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Edit : So, desperate as I was to postpone restarting the map I took the wheel of the medivan and kept doping the dinosaurs. Through this I found that the timer for quarantine ticked down about 4 seconds every so often as long as I herded all of the animals together by circling them and shooting them repeatedly. It has taken over 12 minutes to make a one minute timer tick down.
When each dino was in it's own pen, the clock ticked down. (So seperate every dino thats infected from other dinos)
That doesn't work for a lot of people and also is ludicrous in practice for herd/pack dinosaurs. Have velociraptors, troodons, dilos, etc? Well, now you have to build 2-14 individual cages, if you have compy you might need to build up to two dozen along with any herd animals you might have cohabitated them with. Also, if your quarantine isn't perfect then they will aggro and escape, oops.
It's really just about isolating each case (Even if it's only one left) to trigger the clock ticking down.
That doesn't work in practice, and if that was the intent then it makes no sense for small enclosures with multiple dinosaurs to count down the quarantine. Plus there are missions that fail if dinosaurs die, but these dinosaurs are not given special immunities which means that they have a hardcoded fail state in this instance.
If it was really meant to just be isolation, then I wouldn't have very gradually been able to get it to tick down by circling my 13 sick dinosaurs with a medivan so they were close enough to each other to fulfill its requirement (which seems to obtusely be : All dinosaurs in enclosure are sick and ALSO are in a very specific radius of each other which can be far smaller than the enclosure required space)
Imo if they were going to go the quarantine route it should be done as : Shoot dino, place in paleo-medical facility, bam it's medically quarantined. But that doesn't work.
The pen I dumped them in was roughly 3 full span fence section by 2 full sections in size. Maybe the dinos need to remain in an area that is a certain size? Based on your comment it sounds like they have a maximum distance they can be apart for the timer to progress.
As for the distance apart, I'm not it would make much different I would assume it's down to the territory.
Placing fences and a gate splits them to individual territory, if they share a territory then the disease can spread.
Incidentally if disease spreads via territory, it can give you an idea of whether you should put "sickly" dinosaurs in shared encloses with "resilient" ones. For instance you could have a sickly Saropod (since you might have only one in an enclosure) surrounded by a pack of resilient smaller dino's.
If the Saropod get's sick there would be a lesser chance of it spreading to the smaller pack. Alternatively if the pack gets sick, it's only one extra dino that will likely get sick from the pack.
While ideally it's best to have them all healthy, it's just a way to give you a different configuration in gene editing.