I wouldn't know. I am not an atheist.
However, if all the human diseases were carried on the Ark, Noah and his family would have never survived.
Obviously. Genetic diseases are the result of mutations after the ark. We know mutations occur. Bacterial infections are the result of bacteria. They obviously survived. I'm not sure where viruses came from. They may come from decaying life. They may have survived the flood, or they may have been created or occured afterwards.
What does evolution say about viruses? Are they common descent too?