I think It might be cool to add viruses as anomalies on planets or as events in the game. It should make the game more challenging because some planets would be inhospitable or with low system approval. What's more, different factions might have different reactions to a disease. Some civilisations might go extinct as a result and some might benefit from this anomaly. 

As an event virus would bring either approval or disapproval from player's faction depending on a decision they've made (for example, ignore or find the cure).