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The Brotherhood and its leader, Mohammed Badie, congratulated the church and Tawadros in statements on Sunday.

Tawadros faces tremendous challenges as the country’s transition to democracy is marred by a deep rift between increasingly politically powerful Islamist groups, from which the country’s new president hails, and the liberal and secularist groups who were initially behind the revolt that ousted President Hosni Mubarak last year.

At the center of the political squabbling in Egypt is the role of Islam in the country’s new constitution, currently being drafted. The Christians, along with liberal and secularists, oppose demands by Islamists to increase the role of Islamic Shariah law. The prospects of a stronger role for Islamic law in legislation increase the community’s concern of further marginalization, or of curtailing of their rights of worship and expression.

Mr. Morsi has named a number of Christians as advisers and vowed to work closely with the community, but Christians are skeptical. Late Saturday, Pachomios said during a popular TV program on the private station al-Nahar that Christians have never held senior state posts or leading positions such as university deans in Egypt’s modern history. He also insisted there be no clause in the constitution allowing state monitoring of the church’s finances, a demand often made by Islamists.

Sunday’s papal election comes during a shift in Christian attitudes toward their relation to the state. For years, Christians largely relied on the church to secure protection for their rights, using Shenouda’s close relationship with the authoritarian Mubarak.

But even with that relationship, Copts continued to face attacks from radical Islamists, and local disputes with their neighbors sometimes flared into deadly violence. Rights groups say Mubarak’s police were lax in pursuing and punishing offenders. Few Copts were named to genuinely powerful posts in government.

On New Year’s Eve 2011, the bombing of a Mass in Alexandria killed 21 people — the worst attack against Copts in at least a decade. No suspects are currently in custody in relation to the attack.

In October 2011, after Mubarak’s ouster, soldiers drove armored vehicles into a crowd in Cairo protesting the country’s transitional military rulers’ failure to protect Copts. Twenty-six people, mostly Copts, were killed.

Despite or perhaps because of the Copts’ uneasy status, Shenouda had longstanding critics within the community who asked why a cleric should act as an intermediary between them and the state. Others said that he was too close to the former regime and did not take strong enough stances. Following the uprising and the pope’s death, more Copts, particularly the youth, have been emboldened to act outside the church to independently demand rights, better representation and freedom of worship.

According to Egypt’s state-run MENA news agency, the new pope was born Wagih Sahby Baqi Soleiman. He is a former pharmacist who graduated with a bachelor’s degree in 1975 from the main university in Egypt’s northern coastal city of Alexandria before studying in England in 1985. He briefly managed a government-run pharmaceutical lab in Egypt until he went to a monastery in Wadi Natrun in 1986 where he studied religion for two years. He was ordained a priest in 1989.

Tawadros, whom MENA reported turned 60 the same day his name was selected to become Egypt’s new pope, was formerly an aide to the acting pope.

The process of electing a new pope began weeks ago, when a committee from the church narrowed the list of potential candidates from 17 down to five monks and bishops. On Monday, about 2,400 clergymen and church notables drew up a short-list of three that also included Bishop Raphael, 54, once an aide to Shenouda, and Father Raphael Ava Mina, the oldest among them at 70, a monk in a monastery near Alexandria and a student of the pope who preceded Shenouda.

MENA reported that Tawadros received more than 1,600 votes in Monday’s short-list voting.

None of the candidates attended the ceremony and are instead praying in their respective monasteries. MENA says church leaders will head to Tawadros’s retreat in the monastery complex of Wadi Natrun northeast of Cairo to congratulate him.

Sarah El Deeb contributed to this report.