Your tree is severely infected with cedar apple rust or possibly quince or hawthorn rust.
This is a very common fungal disease and, although this was a particularly bad year for the disease, it will continue to infect your trees as long as the apple and juniper disease hosts are in the same vicinity (spores can travel several miles by wind.) When this disease causes significant defoliation in successive years the tree weakens, branches dieback, and the tree may not rebound.
If you want to saSpraying fungicides to prevent the disease begins early in the season. Please read about and follow the Va Tech spray schedule. And please read our general guidelines on managing tree fruit insect and disease problems. jt
Thank you, I am going to spray with Serenade Garden. Is it OK to remove branches and if so how should they be disposed of?
It is too late to spray this season. The product that you mentioned is not on the Va Tech Spray Schedule listed above and we do not have information on its effectiveness.
If branches are dead, you can prune and discard in the trash.