I just pretend I never heard of the official explanation. It was stupid of them to even respond with such a lame ass reason, which is the one already talked about in this thread that zombie bites induce sepsis. They should have left it up to imagination. In season one the CDC guy Jenner wasn't even sure what the disease is. So I'll tell my theory because why not.

I think that whatever caused the outbreak was due to some sort of biological weapon experiment that went wrong. That or a deliberate attack which was deployed as some sort of doomsday device by a disgruntled employee. As for the pathogen, well, a fungus makes the most sense to me.

In the initial outbreak, the infection had an extremely high mortality rate and was extremely infectious. It was so infectious that every human on the planet was exposed within a month. The fungus created spores that are released by the victim on every exhale, and could travel for miles in the wind and survive for months from -60 to 60C.

However, in order to actually grow inside of a human host, the fungus requires some sort of protein or enzyme that ~95% of the population has in their bodies. Those who had it all died within a month and explains the chicken and the egg problem. Those who do not have the requisite protein/enzyme harmlessly deal with the spores as they would any other mold spore or pollen grain. I believe that the protein requirement really makes sense with my idea of it being a biological weapon gone bad. The weapon was supposed to use a very uncommon protein so that it could make whoever deployed the weapon immune while having nearly 100% efficacy on its target. A country with this weapon could insure that nobody would ever attack them. The ultimate MAD.

What the developers weren't counting on though was this fungus mutating, (or evolving, as it were). It was supposed to produce sterile spores so that it wouldn't spread too far from where the weapon was deployed. Insert typical "don't fuck with nature" cliche.

As to why bites are infectious, well that one is easy. The fungus stores the protein and secretes it into the saliva when the walker is in hunting mode, sorta like snake venom since I believe those are proteins too. Being bit introduces enough of it to allow the infection to take hold. Everyone who has died to bites after the outbreak eventually deplete their stores and become essentially harmless, and this can explain Herschel surviving being bit as he was exposed to a very small amount.

And finally for the reanimation, if you look up some pictures of mycelium you can easily see this organism taking over a human host. Note that in reality there are parasites that take over other organisms, completely controlling them. There's this worm that literally controls the brain of insects. It forces the bug to seek out water so it can lay its eggs. I think this would be too obvious though. Mycelium could easily be confused with rotten veins, and the spores could have been mistaken for pollen in preliminary tests. Practically all disease specialist did die before it could be discovered after all.

Anyway as Jenner says, the fungus is present in the brain stem since that is the only part required for movement and eating iirc. It then extends its mycelium throughout the hosts nervous and circulatory system in order to take control of peripheral nervous system and to be able to deliver nutrients and antibiotics/preservatives to keep the host "alive" for as long as possible. See: penicillin.