I doubt the zombie infection is actually a virus. Viruses require the metabolism of a living cell to reproduce. So what could it be then? Here are two possibilities:

1. It's an ancient organism unearthed, say, by a natural gas fracking operation (damn oil companies!). There have been a number of mass extinctions in Earth's history. The one that came closest to wiping out all life on the planet was the Permian-Triassic Event around 250 million years ago. Suppose back in the Permian Era there was a necrotizing parasitic slime mold. A parasite that required a dead host. Certain species of animal carried the slime mold in their bodies; most (or all) members of those species would've been carriers but suffered no ill effects because the mold remained dormant until their deaths. Then the animal "came back" and wandered around in its reanimated state, attacking other creatures, eating them when possible, creating the occasional new walker, until slow decomposition incapacitated it.

Perhaps the undigested remains of victims contained the parasite and so zombie droppings helped to spread it around. Slime molds can take on several different forms during their life cycle, including these things called fruiting bodies that look a bit like mushrooms growing in the woods, and a fluid-like state called plasmodium which is how you'd find it in walker blood. All this would've been a normal part of the ecosystem. A certain percentage of compatible animal hosts would be undead. Most though would be living. Because no species would exist in the excessive numbers of modern day humanity the balance would be maintained. No ZA-like uncontrolled spread. No vast herds of undead. When the mass extinction occurred, all compatible host creatures were wiped out and the slime mold disappeared from biological history ... until now.

Humans have the bad luck to re-develop a random gene that makes them the first viable hosts since the Permian. When an intact pocket containing the organism is exposed, it begins to take hold. Our overpopulation, and especially our cities with millions of people packed in like sardines, provide the perfect environment for the ancient slime mold to wreak havoc.

2. The pathogen is an out of control piece of self-replicating nanotechnology. Perhaps they were created by a deranged individual or group for the purpose of bringing down civilization. Or they might've been medical in nature, intended to repair the human body from within, but got out of containment before they were finished and so can perform only a few of their original intended functions properly.

This would explain why humans alone are affected. It would also explain what's powering the walkers. Nanites can scavenge energy from sunlight and wind, ambient temperature differences, energy storing chemical compounds in the environment, even electricity (although that source isn't available most places anymore). If they really are med bots, people reanimating could simply be the stupid little machines trying to do their thing. Being incomplete they can't actually fix up a patient and restore their life - but they won't let them die and rot away in peace either. On the other hand, if the zombie outbreak was the ultimate act of terrorism they need to track down the people responsible. The details of how the nanites work could directly result in a deployable counteragent. At the very least, you know they must have inoculated themselves against their creation. So there'd be a vaccine all ready to go.

● Any thoughts? Additional theories? This is one of the central mysteries of the series and yet they've avoided giving us any more answers than we had in season 1, from their brief encounter with Jenner at the CDC.