Lee, who was kept in a detention centre while awaiting the court's decision, was directly arrested on early Saturday, Yonhap said.
As of July 19, those connected with the church made up 38 percent of all confirmed coronavirus cases in the country, according to the Korea Centers for Disease Control and Prevention.
Prosecutors allege Lee conspired with other sect leaders to withhold information from authorities, including their meeting places and the number of participants at their gatherings as authorities tried to trace infection routes in February.
Lee, 89, is also suspected of embezzling about 5.6 billion won (4.69 million US dollars) in church funds, including spending around five billion won to build a retreat, and holding religious meetings in regional government property without permission.
"There is some room for contention about the suspect's alleged crimes, but some charges have been ascertained".
Judge Lee Myeong-chul said "there have been circumstances indicating systematic attempts to destroy evidence" and considering Lee's status, "it can not be ruled out that there will be similar attempts in the future". "Considering his status, it can not be ruled out that there will be similar attempts in the future", said Judge Lee Myeong-chul. The judge noted that though Lee is old and has chronic ailments, he is not deemed unfit for imprisonment.
"The court's issuance of an arrest warrant doesn't mean a guilty verdict".
The sect said in a statement that Mr Lee was concerned about government demands for members' personal information but never tried to hide anything.
Some 4,000 followers, most of whom were from its branch in the southeastern city of Daegu, were infected with the coronavirus.
The measures come after North Korean leader Kim Jong Un declared an emergency on Sunday after a person who defected to South Korea three years ago returned across the highly fortified demilitarized zone (DMZ) to Kaesong this month with symptoms of COVID-19, KCNA reported. More than 5,000 of them are infections associated with Shincheonji.
McPherson county reports four new cases of COVID-19
There have been 1,029 Marshall County residents who have recovered from COVID-19 and 31,879 have recovered throughout the state. Twenty people are hospitalized for COVID-19 in Clark County, with 10 more people in the hospital awaiting test results.
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