Heavily-armed Islamists, many linked with Al Qaeda, have deepened their presence in the Syrian uprising and threaten Christians with death if they don’t work against Assad.

They warned two Christian towns on Saturday they will be attacked if they do not evict regime forces, as the new Greek Orthodox patriarch said Syria’s often-fearful Christians will stay put and urged a peaceful end to the conflict, according to AFP.

Yet a key opposition group said Syria’s conflict is not a sectarian one, contradicting warnings this week by a UN team that increasing sectarianism is threatening whole communities.

In a video message to the Hama provincial towns of Mharda and Sqilbiya, one of seven men armed with Kalashnikovs warned residents to expel “gangs” of Syrian President Bashar Assad and the pro-regime terrorist group shabiha “from your towns and convince them not to bomb our villages and families.”

“If not, we will immediately attack the hideouts of Assad’s gangs and shabiha,” added the man, who identified himself as Rashid Abul Fida, head of the Al-Ansar Brigade in Hama.

Syrian Observatory for Human Rights director Rami Abdel Rahman said the towns both had pre-war populations in the tens of thousands but that most of their residents have already fled.

As the news circulated, Syria’s new Greek Orthodox leader called in Damascus for Christians to remain in the country despite the conflict.

Patriarch of Antioch and All the East Yuhanna X Yazigi also appealed to warring parties to renounce violence “in all its forms” and to start a process of dialogue.

In his first press conference since succeeding Ignatius IV Hazim, who died on December 5, he said, “We Christians are here in the country and we will stay here.”

The patriarch sought to play down dangers faced by Christians.

“What is happening to us is happening to others too. We are in the same situation as everyone else, Muslims and Christians, shoulder to shoulder, facing the difficulties,” he said.

There are some 1.8 million Christians in Syria.

Many have remained neutral in a conflict that erupted in March 2011 and has killed an estimated more than 44,000 people. Others, fearing a rise of Islamism, have taken Assad’s side.

The messages came two days after UN investigators described the 21-month conflict as “overtly sectarian in nature.”

In response, the opposition Syrian National Council, hit out against the UN Commission of Inquiry on Syria, saying the “revolution is neither sectarian nor bloody.”

“The only division that Syrian society is witnessing is between a bloodthirsty, oppressive regime… and people calling for freedom and equality,” said the SNC, whose chief George Sabra comes from a Christian background.

On Thursday, the commission said the conflict threatened whole communities, and warned that newly formed armed Islamist groups were increasingly operating independently of the main rebel force, the Free Syrian Army.

Fabrice Balanche, director of the French research center Gremmo, says 80 percent of Syrians are Sunnis, around 10 percent belong to Assad’s Alawite community, five percent are Christian, three percent Druze and one percent Ismaili.

Meanwhile, there was no let-up of violence, as a car bomb in the northeast Damascus district of Qaboon killed five people, the Britain-based Observatory said.

And Haidar al-Sumudi, a cameraman for state television was gunned down outside his Damascus home, the broadcaster said.