The civil war in Syria is reigniting the sectarian civil war in Iraq. A vast area of eastern Syrian and western Iraq is turning into a zone of war. Well-armed and well-organised al-Qa’ida-linked movements are launching attacks with suicide bombers from the shores of the Mediterranean to the Tigris River. They may also be over-playing their hand and risk provoking a counter-reaction by all those with a reason to fear al-Qa’ida and its fanatical Sunni fundamentalism.

No doubt groups like the Islamic State of Iraq and Syria (Isis) are growing stronger by the day. Its advance in Syria has been well publicised and has done enough to frighten the US and its allies into doubting how far they want to see President Bashar al-Assad replaced by Sunni fanatics. Less well publicised is the tightening grip of Isis over great areas of western Iraq where it has not been a power since the confrontation with the Americans and the Sunni tribes six or seven years ago.

This is not a well-reported part of the world because of the growing dangers facing foreign and local journalists. Some 16 foreign reporters have been kidnapped in northern Syria this year, so even the most intrepid are no longer going there. Syrian rebel commanders who protected journalists can no longer defend themselves against Isis, the al-Nusra Front or or Ahrar al-Sham. Iraq, which once had hotels filled with foreign journalists, has long fallen off the media map.

Unsurprisingly, important developments such as the weakening government grip on Anbar – the vast Sunni province west of Baghdad centred on the towns and cities of the Euphrates – have not been properly reported. Al-Qa’ida is once again making ground attacks on cities like Fallujah from which they were driven by US Marines in 2004. The same is true of the city of Mosul in northern Iraq, where Isis is reported to levy protection money on everybody from the local green grocer to satellite phone and construction companies – bringing in monthly revenue of $8m.

This is happening because al-Qa’ida reinvigorated itself by its gains in Syria, and the Sunni community in Iraq – heavily defeated after the fall of Saddam Hussein in 2003 – could see the regional balance of power changing in its favour.

Dysfunctional and crudely sectarian at the best of times, the Shia-dominated government in Baghdad has progressively alienated the Iraqi-Sunni by discrimination and repression. The result is that al-Qa’ida has gained popular support and has been able to launch a wave of bombings that has been killing up to 1,000 people, mostly Shia civilians, every month.

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But the last time al-Qa’ida did this, in 2006, it provoked a savage sectarian counter-attack by the Shia, who make up 60 per cent of the Iraqi population. The outside world never really took on board that an outcome of the Iraqi civil war was that Baghdad moved from being a mixed Shia-Sunni city to one dominated by the Shia with only a few Sunni enclaves left, mostly in the west of the capital. If al-Qa’ida’s bombings go on, these areas will be at risk of further sectarian cleansing. There are detailed reports, denied by the government in Baghdad, that the few remaining Sunni in and around Basra in southern Iraq are being killed or forced to flee.

In a different way in Syria, al-Qa’ida’s ferocity may make it formidable on the battlefield but it creates a counter-reaction among Sunni as well as Alwaites, Christians and the other minorities. Damascus is full of people who do not much like Assad, but still think Isis or the al-Nusra Front are worse. Much the same thing happened in Sunni neighbourhoods in Baghdad in 2006 when al-Qa’ida terrified people by shooting barbers who gave un-Islamic haircuts or were rumoured to be chopping two fingers off the right hand of people caught smoking a cigarette. In the last few weeks there have been signs of the way in which Isis has weakened the loose coalition against Assad, by starting a war in north east Syria with the Kurds, about 10 per cent of the Syrian population.

A motive for the fighting is control of the oil wells that are concentrated in this area. Some 50,000 Kurdish refugees have already fled but others have been forced to rely on the disciplined fighters of the Kurdistan Workers Party which has been fighting the Turkish army for years.

The outcome of these struggles is likely to be a divided Iraq and a divided Syria. Where there are Sunni minorities in Iraq they will be killed or forced to flee. This might well include Baghdad. In the Sunni heartlands al-Qa’ida will grow stronger, though in Syria the movement is vulnerable to a backlash. The governments in Baghdad and Damascus will be strengthened not because they are well liked but because people dread the alternative to them.

Is there any way this bloodbath could be ended? The chances of the so-called Geneva 11 peace meeting getting off the ground do not look good with the deeply divided opposition leadership refusing to attend if Assad plays a role. But there is no reason for him to depart since he is militarily and politically stronger than a year ago.

Perhaps, the only way to exercise influence on al-Qa’ida and the 1,200 other rebel groups is to threaten them with closure of the 500-mile long Turkish border which they need to keep open if they are to continue to fight.