Fears are growing across the Middle East that coronavirus has infiltrated a main pilgrimage route, which could lead the deadly pathogen to vulnerable refugee populations, causing perhaps unprecedented public health crises across the region.

Concern is centred on the Iranian shrine city of Qom, which is thought to be a hub of the disease and the likely source of its spread elsewhere in the country and in neighbouring states, where infected travellers have been diagnosed in recent days.

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Shia Muslim pilgrims who travelled to Qom are thought to make up the majority of the so far small numbers of those infected, in Kuwait, Bahrain, Iraq and Lebanon.

Adding to the fears that pilgrimage routes may have spread the disease was the diagnosis on Monday of an infected worshipper in Najaf, Iraq. Local health officials closed and disinfected the Imam Ali mosque after the case was confirmed, and public health experts warned of a pending emergency if the virus was not contained quickly .

“In Iraq, [coronavirus] poses a major public health threat because the Iraqi health system is very weak,” said Dr Adam Coutts, a specialist on public health in the Middle East at Cambridge University.

“It potentially could wipe out thousands of people. And there’s no way of tracking it once it gets into a refugee population, given the mobility. These viruses or diseases expose the politics and fragility of public health systems.”

Refugees and internally displaced populations across Iraq and Syria have been identified as the most vulnerable groups in the region, should the spread of the virus become a pandemic. Health officials in both countries remain under-equipped to deal with such a a reality that seems more possible with each passing day.

Facebook Twitter Pinterest A bus passenger wears a protective mask in Tehran. Afghanistan, Turkey and Iraq have closed their borders with Iran. Photograph: Atta Kenare/AFP/Getty

Coutts said: “The major issue we have been worrying about is coronavirus getting into the Syrian and Iraqi refugee population, given the conditions in which they live. Overcrowded with no sanitation, plus a lack of access to healthcare.”

Iraq, Turkey and Afghanistan have closed their borders with Iran, where officials scrambled on Monday to deny that 50 people had died of the virus in Qom.

“In the whole country, 47 have been diagnosed with Covid-19. Unfortunately, 12 of them have died of the disease so far,” said the spokesman for the Iranian parliament, Assadollah Abbasi, contradicting the reports out of Qom.

Panic buying and lockdowns spread through the city after local news reports citing regional health officials circulated on Monday morning. The local governor, Barham Sarmast, said enough was being done to stop the virus.

“Quarantining Qom is not an effective way to contain the coronavirus – we have to look for more effective ways,” he said. “Qom is geographically located in the crossroads of 17 provinces of the country and a pilgrimage centre. So if we could adopt a quarantine strategy, we would have adopted it already.”

A local news agency in the city tweeted: “The situation in Qom is very bad. Don’t come to Qom and no one should get out of Qom. Qom should be closed. We need a lot of medical help here. We don’t think we have enough medical staff in the city.”

Amid increasing alarm that officials had been slow to realise that coronavirus had taken root in parts of Iran, and could now no longer stop its spread, schools and universities were closed in several cities and Tehran’s public transport system disinfected.

Facebook Twitter Pinterest A passenger in Jdaydet Yabous, Syria, is tested for coronavirus at a border crossing with Lebanon. Photograph: Omar Sanadiki/Reuters

Religious pilgrimages to Iraq have been suspended. Theatre sessions have also been cancelled and football matches are to be played without spectators, Iranian media reported.

Elsewhere, officials were attempting to track those who had returned from Iran in recent weeks and summons them for urgent screenings. Particular attention was being paid to Shia pilgrims who may have unwittingly carried the virus with them on their journeys home.

Iraq, Syria, Lebanon and Turkey are home to at least 12 million refugees and internally displaced people, many of whom live closely together in conditions of poor hygiene and with already compromised immunity systems. All three factors are considered ideal conditions for the spread of the disease, which health officials worldwide believe could survive on surfaces for up to nine hours.