VATICAN CITY (Reuters) - Pope Francis flies to Cairo on Friday, less than a month after church bombings killed 45 people in two Egyptian cities as part of a concerted campaign by Islamist militants to rid the Middle East of Christians.

Pope Francis' wears his skull cap during Wednesday general audience in Saint Peter's square at the Vatican, April 26, 2017. REUTERS/Tony Gentile

Home to some of the faith’s earliest churches, the region’s Christian communities have been in decline for decades, but wars this century in Iraq and Syria, and the emergence of Islamic Stat have put their future in doubt.

Francis said on Tuesday he hoped his visit could be a “consolation and ... encouragement to all Christians in the Middle East”. He also wants to improve dialogue with Islam.

“The pope is very conscious of the fact that the Middle East may lose its entire Christian presence,” said Nina Shea, the head of the Center for Religious Freedom at the Washington-based Hudson Institute think tank.

“These are ancient communities that have their roots in the earliest Church. They aren’t grafted on, or the result of Western evangelization. They are unique and they are being lost,” she told Reuters by telephone.

The largest exodus has been in Iraq, where Christians were caught up in the sectarian violence that wracked the nation following the U.S.-led invasion in 2003 and then actively persecuted as the Islamic State grew in power from 2014.

No precise figures exist, but Shea said Christian numbers had fallen from 1.5 million in 2003 to between 100,000 and 200,000 today. Others say up to 400,000 may still live there, but many have lost their homes and been displaced.

As Islamic State, also known as Daesh, started to seize towns and cities across Iraq, they ordered Christians who fell into their clutches to convert, pay a tax or face death.

Those Christians who could, fled abroad or to Kurdish-held areas in the north. They appear highly reluctant to return to their old homes even as Iraqi forces gradually retake lost territory, including large swathes of the city of Mosul.

“Daesh were people from Mosul, there were friends, people we know,” said Kharallah Jamil, the Christian owner of a construction company who escaped with his family to the Kurdish city of Erbil after Islamic State forces seized his property.

“I can’t say whether we will go back. We were betrayed. People in Mosul were cooperating with Daesh, following their interpretation of Islam.”

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Christianity spread through the Middle East during the first century, overtaking pagan Eastern cults and co-existing with older faiths, like Judaism and Zoroastrianism. Although Islam gained predominance in the region from the 7th century, many Muslim rulers allowed Christians freedom of worship.

Centuries of status quo frayed with the collapse of the Ottoman Empire in World War One. At the time, Christians made up some 15 percent of the regional population, but the figure now stands below four percent, according to the Pew Research Center.

The figures vary from country to country. While Saudi Arabia officially has no Christian nationals, up to 40 percent of Lebanon’s population is Christian, according to the U.S. Central Intelligence Agency.

Lower birth rates among Christians by comparison with Muslims has helped lower the overall ratio. Economic emigration has also played a part, with Western countries traditionally more willing to welcome in Christians than Muslims.

There are more Christians from Jerusalem living in Australia than there are Christians left in the Holy City, according to Palestinian data, with the Palestinians saying Israeli occupation has convinced many local Christians to move abroad.

While Christian migration from the Israeli-occupied West Bank has been a constant trickle, it has turned into a flood in nearby Syria, torn apart by six years of civil war.

From a population of some 1.25 million in 2011, less than 500,000 remain today, according to ADF International, a Vienna-based group which promotes religious freedom.

As in Iraq, the minority group has been persecuted by Islamic State, which has publicly executed Christian men and sold Christian women into slavery.

Even in areas still under control of President Bashar al-Assad, the mood is grim.

“There’s not many left here. Most of our relatives, friends, maybe 70 percent have traveled or migrated abroad,” said Suzanna Tannous, a Christian housewife from the Ghassani district of Damascus, only a kilometer from rebel-held Jobar.

“There’s no future for us here,” she said, speaking in a cafe, the sound of falling shells thudding in the distance.

INTIMIDATION AND MURDER

It is a sentiment heard across the region, but the sheer numbers seeking to get out is clogging up the system.

“The embassies won’t take everyone ... and even if the embassies opened their doors to Copts, they won’t even take one out of 500,” said Bishop Macarius, the head of a Christian Coptic diocese in Minya, south of Cairo.

Egypt’s Copts make up some 10 percent of the country’s 92 million people, by far the largest Christian minority in the Middle East. But despite having roots that date back to the Roman Empire, they feel marginalized and persecuted.

Islamic State, which is battling President Abdel Fattah al-Sisi, has declared war on the nervous Coptic community, hoping to destabilize the Arab-world’s most populous nation.

Besides the Palm Sunday attacks, it claimed responsibility for the bombing of a Coptic cathedral in Cairo last December that killed 28 people and is chasing Christians from the Sinai, using intimidation and murder to force them out.

Egypt’s highest Islamic authority, al-Azhar, froze all dialogue with the Catholic Church in 2011 after former Pope Benedict denounced what he called “a strategy of violence that has Christians as a target”.

Pope Francis has worked hard to improve relations with the Muslim world, but the Hudson Institute’s Shea said he would have to address directly the issue of religious persecution this week.

“The context of this visit is the broad religious genocide against Christians in the Middle East,” Shea said. “It is the elephant in the room, but it cannot be ignored.”