Rome had spent months prepping up for the Roman Catholic Church Jubilee. It built tunnels, opened up squares and scrubbed moldy fountains. Now thousands of pilgrims were flocking from all over the world for the occasion — a year of penance and forgiveness that takes place every quarter century.

The only thing missing was the pope.

For the past three weeks, Pope Francis, leader of the world’s nearly 1.4 billion Catholics, has been in seclusion on the 10th floor of the Gemelli hospital, where he is being treated for pneumonia and other infections. He has missed his regular Wednesday general audiences, where he greets visitors and pilgrims, and his Sunday Angelus prayer, and on Ash Wednesday he entrusted his homily to a cardinal.

A brief audio recording of the pope faintly giving a blessing in Spanish was all the faithful received on Thursday, as they gathered for a rosary for Francis in St. Peter’s square.

“We were hoping we could see him,” said Dinora Ramirez, a pilgrim from Honduras, who prepared to cross St. Peter’s basilica’s holy door as tears filled her eyes. “Our hearts are aching.”

Doctors speak of a “guarded prognosis” for the pope. They have offered mostly terse reports about his condition, which has alternated between crises and stable moments, leaving ample room for conspiracy theories to flourish about his health and his intentions to resign, and even false reports of his death.

But the one undisputed reality is the pope’s prolonged absence.

It is especially notable for a pope who has made a point of being among the people, frequently venturing into crowds, embracing the faithful and engaging in impromptu conversations. And it is even more deeply felt as thousands of pilgrims have been coming to Rome hoping to catch a glimpse of Francis, and as Roman Catholics prepared for Easter celebrations.