Dr. Craig Spencer at first told officials that he isolated himself in his Harlem apartment — and didn’t admit he rode the subways, dined out and went bowling until cops looked at his MetroCard the sources said.

“He told the authorities that he self-quarantined. Detectives then reviewed his credit-card statement and MetroCard and found that he went over here, over there, up and down and all around,” a source said.

Spencer finally ’fessed up when a cop “got on the phone and had to relay questions to him through the Health Department,” a source said.