CDC blew up two years ago and the prison is not that far from Atlanta. I can't imagine the flu taking that long to reach the prison.

 

The CDC was actually rigged to blow up not to contain the pathogens, but to destroy them.

http://walkingdead.wikia.com/wiki/Center_for_Disease_Control

 

Assuming that the system worked perfectly. They could have been working on a disease that kills walkers derived from human diseases. Any walker in the area could be a carrier for that disease and it just slowly spread through random walker movement and proximity. Then again that is highly doubtful considering that the explosion was quite big and it seemed to destroy the facility thoroughly.

 

The other thing to keep in mind is that diseases will develop in any post-apocalyptic scenario. Waters are contaminated and the lack of oversight, hygiene, nutrition, and social containment will let any emerging disease spread. The same thing would happen today if mega poop hit the fan and our society collapsed. Diseases would run rampant.

 

You also have to figure that there's bound to be some new types of diseases developing just from all the rotting corpses walking around everywhere. It was only a matter of time before they encountered something like that, if you really think about it.

 

Dr. S said that people had this disease/illness before the walkers came along, so maybe someone near the prison that had the disease/illness died in/near the water that's by the prison. If that person or group died near the prison they might have reanimated and walked in the water and that's where they get some of their water (In a river or a lake). The walker that had that illness could have fell in one of the water buckets and the group thought that they cleaned it out, but they didn't. So that's three ways that the water could get infected

 

The flu virus isn't transmitted via water.

 

Omg rick broke the window before the HITs could destroy all the viruses!!!!!!!

 

I don't think it's the CDC. With the ZA the clock has been turned back. Prior to the 20th century people would sometimes die of stuff that simple anti-biotics knock out today. Also, they can't properly disinfect things and in this ZA world both new and old viruses can be lethal.

 

plus surely people are going to be physically run down. Their diet is poor, they must be going hungry and the last two years must have been hard in their overall health. They must be physically vulnerable.

 

I think you hit the nail on the head. The thousands of half living- half dead rotting sacks of flesh roaming around in close proximity to each other (see super herd, and think major cities) are the likely source of this new infection. Sure the lack of sanitation may lead to the resurgence of common illnesses but this new super strain is something entirely unique in its lethality and extreme contagion and the zombies are its likely breeding ground. You have to consider people lived in much larger cities with an even lesser understanding of disease and even poorer conditions in the history of man, during the middle ages for example. This is a small isolated pocket of people who's living conditions actually seem somewhat reasonable.

 

There's a red-eyed zombie at the fence. There are several instances where the camera focuses on him. I believe both Rick and Carl stop to look at him. He is clearly not right, even for a zombie. It's safe to assume that the infection killed him, he is carrying it with him, and he is the cause of the infection in the pigs and the people. (I'm only on episode 4 of season 4, so I don't have a lot perspective on that yet).