We first derive the boundary theory from the U(1) Chern-Simons theory. We then introduce the Wilson line and discuss the effective action on an $n$-sheet manifold from the back-reaction of the Wilson line. The reason is that the U(1) Chern-Simons theory can provide an exact effective action when introducing the Wilson line. This study cannot be done in the SL(2) Chern-Simons formulation of pure AdS$_3$ Einstein gravity theory. It is known that the expectation value of the Wilson line in the pure AdS$_3$ Einstein gravity is equivalent to entanglement entropy in the boundary theory up to classical gravity. We show that the boundary theory of the U(1) Chern-Simons theory deviates by a self-interaction term from the boundary theory of the AdS$_3$ Einstein gravity theory. It provides a convenient path to the building of minimum surface=entanglement entropy in the SL(2) Chern-Simons formulation. We also discuss the Hayward term in the SL(2) Chern-Simons formulation to compare with the Wilson line approach. To reproduce the entanglement entropy for a single interval at the classical level, we introduce two wedges under a regularization scheme. We propose the quantum generalization by combining the bulk and Hayward terms. The quantum correction of the partition function vanishes. In the end, we exactly calculate the entanglement entropy for a single interval. The pure AdS$_3$ Einstein gravity theory shows a shift of central charge by 26 at the one-loop level. The U(1) Chern-Simons theory does not have such a shift from the quantum effect, and the result is the same in the weak gravitational constant limit. The non-vanishing quantum correction shows the naive quantum generalization of the Hayward term is incorrect.
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