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The 68-year-old former international cricketer received his first dose of China's Sinopharm coronavirus vaccine on Thursday. The Sinopharm shot is the only Covid-19 vaccine available in Pakistan.
Pakistan's health ministry said it can take a few weeks to develop immunity to the virus after getting vaccinated, and has urged the public not to be deterred from getting a shot based on Khan's diagnosis.
"Prime Minister Imran Khan was not fully vaccinated when he contracted the virus. He only got the 1st dose and merely 2 days ago which is too soon for ANY vaccine to become effective. Anti-bodies develop 2-3 weeks after 2nd dose of 2-dose COVID vaccines. #VaccinesWork," Pakistan's health ministry tweeted Saturday.
The South Asian nation of 220 million people has recorded 13,799 deaths and 623,135 cases during the pandemic, according to Johns Hopkins University in the United States.
Cases have increased in Pakistan in recent weeks, though the pandemic has remained largely under control. Lockdown restrictions have been reinforced in some parts of the country in response to rising infections.
Pakistan's vaccine rollout, which began on March 10 with the elderly, has been met with hesitancy among some parts of the population and footage of Khan receiving the shot was broadcast in an apparent attempt to ease concerns.
Khan's spokesman Shahbaz Gill was quick to distance the Prime Minister's positive test result with the Sinopharm shot.
Gill said that Khan had a slight cough and fever, and prayed for him to have a quick recovery.
Khan has been holding regular meetings and recently attended a security conference in the capital Islamabad, where he addressed a crowd without a mask.
Khan's special assistant on overseas Pakistanis, Syed Zulfi Bukhari, said the Prime Minister had likely been infected before he was vaccinated on Thursday.
"Vaccines are safe & must be taken, #PMIK had his first shot just a day ago, before which he was exposed already. Please do get yourself & loved ones vaccinated and fight the fake news," Bukhari tweeted Saturday.
CNN's Sophia Saifi reported from Islamabad. Eliza Mackintosh wrote and reported from London. CNN's Hamdi Alkhshali in Atlanta contributed to this report.