The ending of the episode shows that Patrick, the "nerdy" kid is infected!
Who/what infected him?
I did notice something funky with his eyes and there were at least 2 closeups on the same zombie in the episode where the camera zoomed in on the zombie's eyes which were also funky looking...
Is this some new threat/infection form?
It's likely this isn't the zombification virus. Shortly before that scene, Rick found one of the pigs dead. It's likely they're going for a swine flu sort of situation here, where one of the pigs got ill, the virus mutated and infected some humans, and next episode will see everyone take ill. This jives with how the boy was feeling ill earlier that day, and there were no scenes showing him coming into contact with zombies.
The main quirk here is that if someone dies from the flu, they need to quickly be killed again, since they'll turn into a zombie and become a different sort of danger.
Unfortunately, we are left with little more than speculation at this point. That said:
As a writer, I can follow a narrative thread and recognized the foreshadowing of the conversation with Rick and his son over the naming of the pig and her state of health. This conversation appears innocent enough but will serve as a sign of hidden infection in the group.
Later...
We see Patrick, sick, fevered, coughing with flu-like symptoms, dare we say "swine flu-like" symptoms. The foreshadowing is after Rick noticing the dead pig after he returns from his harrowing event with Clara.
Everything going wrong...
Adding insult to injury, the foraging party returns after losing one of their own, it appears the "30 days without an Incident" period is ended both from without and now from within, as Patrick succumbs sweaty, fevered, barely coherent (coughing over the shower water...didn't anyone notice his increased coughing? Where does he live that no one noticed this?) and dying in the shower, inside the compound with no gates between him and many potential victims...
Honestly, seeing that he was likely added in the off-season, picked up from outside of the normal and safe populations of Woodbury, how he got infected was less important THAN he got infected and there were no protocols to notice this. Curiously enough we haven't seen much in the way of infection in the series. I would think with all of the dead lying about, disease should be much more of a player than it has so far.
In a world where everyone is infected with the Zombie virus, a health survey on a daily basis, checking for infections, scratches, colds and flu symptoms, as well as a watch set on anyone who is sick (or extremely old) should be a mandatory thing.
But if they did this, they would not be on television. This is not a show about people doing the right things, but how under stress, they can make simple mistakes with long lasting repercussions.
Everybody is infected because the virus is in the air. When you're bitten there's just more virus in your body, so you die quickly.
