It has been confirmed that Ashley Graham, the President’s daughter who appeared in Resident Evil 4, has been infected and turned into a zombie. She turns on her father, then bites him and infects him with the C-Virus, which answers your questions on how the President eventually turned into a zombie. The zombie President then turns on  Leon and his partner. Leon and Helena are both under arrest warrant by the U.S authorities because someone must have saw them murdering the President and reported it.
Leon and Helena immediately contact Ingrid Hunnigan (secret service agent who supports Leon on his missions and provides feedback on his progress) on a private call to fake their deaths as they leave for China for some unfinished business.