the city where the active player's pawn is located. Furthermore, since you are able to discard multiple cards, it doesn't make any sense that the cities on those cards would be "yours". 

"Your city" is the city where you are.