A total of 180 cases of influenza have been detected in Mexico City since October 2015 until date.
Agents of the Office of the Attorney General of Mexico City were on the case and faced police officers.
The mayor said that there is no epidemiological alert in the city.
The pontiff thanked those who received him at the Vatican embassy.
The Pope spoke to the faithful surrounding the embassy and took some pictures with them.
Boston Cardinal Sean O'Malley went beyond the Vatican's guidelines for bishops.
He urged people: "Don't forget to pray for me."
A little girl in a wheelchair presented Francis with a handmade Valentine's Day card.
"We could go until 4 a.m.?" the pope asked. "Yesss," the crowd answered. "Well, but that could be a little long," he responded.
The Pope is conducting a mass in the Basilica of Guadalupe in front of 30,000 faithful.