Pope Francis praised Pope Emeritus Benedict XVI’s “acute and gentle thought” during a general audience in the Vatican, as tens of thousands of admirers of the retired pontiff filed by his body lying in state in Peter’s Basilica on the final day of viewing.

By the time the basilica’s doors were shut to the public on Wednesday night (local time), some 200,000 people had paid their respects over three days of viewing.

After the closure, Vatican officials were preparing to place the 95-year-old German churchman’s body into a wooden coffin, ahead of Thursday morning’s funeral in St Peter’s Square.

Among the last viewers were a married couple from Calabria. Gaspare Guadagnuolo, 73, and Lina Proto, 62, said they remember a visit by Pope Benedict to that southern region years ago.

“I was struck by people’s participation,” Ms Proto said. “There was a lot of intense emotion.”

At his customary weekly audience, Pope Francis was greeted by an enthusiastic crowd in Paul VI auditorium and shouts of “Viva il papa!” or “Long live the pope.”

“It is my duty to come,” said Małgorzata Nowska, a Polish resident of Rome as she paid tribute Wednesday. She said she wanted to give Pope Benedict “a last hug, a last prayer.”

Pope Francis will preside over Pope Benedict’s funeral, an event drawing heads of state and royalty despite Pope Benedict’s requests for simplicity and Vatican efforts to keep the first funeral for an emeritus pope in modern times low-key.

Only Italy and Germany were invited to send official delegations, and German President Frank-Walter Steinmeier and Italian President Sergio Mattarella confirmed their participation.

But other heads of state and government have decided to take the Vatican up on its offer and come in their “private capacity”. They include several other heads of state, at least four prime ministers and two delegations of royal representatives. All will attend in what the Vatican describes as a “private” role.

In a further sign of officialdom, the Italian government announced it would lower all Italian and European Union flags to half-staff on public buildings across the country on Thursday.

Pope Francis drew applause when he opened his remarks by giving a shout-out to all those who were outside paying tribute to Pope Benedict, whom he called a “great master of catechesis.”

“His acute and gentle thought was not self-referential, but ecclesial, because he always wanted to accompany us in the encounter with Jesus,” Pope Francis said.

Later on Wednesday, Vatican officials were to place Pope Benedict’s body in a cypress coffin – the first of three coffins – along with a brief, written summary of his historic papacy, the coins minted during his pontificate and his pallium stoles.

After the funeral in the piazza, the remains will be carried back into the basilica, where the coffin will placed inside a zinc one, and then finally into another made from oak.

In keeping with Pope Benedict’s wishes, his remains will be placed in the crypt once occupied by the tomb of St John Paul II in the grottos underneath the basilica.