I haven’t watched The Last of Us (yet), but it seems to be based on a scenario I’ve discussed before of how a zombie outbreak could (semi-plausibly) happen:
We know that fungi can infect humans. We also know that fungal networks exist in most of the world’s forests. These mycorrhizal networks have a symbiotic relationship with trees and other plants in the forest, exchanging nutrients for mutual benefit. These networks can be quite large, and there are studies that demonstrate the potential for chemical signals to be transmitted from one plant to another via the mycorrhizal network. That, in turn, means that fungal filaments could perform both vascular and neural functions within a corpse.
This leads us to the following scenario: microscopic spores are inhaled, ingested, or transmitted via zombie bite. The spores are eventually dispersed throughout the body via the bloodstream. Then they lie dormant. When the host dies, chemical signals (or, more accurately, the absence of chemical signals) within the body that occur upon death trigger the spores to activate, and begin growing. The ensuing fungal network carries nutrients to muscles in the absence of respiration or normal metabolism.
Part of the fungal network grows within the brain, where it interfaces with the medulla and cerebellum, as well as parts of the brain involving vision, hearing and possibly scent. Chemicals released by the fungi activate basic responses within these brain areas. The fungi/brain interface is able to convert the electrochemical signals of neurons into chemical signals that can be transmitted along the fungal network that extends through much of the body. This signal method is slow and imperfect, which results in the uncoordinated movements of zombies. And this reliance on the host’s brain accounts for the “headshot” phenomenon, in which grievous wounds to the brain or spine seem to render zombies fully inert.
In “zombie” ants, the fungus bypasses the brain and directly takes control on the ant’s muscles.
John Ringo’s Black Tide Rising series postulates a bio-engineered hybrid virus (flu/rabies) as the cause of a “zombie” pandemic. The latter pathogen destroys higher brain function in the infected leaving a fully functioning organism driven by mid-brain impulses only.
The main problem with trying to use viruses as tailored bioweapons is the rapidity with which they mutate; generally, towards lower morbidity, in order to maximize the chances of its ‘hosts’ spreading it around.
You can see this in the facile attempt by the club of rome’s fanclub to exterminate people with coof (though they made up for it by exterminating people with their mutagenic serum instead).