Sister Leonella Sgorbati, 65, left, was shot four times in the back by two men at the entrance to the hospital in the capital, Mogadishu. Her bodyguard was also killed. The Vatican said that it hoped that the “horrible tragedy” was an isolated incident.

The killing came after Benedict XVI expressed deep regret yesterday at the furious reaction to his remarks on Islam and holy war, saying that the text he quoted last week did not reflect his personal opinion.

Sheikh Mukhtar Robow, deputy head of security at the Islamic Courts in Somalia, which control the capital, said that there was a “concrete possibility” that the murder of Sister Leonella at the Austrian-run hospital in the north of the capital was “a reprisal for the Pope’s remarks on Islam”. One person had been arrested.

Despite the storm, the Pope appeared relaxed, chuckling as the faithful below repeatedly shouted words of encouragement, and joking about the heavy rain, observing in an impromptu aside that “water from Heaven is a sign of the Holy Spirit”.

In his Angelus address — his first public appearance since the furore broke out — he said that he was sorry that a passage in his address at Regensburg last week, quoting from a 14thcentury Byzantine emperor, had been construed as “offensive to the sensibilities of Muslims”.

“These words were in fact a quotation from a medieval text which do not in any way express my personal thought,” he said. “I hope that this serves to placate souls and to clarify the true meaning of my address, which in its totality was and is an invitation to frank and sincere dialogue, with great mutual respect.”

Unusally the passage dealing with Islam was distributed in English and French as well as Italian, the language used by the Pope and Vatican officials.

At the university, where he had once been a theology professor, the Pope cited the words of Manuel II Paleologus, one of the last Christian emperors, who when Constantinople was under threat from Muslim forces described the teachings of the Prophet Muhammad as “evil and inhuman” and accused him of “spreading faith by the sword”.

His remarks led to angry complaints and demands that the Pope’s scheduled trip to Turkey in November should be cancelled.

Mehmet Aydin, the Turkish Minister of State, said that the Pope seemed to be saying he was sorry for the outrage but not necessarily the remarks themselves. “You either have to say this ‘I’m sorry’ in a proper way or not say it at all,” he said. “Are you sorry for saying such a thing or because of its consequences?” However, Abdullah Gul, the country’s Foreign Minister, said that he saw no reason to cancel the Pope’s trip to Turkey in November, a view echoed by Cardinal Tarcisio Bertone, the Pope’s new Secretary of State (Prime Minister).

Seven churches in the West Bank and Gaza were set on fire. Religious seminaries closed down in protest in Iran, where Ahmad Khatami, a leading cleric, told students at a mosque in the holy city of Qom that the Pope’s remark’s were inflammatory. The Tehran Times said that the Pope’s remarks were “code words for the start of a new Crusade”.

Morocco recalled its ambassador to the Vatican and there were further street protests by Muslims in Pakistan, India and Turkey. An Iraqi insurgent group, the Mujahidin Army, threatened a suicide bomb attack against the Vatican on a website used in the past by militants. Addressed to “the dogs of Rome”, it said: “Our minds will not rest until we shake your thrones and break your crosses in your home.”

But Muhammad Abdul Bari, general secretary of the Muslim Council of Britain, said: “It’s certainly a welcome step that the Pope recognises the hurt that his speech caused.”

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