I interpret AP here as saying "[China] denied these claims, saying that they are lies"
As I read it now, the text of the article says "refuted the claims *as* lies" (emphasis mine). AP is not themselves calling them lies. And looking up "refute" in MW, while the first definition is disproving, the second definition is denying.
In general, pro-China is not a bias I'd expect from a mainstream western news source.