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Bishops from the Iraq-based Chaldean Church chose the archbishop of Kirkuk as their new patriarch on Friday at a synod held in Rome for security reasons, websites and the church leader said.
Louis Sako will replace Emmanuel III Delly who retired in December after reaching the age limit of 85 in the Christian church which recognises the authority of the pope.
Sako was elected by 15 bishops from Iraq and other parts of the Middle East, as well as areas of North America and Europe with large Iraqi diasporas.
The election was announced by Iraqi Christian websites and the synod was presided over by Cardinal Leonardo Sandri, prefect of the Vatican's Congregation for the Oriental Churches, in Rome rather than Baghdad for security reasons.
Sako told AFP in Baghdad by phone from Rome that he would be "honoured to meet the Pope on Sunday morning."
"This is a big responsibility, and I will work for (Iraq's) national unity," he said. "I am as close to the Christians as to the Muslims, the Arabs, the Kurds and the Turkmen.
"I will do my best to stop the emigration of Christians from Iraq," he added.
Sako will take on the official title of Patriarch of Babylon of the Chaldeans. He is seen as pro-Kurdish and has favoured co-operation with Muslim leaders in his archdiocese.
The Chaldean church, which has 700,000 followers and uses Aramaic -- the language that Jesus Christ would have spoken -- belongs to one of the oldest Christian communities in the world.
But along with other Iraqi Christian communities, it has suffered persecution, forced flight and killings in the aftermath of the 2003 US-led invasion.
Before 2003 there were more than a million Christians living in Iraq. Now they number around 450,000.
According to the UN High Commissioner for Refugees, many thousands fled after 44 worshippers and two priests were killed in an attack on a Syriac Catholic church in Baghdad on October 31, 2010, an atrocity claimed by Al-Qaeda.
Between 2003 and May 2012, some 900 Christians were killed, while 200 were kidnapped, tortured and ultimately released for exorbitant ransoms, according to the Hammurabi Human Rights Organisation in Iraq.