Bashir comes to this conclusion in a later episode, "The Dogs of War":
BASHIR: Odo, there is something you need to know. When I first discovered that you'd become infected with the morphogenic virus, I assumed you'd contracted it from the Founders.
ODO: Didn't I?
BASHIR: No. The fact is, it was you who transmitted the disease to them.
ODO: But how did I get it?
BASHIR: You were deliberately infected.
ODO: By whom?
BASHIR: Section 31. They used you as a carrier, hoping you would pass on the disease to the Founders. I'm sure you were never meant to develop symptoms.
ODO: I don't care whether they meant to kill me or not. The reality is the Federation set out to destroy my people.
Bashir's conclusion is logical, considering that Section 31 did not want itself or the Federation to be tied to the infection of the Founders.
As for why Odo did eventually show symptoms, Odo was taxing himself towards the end of the war with frequent shapeshifting. From "Tacking Into the Wind":
GARAK: My approach may have been quiet, but I assure you, I had no intention of sneaking up on you. My apologies. If I may ask?
ODO: Why have I deteriorated so rapidly? I've been assuming dozens of different forms over the past few weeks. Changing shape seems to accelerate the progress of the disease.
GARAK: Perhaps you should stop.
ODO: And do what? Lie here waiting to die? I came to work and work is what I'm going to do.
Granted, Odo is speaking about why the disease is accelerating in him, but we can surmise that his general shapeshifting had been increasing over the course of the war, and the protection Section 31 gave to Odo from the virus eventually failed because of this.
That being said, Section 31 probably reckoned that Odo would join the Great Link or merge with another shapeshifter yet again at some point, at which time any symptoms he might develop could be attributed to that most recent link. This is indeed exactly how things played out, before Bashir pieced together the truth.
The exact technical details of how Section 31 engineered the virus so that Odo would be immune are unknown. Nothing about this is mentioned in the episodes or in any writer's guides / notes, nor is it referred to in the DVD commentary for Season 7. There seem to be no further speculations in the novels either.
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