South Sudan Vice President Contracts Covid-19
Mr Machar said as several other members of the task force were infected a new team was taking over their work.
His wife, who is Defence Minister Angelina Teny, some bodyguards and other staff also have the virus.
Experts worry that decades of conflict has left South Sudan incapable of dealing with a surge in new infections.
So far South Sudan has recorded 236 cases of Covid-19 and four deaths.
Last week, the authorities announced the virus had reached a UN refugee camp in the capital, Juba, where some 30,000 people have sought seeking shelter and protection.