Is the human disease as bad as the Colonel believes it to be?

In the 1968 movie, humans were very primitive.

So, without any more evidence, and supposing the new trilogy is a reimagining, but essentially trying to walk towards the same situation (a planet ruled by apes, where humans are subjugated), I'd say the new virus is very likely to be the downfall of all humanity, and the Colonel had a good reason to fear it.

So exactly at what level of intelligence does the disease leave humans? Again, falling back in the 1968 original, it leaves humans at roughly the "ape" level. The only real long term evidence we have in War of the Planet of the Apes is Nova, and we don't exactly know how smart Nova was before the virus, so it isn't a fair comparison. All the things Nova did, apes can do in real life, in particular signaling.

Let's presume Nova was a healthy kid, with normal functions before the virus. Post-virus she didn't seem smart enough to understand dialogue, or have that much situational awareness. She didn't just lose her ability to speak, she lost her ability to understand words at a higher level.

On more than one occasion she disobeyed a direct order, not out of stubbornness but just absent mindedness. She still walked around without any fear on the base, where she saw a huge number of armed men, who were dangerous and prone to hurting the apes. She didn't attempt to sneak or hide. She didn't seem smart at all for a human. She clearly was much more primitive than a regular human.

The colonel represents human fear, panic, doubt. An animal cornered by things it can't fight. He represents madness, hatred and prejudice. He was given an opportunity to stop fighting but doesnt. He is ordered to stand down but doesn't. He kills anyone that represents the enemy, the virus that made apes smart and killed 90 percent of the population in a span of a decade. Be that defenseless apes or humans, family even. At the end, he Has become fanatical. A cult leader. He is not a rational source of information.

He considers the virus like he does any enemy. It must be destroyed at all costs. Other, mostly rational humans consider the virus like any other, something that can be handled within the means of medical science.

We know that Nova and her father had gone awol just months prior, but after the soldier was branded with the Alpha Omega symbol , based on the Colonel' s dialog to Ceasar. We know that he will have anyone that is infected killed, and anyone that refuses to kill the infected, so we can be sure that he will do it immediately when they are found to be infected.

What we don't know is the long term effects or the vector of the mutates virus. It could do nothing but render them mute. It could be spread by infection by other humans or it's a mutation of their existing infection of the original virus or carried by the Apes.

But the biggest thing we know is that the effects of the virus manifest themselves immediately. The movie heavy implies by cutting to a shot of Nova's blood soaked doll after Ceasar finds a bloody Colonel in his bed, that the Colonel got infected by Nova's doll. This juxtaposition of the doll makes it a clear cause and effect.

Unlike the original films where mute-ness is because the humans do not know how to speak after an uprising by apes killing humans, this version makes both due to a fatal virus. Without knowing how humans will be effected in the long run, all we can say is that the virus is quick acting and widely infecting. It is a pandemic, but we can't say to what extent. The Colonel's explanation of ape-like behavior is suspect due to fanatical racism.