At least 51 people have died in Saudi Arabia over the last year from Middle East Respiratory Syndrome, or MERS, a virus related to SARS, which killed hundreds worldwide a decade ago.
Limits on visas for foreigners hoping to take part in the pilgrimage that all able-bodied Muslims are expected to fulfill at least once in their lifetime cut the number arriving from abroad to 1.38 million, the Public Statistics Department said in a statement carried by the state-run Saudi Press Agency.
Domestic attendance was down even more sharply, with only 117,000 permits issued within the kingdom, the news agency reported.
Authorities turned back some 70,000 would-be pilgrims who arrived without permits, the news agency said, and 38,000 others were arrested after participating in the hajj without permission.
Still, Middle East news agencies covering the four days of spiritual cleansing followed by the Eid al-Adha holiday reported a reverent culmination of the hajj with Tuesday's ritual "stoning of the devil" in the Mina valley.
"An endless torrent of pilgrims, dressed in the ihram, a two-piece seamless white garment, cried 'Allahu akbar' (God is great) as they hurled pebbles they had collected overnight at nearby Muzdalifah at concrete pillars representing the devil," Arab News reported from the scene.
Perhaps due in part to the smaller crowds - fewer than half the 3.2 million pilgrims who came to Mecca and other hajj sites last year - Monday's gathering at Mount Arafat and Sunday's circling of the Kaaba in the Grand Mosque at Mecca were unscathed by stampedes or attacks of the type that have marred the rites in other years.
In his annual sermon at Mount Arafat, Saudi Arabia's top cleric, Sheikh Abdulaziz Sheikh, made vague reference to the civil war pitting Muslim sects against each other in Syria in appealing for unity and peace.
"Your nation is a trust with you. You must safeguard its security, stability and resources," the cleric said of Islam's tenets of respect and serenity, the Pakistan Daily Times reported. "There is no salvation or happiness for the Muslim nation without adhering to the teachings of the religion."
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