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A war of extraordinary brutality is being waged across the Muslim world which is largely ignored by the media. It is a war in which victims are assassinated or massacred with no chance to defend themselves. Most of those who die are poor people murdered in obscure places without the world paying any attention.

Few places are more obscure than a dusty road at Mastung, 30 miles south of Quetta in Balochistan province, Pakistan. But it was here late last month that between eight and 10 gunmen stopped a bus filled with Shia pilgrims on their way to Iran. According to the bus driver, the gunmen ordered the pilgrims off his bus and opened fire, killing 26 and wounding six. The Sunni fundamentalist group Lashkar-e-Jhangvi claimed responsibility. A year ago there was an even worse atrocity in the same area, when a suicide bomber blew himself up at a Shia rally and killed 57 people.

Earlier in the month, 1,500 miles away at Nukhayb in Al Anbar province, western Iraq, there was a similar incident to the massacre at Mustang. A bus carrying Shia pilgrims from Karbala to a shrine in Syria was stopped at a fake checkpoint and uniformed men told the women, children and old men to stand to one side. The rest of the pilgrims were taken to another location and slaughtered. It is fair to assume in overwhelmingly Sunni Anbar that the killers were Sunni.

The conflict between Shia and Sunni has been becoming deeper and more dangerous ever since the triumph of militant Shi’ism in the Iranian revolution of 1979. Sectarian hostility became worse when, in 2005, Iraq became the first Shia-dominated Arab state since the time of the Fatimids 800 years ago. The civil war between Sunni and Shia in Iraq which followed in 2006-7 has left a legacy of hatred and fear that has not abated. Tens of thousands were tortured and killed. Al-Qa’ida in Mesopotamia slaughtered Shia, and the Mehdi Army and the Shia-dominated security forces butchered Sunni and drove them out of most of Baghdad.

Since the start of the Arab uprisings this year, Shia-Sunni hostility has deepened again wherever the two communities seek to live side by side. Rulers have appealed to the Sunni and Shia loyalties of their people to stay in power. In Syria and Bahrain the democratic movement against authoritarian rule, the Arab Awakening, has been thwarted by officially sponsored sectarianism. In Syria, President Bashar al-Assad has been clinging to power by playing the sectarian card for all it is worth. The ruling elite, drawn from the Alawites, an offshoot of Shi’ism, is being told that they must sink or swim with the Assad regime or face elimination or exile. Assad and his family rely on Alawite officers and Alawite-dominated units to shoot demonstrators and control the main towns and cities. The Sunni majority understandably react by holding Alawites as a whole responsible for the atrocities.

The same thing has happened in Bahrain. Cherif Bassiouni, the American-Egyptian lawyer conducting an inquiry sponsored by the Bahrain government into the events of earlier this year, told me he had seldom seen a more polarized society. He compared the situation to Sarajevo in 1992 when Serb gunners firing at Muslim civilians told him they were avenging the defeats suffered at the hands of the Turks by their Christian ancestors over the past 600 years.

Sectarianism in Bahrain pervades every aspect of life. When repression started in March, the government portrayed democratic protests as a Shia coup d’etat orchestrated by Iran. Respected consultants at Salmaniya hospital were tortured to make them confess that they had stored weapons, splashed blood on uninjured demonstrators, and even secretly killed patients by deliberate neglect. Shia shrines and mosques were bulldozed.

Bahrain’s King Hamad bin Isa al-Khalifa is finding the sectarian genie is difficult to get back in the bottle. In a speech at the end of last month he spoke of Bahrainis’ “common future, regardless of the diversity of our sects” and “the inevitability of co-existence”. But last week the Bahraini government closed the door on compromise when a military court gave 20 medical practitioners long sentences for helping those injured in the protests. Thirteen received 15 years in prison and two others were sentenced to 10 years. This can only suggest that the al-Khalifa royal family intends either to remain in a state of simmering war with the majority of Bahrain’s Arabs or that it plans to drive them out and replace them with Sunnis. Either way, the violence is likely to get worse.

While decrying sectarianism, the United States and its allies have done their bit over the years to pump it up. In Iraq, US ambassadors and generals were continually pretending that Shia militants were the pawns of Iran. This fed into the extreme and not-so-extreme Sunni claim, made in Pakistan, Afghanistan, Lebanon, Bahrain and Saudi Arabia, that any drive by the Shia for civil and political rights, is an Iranian inspired plot. Communities which benefit from Sunni or Shia sectarianism find it hard to give up. In Iraq, it determines the chances of staying alive and getting a job. The two are intertwined: a few years ago I had a Sunni driver in Baghdad who, through various connections, was offered a well-paid Interior Ministry job as a computer specialist. I remember him agonising for weeks over whether to take the job in this mainly Shia ministry until deciding it was just too dangerous and he would probably be killed if he did.

A similar pattern is repeated elsewhere. In Bahrain, sacked Shia point out that Sunni who have taken their jobs are in no hurry to give them back. In Syria, Alawites provide not just most of the senior army officers but some 60-70 per cent of ambassadors, 50 per cent of university professors and a majority of oil and gas executives, according to the opposition. Given that Alawites are some 12 per cent of the Syrian population, equal rights for the Sunni means that a lot of these people will be out of a job.

Sectarianism is likely permanently to enfeeble Iraq and Syria, two of the Arab states who once helped determine the region’s future. It will absorb the attention of the Sunni monarchies of the Gulf and put them at odds with Iran and Iraq. It explains why the democratic uprisings that succeeded in Egypt, Tunisia and Libya are faltering east of the Egyptian border.

Patrick Cockburn is the author of Muqtada: Muqtada Al-Sadr, the Shia Revival, and the Struggle for Iraq.