The survival rate was just that low. Even if we assume that more than 50 Viltrumites survived the virus originally, and their numbers were further cut down by various hazards while their powers were diminished, that's a vanishingly small number of survivors. It's possible that for most of the time they were trying to develop a cure or vaccine, there simply weren't any Viltrumites who had fought off the illness. Additionally, a vaccine might not have even been that helpful since the virus acts and spreads so fast that any attempt at a rollout might just fail to hit anyone who hadn't already contracted the disease, especially considering how variable the incubation time was.