The Last Wild by Piers Torday

This is a story about a boy named Kester. He is extraordinary, but he doesn't know that yet. All he knows, at this very moment, is this:
1. There is a flock of excited pigeons in his bedroom.
2. They are talking to him.
3. His life will never be quite the same again...

Kester lives in a land in quarantine. A deadly virus has killed all the animals except pests and it's expected to be equally dangerous to humans. But when Kester realises he can talk to the pests, he finds they have great hope invested in him.