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Aden - Yasmine El Tohamy - Two Qatari citizens who who were evacuated to Doha from Iran tested positive and are in stable condition, the ministry said.
They had arrived among a group of citizens who were repatriated from Iran on February 27 and are under quarantine.
A 36-year-old Qatari man who was also evacuated from Iran tested positive on Saturday. All repatriated citizens have been confined to a 14-day period of quarantine, the government assured.
The health ministry said the infected patients had been admitted to hospital.
"The Ministry of Public Health assures that the infected people have not had contact with community members since their arrival, and the outbreaks of the disease in the State of Qatar are still very low," a statement read on Sunday.
"This had been expected because of the virus's spread across the region and other countries, alongside the exponential increase in the number of cases," the health ministry said in an earlier statement on Saturday.
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The announcement on Sunday came after Iran's health ministry reported 11 new deaths from the novel coronavirus and 385 infections, bringing the overall number of lives lost to 54 and cases to 978.
Tehran has dismissed as "rumours" a BBC Persian report, citing unnamed sources in the Islamic republic's health system, that at least 210 people have so far died from the outbreak inside the country.
While Iran has rejected the claim as rumour, it has has scrambled to bring the outbreak under control, shutting schools, suspending cultural and sporting events.
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It has even halted meetings of the cabinet and parliament, amid the disease's spread among the country's political elite.
On Saturday, recently-elected Iranian MP Mohammad Ali Ramazani died after being tested positive for the deadly virus a few days earlier, The Independent reported.
Iran's coronavirus death toll is the highest for any country other than China - where COVID-19 first emerged.
One of Iran's seven vice presidents, Massoumeh Ebtekar, and Deputy Health Minister Iraj Harirchi are among several senior officials who have been infected.
Gulf countries have announced a raft of measures to cut links with Iran to prevent the coronavirus spreading, after infections emerged among people returning from pilgrimages or trips to the Islamic republic.
On Friday, Saudi Arabia barred citizens from the six-nation Gulf Cooperation Council, which includes Qatar, from entering two of Islam's holiest cities amid fears over coronavirus.
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