Botswana is the current chair of that division, which is tasked with promoting peace and security in the region.
Vice-president Slumber Tsogwane will lead Botswana’s delegation to the summit, the president’s press secretary Batlhalefi Leagajang said in a statement.
Leagajang said President Mokgweetsi Masisi’s self-quarantine was “out of an abundance of caution”.
Botswana has recorded more than 45,850 coronavirus infections and more than 690 deaths since the pandemic began, according to a Reuters tally.