Of the 52 new cases, 39 are linked to the Shincheonji Church of Jesus in Daegu, where the 31st patient, the country's probable "super spreader", attended worship services, the KCDC said.
It said authorities were investigating the exact cause of his death.
The surge of infections in the Daegu area and several cases in the capital, Seoul, where infection routes weren't immediately traceable, forced government officials to acknowledge Thursday for the first time that the virus has begun to circulate in the local population.
A 61-year-old South Korean woman, who tested positive for the virus earlier this week, attended worship services at the church on February 9 and this past Sunday.
All 74 sites operated by the Shincheonji Church have been closed and worshippers have been told to instead watch services online for a sect whose leader claims to be an angel of Christ, but who is dismissed by many outsiders as a cult leader.
She said: "This is the case where some individuals can either be much more infectious than others so that they may go on and infect many people or, equally, it can be related to their contact patterns".
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Those included shutting down for the first time the Thousand Islands Bridge border crossing near Kingston, Ont. The counter-demonstrators said they are fed up with the blockades that have been found around the country.
The central government on Friday declared Daegu and Cheongdo as "special management zones".
"Most of the hospital's patients who have been diagnosed are those who had been staying as inpatients for mental illnesses", Seoul's vice health minister Kim Gang-lip told reporters.
"It seems that the novel coronavirus is spreading quickly across the country, and if manufacturing sites are contaminated, there will be production and supply disruptions", said an official at a local electronics firm. Ninety are showing symptoms of Covid-19.
The city, located in the southern part of the country, is home to about 2.5 million people.
Also on Friday, the country's defense ministry limited military personnel from taking vacations and outside trips as well as banning visitors to military facilities after a Navy sailor visiting Jeju Island contracted the coronavirus, Chosun Ilbo newspaper reported, citing ministry officials. The decision directly impacts thousands of Iranians who travel to Mecca and Medina for Islamic pilgrimages, effectively barring them from the kingdom.
The man, who was not identified, died at Daenam Hospital in Cheongdo, where he had been hospitalized in the psychiatric ward for the past number of years due to schizophrenia.
A dozen towns in northern Italy were on effective lockdown Saturday.