The Egyptian revolution began on 25 January 2011 when protests erupted throughout Egypt, focusing on the symbolic Tahrir Square in Cairo, and eventually led to the resignation of President Hosni Mubarak after 20 years of authoritarian rule. And at the end of 2011, the revolution was arguably still ongoing, as opposition strengthened against the SCAF, which assumed power after Mubarak's departure. The SCAF has continued to use the repressive practices of the Mubarak era, including bringing its critics before closed military trials. In terms of women's rights, the most prominent violation was the so-called 'virginity tests' on female protesters arrested by army soldiers; the practice reportedly continued into 2012, despite widespread protest.

While the Egyptian revolution created an atmosphere of national solidarity as Egyptian Muslims and non-Muslims united to topple the Mubarak regime, religious and ethnic minorities continued to face discrimination and sectarian attacks. Muslim fundamentalists have been responsible for a number of sectarian attacks on minorities. The SCAF has also been complicit in attacks against minorities, either by ignoring cases of sectarian violence, failing to investigate them or actively engaging in violence alongside extremists. Human Rights Watch (HRW) found that public prosecutors often encouraged extra-legal settlements, thus reducing sectarian attacks to personal disputes. This has fostered a climate of impunity, allowing extremists to target minorities without fear of punishment.

The year 2011 was a grim one for Coptic Christians, who represent between 6 and 9 per cent of the population. Over 10 major attacks occurred against Copts, most of them involving disputes about whether they had permission to build or renovate a church. Under existing laws, Copts must obtain an official endorsement and permission from the local Muslim community to build or renovate a church.

On 1 January, a bombing occurred at a church in Alexandria during the New Year's prayer service, in which at least 21 people were killed and over 70 injured. In March, a crowd burned down a church in the town of Atfih, south of Cairo. Lawyers representing the church told HRW that they had presented the names of 100 suspects alongside video evidence of the arson attack to the local prosecutor, but none of the suspects were prosecuted. In protest, Copts held demonstrations in Cairo, during which at least 13 people were killed and nearly 150 injured in clashes. A crowd attacked the demonstrators, while the Egyptian military apparently stood by for hours without intervening. Also in March, a group of men, alleged to be members of the Salafi movement, adherents of an interpretation of Islam that seeks to restore Islamic practice to the way it existed at the time of the prophet Mohammad, set fire to a flat in Qena owned by a Coptic Christian. The authorities made no efforts to arrest the perpetrators.

In May, Salafists attacked and badly damaged two churches in Cairo's Imbaba district, acting on rumours that a female convert to Islam was being held in a church. The government later reported that 12 people had died in the violence. The Egyptian Initiative for Personal Rights said that security forces knew in advance that Salafists were gathered outside the churches, and failed to take any preventive measures. Christian houses and businesses were also vandalized.

On 30 September, a group of local residents in Al-Marinab village, Edfu Province, set fire to Saint George's church as it was undergoing reconstruction, because they believed that the congregation did not have a permit and objected to the height of the steeple that bore a cross. Authorities confirmed that the church did have a permit. Copts were angered by the governor of Aswan who appeared to justify the attack.

In October, thousands of Copts demonstrated outside the Maspero government building in Cairo, to protest the authorities' failure to punish attacks on Christians. They were met with armoured personnel carriers and hundreds of riot police who opened fire on the crowd. An estimated 24 people were killed, mostly Copts, and about 250 injured. The state media was allegedly also instrumental in inciting sectarian unrest. The SCAF was criticized, as generals denied the use of live ammunition despite video evidence, and the inquiry set up to investigate the incident was headed by a military prosecutor.

In June 2011, a draft law on the construction of religious buildings was issued by the government to replace the previous Hamayouni Decree, dating back to the Ottoman era, which regulated church construction but did not apply to mosques. The law sought to promote religious equality by applying equal regulations to mosques and churches, but was opposed by the Muslim Brotherhood for not abiding by 'measures of justice that are espoused by Islamic sharia [law]'. Coptic Christians also expressed dissatisfaction with the draft law, since they still had to receive permission from governors to build places of worship.

In 2011, Sufi Muslims, who adhere to the esoteric, mystical dimension of Islam, faced attacks and harassment from Salafists who consider them to be heretics. Salafists attacked 16 historic Sufi mosques in Alexandria where half a million Sufis live and which has 40 Sufi mosques. Aggression against the Sufis in Egypt included a raid on a mosque named after and containing the tomb of the thirteenth-century Sufi al-Mursi Abu'l Abbas. Another target was the Qaed Ibrahim mosque, where mass protests were organized during the revolution. Sufi residents of the Egyptian governorates of al-Minufyia and Aswan have also demanded state protection of Sufi institutions and buildings.

Bahá'ís in Egypt have historically suffered from state-sanctioned discrimination and persecution. Most Egyptian Bahá'ís do not have official identity cards which are necessary for access to education, employment, opening bank accounts, receiving pensions and carrying out business transactions. In addition, they have been barred from holding government jobs. Bahá'í marriages are still not recognized in Egypt. While the Supreme Administrative Court ruled that Bahá'ís could obtain official identity cards back in 2008, the implementation of this ruling has moved slowly. Bahá'ís are still banned from forming spiritual assemblies in Egypt.

The Egyptian paper Youm al Sabe' reported that on 23 February two homes of Bahá'ís were set on fire and burgled in Shuraniya village, in the Sohag governorate. According to the Egyptian Initiative for Personal Rights there was strong evidence that state security officers incited the attack.

Following the 2011 revolution, ethnic Nubians began to demand their right to return to their homeland around Lake Nasser. Egyptian Nubians are an ethnic group with a distinct culture and language, and live mostly in the Upper Nile region. Developmental projects in their ancestral lands have led to the loss of their livelihoods which are dependent on farming. In the 1960s, during the construction of the Aswan High Dam, when the surrounding region was flooded to create Lake Nasser, 50,000 Nubians were relocated to less fertile government lands in Upper Egypt. But Lake Nasser has receded over the past decade, making fertile land available again. Nubians were subject to repression under Mubarak's regime because of the strategic location of ancient Nubia on the site of the Aswan Dam and have also seen Egyptian Arab communities settled by the government on the land they claim as their homeland.

In early September, about 2,000 Nubians protested in Aswan City against their marginalization and the elimination of their traditional rights to the land. Protesters set fire to the Aswan governorate headquarters.

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