The deer king - Nahoko Uehashi

Van, a former soldier made slave, toils away endlessly in a salt mine. An unexpected chance at liberation drops in his lap when a pack of infected dogs passes through, killing everyone but him and a young girl he names Yuna. Van hopes to make a peaceful life for them both now that they've escaped. However, the disease that cleared out the mine begins to spread, endangering the nation and placing Van and his ward at the center of a conflict greater than any the world has ever seen. Thus begins a tale of ecosystems, viruses, and cultural relations.