So.... a virus maybe?
I've just got back to running myself after fighting with a virus that took me out totally for two weeks.
Take your time. you'll probably have a couple of days again soon where you don't feel so good. Take it easy on those days and then you should come right (fingers crossed).
Possibly, would make sense considering how long rides/runs suppress your immune system a bit. But I'm pretty sure I'm all good now. Gunna hit the road on the bike this afternoon after getting some revision done and see how it goes.