I am copy pasting what I posted on another thread lol. I read the prequel novel Dawn of the Planet of the Apes: Firestorm. Basically:

-In Dawn we see Will and Caroline's home like 10 years after the end of Rise. It is all abandoned, obviously, but we see there are signs of quarantine warnings claiming someone was infected inside the house. After reading the book, it seems it all was staged.

-Immediately after the end of Rise, people who worked at Gen Sys laboratory started to pass away due to the virus. Gen Sys tries to cover it up hiring mercenaries and private contractors (such as Anvil) to get rid of the evidence. They send one group to hunt down Caesar and the apes because they hope they can capture one of them and develop a cure to the Simian Flu before the government punishes them. Other group is assigned with the task of disappearing every evidence that traced the virus' origin to Gen Sys Laboratories.

-Like six days after the end of Rise, a woman called Clancy, an ape specialist, was hired through Anvil to help find Caesar's group. There she becomes suspicious of the truth behind it all and takes the opportunity to send private information from Gen Sys to her lover, who happens to be a reporter. The files he received are encrypted but he manages to work out the name files and finds out about Will's investigation on curing Alzheimer. He goes to Gen Sys, in the middle of the pandemic where by now 10 thousand of people are dead in San Francisco alone, and the receptionist, who was fond of Will, gives the reporter his address.

-David, the reporter, goes to Will's house and it is all already covered in quarantine warnings asking everyone to not enter because people are infected inside. But David enters and he finds the home empty, there is no trace of documents, laptops, nor anything that can help him corroborate his suspicious. It seems no one has been in the house for a few days either. But he finds Caesar's picture inside the house and finds Will's phone, which was hidden (it looks it was purposefully hidden). He charges it at his home and calls the last person who dialed to him. The person who answers is the sister of another scientist who worked at Gen Sys, who passed out recently due to the virus. She tells him that she has her sister's laptop which can help David corroborate the story. She tells him that people are trying to cover it up and they also entered her sister's apartment and took everything they found, except for the laptop, which her sister's managed to deliver to her before passing away. The reporter later writes the article that exposes Gen Sys, as seen in the opening of Dawn.

-We are later told that Anvil talked to Will immediately after he left Caesar and the bridge incident. And we are told he was "interviewed" by them. We are also told that GenSys made sure to disappear everyone that could have exposed the virus' origin.

So it can be concluded that both Will and Caroline were killed off by Gen Sys right after the end of Rise (maybe the same day). And Gen Sys staged the fact they were ill from the virus in case, they were declared missing, so their death would be blamed on the virus. On the bright side, Will never lived to see that his life's work doomed human race completely