There are several implants/powers/qualities that give resistance to disease, but there are no disease rules. How do they work?

http://forums.dumpshock.com/index.php?showtopic=17378 talks about this in relation to SR4.

I suspect the SR5 rules will be similar to SR4, so see Augmentation, pp. 129 - 135.

Tzeentch is correct. They're probably going to be very similar to the rules in SR4. At least if I wind up writing them (and this is far from certain).

Of course not to be left behind, some bugs have gotten smart.. matrix smart......

Influenza 2.0
Vector: Inhalation
Speed: 12 hours (14)
Penetration: 0
Power: 2
Nature: Viral
Effect: Stun Damage, Disorientation
The flu causes fatigue, muscular aches, stomach distress, and a
runny nose. It is an extremely common viral affliction, in no small
part because it mutates extremely quickly.

Wireless Bonus: Mutates faster to better match it's victim's physiology.
+2 Penetration, +2 Power.
Also causes Interrupt Action: Cough (-5 Initiative) every combat turn.

Does this mean that our decker can brick influenza? sweet!

Only Influenza 2.0, and only if its Wireless capabilities are enabled at the time.

... See, you're joking, but Code Induced Diseases ARE a thing - they were introduced in Unwired as a Dissonant Echo. There's no reason this isn't a viable option for one (though as far as the list of "viable options for CID's" goes, this is rather tame).