the core idea is that there are 3 different strains of the virus (red, green, blue), and the player is made to specialize in 1 of them via research. the infection logic would use a rock-paper-scisors system - red beats blue, blue beats green and green beats red.
possible effects of virus strains:
red: increase/decrease weapon damage;
green: increase/decrease movement and production speed; mess with movement orders;
blue: increase/decrease energy production and shield power; turn off shields;
now about the research, you can make it so you have to chose 1 strain that you get immunity to / positive effects from, that leaves u with 2 good strains and 1 bad one that u can now deal with in new ways (if there is mainly green virus in an area, the red virus will have a hard time spreading).
so basically it doesnt just matter if you got the virus or not, later on it will matter which strain of the virus you got in which area etc.
this would make the virus also a relevant weapon in pvp again :D
ps: obviously some people wont like this, so you can make it an option in the map settings or whatever
