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Al Qaeda chief Ayman al-Zawahiri has ordered the Iraqi faction of his network to stop meddling in Syria and anointed Al-Nusra Front jihadists to carry the network's banner in the civil war.
The demand for the Islamic State of Iraq and the Levant to shut down in Syria was included in an audiotape broadcast by Al-Jazeera Friday that confirms a written order issued in June that has so far gone unheeded.
It came as loyalists fought rebels, including from ISIL, in the north and centre of the country.
The Britain-based Syrian Observatory for Human Rights said troops, backed fighters from Lebanon's Shiite militant group Hezbollah, recaptured parts of Base 80 in the north.
Loyalists were also locked in fighting with rebels in central Syria around a key weapons depot.
Western hesitation to back mainstream rebels in the uprising against President Bashar al-Assad that erupted in March 2011 has strengthened the position of radical Islamist fighters, including ISIL and the Al-Nusra Front.
Al-Nusra, created in January 2012, joined Al Qaeda in December of that year and is on a US list of foreign terrorists organisations.
It has carried out some of the deadliest attacks against the Syrian regime, including several suicide bombings.
Zawahiri said Al-Nusra was the jihadist's group only branch in Syria, tasked with reporting "to the general command," and will no longer operate under the banner of Al Qaeda's Iraq affiliate.
"The Islamic State in Iraq and the Levant (ISIL) is to be abolished, while the Islamic State of Iraq (ISI) remains functioning," he said.
The dispute dates back to April of this year, when ISIL leader Abu Bakr al-Baghdadi had claimed that Al-Nusra was now its branch in Syria, but that was rejected by its Nusra commander Abu Mohammad al-Jawlani, who affirmed allegiance to Zawahiri.
The tape aired by Al-Jazeera confirmed a letter carried by the network in June, attributed to Zawahiri and addressed to the leaders of Al Qaeda factions in both countries.
ISIL blamed for abuses
But Baghdadi defied Zawahiri's orders at the time and has continued to operate in Syria, where opposition activists have blamed ISIL for an escalating abuse against Syrian rebels and civilians.
These have included kidnappings and public executions in areas under its control.
On the ground, tensions remained high and rebels were reportedly beefing up their ranks after new clashes with loyalist troops.
The Observatory said 15 rebels were killed in fighting with the army, which recaptured parts of the military's Base 80 near the international airport of second city Aleppo.
"Regime troops have advanced inside the base and now control large parts of it, and rebel groups and the Islamic State are bringing in reinforcements," said the Observatory.
A senior security official confirmed the army was making advances in the area near the town of Sfeira.
The Observatory, which relies on activists and medics on the ground for its reports, also reported fighting around a key weapons depot near the town of Mahin in central Homs province.
Rebel groups, including Al Qaeda-affiliated battalions, seized part of the depot earlier this week, and the Observatory said both sides were bringing in reinforcements
The war in Syria has killed so far more than 120,000, according to the Observatory, while UN figures show that it has displaced some seven million people, including two million who have fled the country.
On the humanitarian front the United Nations said emergency plans were underway to vaccinate more than 20 million children in the Middle East after polio resurfaced in Syria.
The region's largest-ever polio campaign was unveiled by the UN Children's Fund (UNICEF) and World Health Organisation (WHO) as experts sound alarm bells over deteriorating conditions in Syria.
Experts have said malnutrition is on the rise and health conditions are deteriorating, particularly in areas where troops have laid siege to rebel strongholds for months, such as in suburbs of Damascus.
The polio campaign will be carried out over six weeks in Egypt, Iraq, Jordan, Lebanon, the West Bank and Gaza Strip, Syria and Turkey.
"The polio outbreak in Syria is not just a tragedy for children; it is an urgent alarm -- and a crucial opportunity to reach all under-immunised children wherever they are," said Peter Crowley, who heads Unicef's polio division.