Malawi was the latest to close schools when President Lazarus Chakwera announced that they would close for three weeks after a sharp rise in numbers.
A girls secondary school in the capital Lilongwe had 137 students who tested positive, according to local media reports.
The country had reported no cases for more than two months but now they have spiked and a third of the 353 total deaths have occurred in the past two weeks, according to John Hopkins University data.
"The time has come to enforce these things for the common good," Chakwera said in a television address on Sunday. Students in boarding schools will however remain on campus until health authorities determine whether it is safe for them to go home.
Government officials have died from the virus including Malawi's transport minister and another senior cabinet member who passed away last week.
Zimbabwe's foreign minister, Sibusiso Moyo, died on Wednesday after contracting the virus, as did South Africa's Minister in the Presidency, Jackson Mthembu, on Thursday.
Chakwera said he has ordered an increase in the number of testing sites and recruited additional medical personnel, noting that the facilities in the country are terribly understaffed. The president said he has directed the Minister of Finance to allocate around $23 million as soon as possible' to meet the demands of the current disaster.
In neighboring Zambia, schools were scheduled to reopen on January 18 but this has been delayed by a further two weeks due to rising case numbers. They will now open on February 1, authorities said.
Zimbabwe, like Malawi, has only allowed examination classes to open, but under strict Covid-19 rules.
Rwanda has closed schools in the capital, Kigali, with the possibility of school closures in other regions too if more cases are confirmed, according to the country's education minister. The cabinet ordered a total lockdown of the city on Monday.
However, in Nigeria, Africa's most populous country, schools reopened on January 18 despite opposition from some lawmakers and a rising number of cases in the country.
"After extensive consultations with relevant stakeholders... the consensus of opinion is that the resumption date of 18th January should remain, while parents and respective institutions must ensure full compliance with COVID-19 protocols..." the federal ministry of education said in a a statement.
Nigeria registered 1,386 new cases and 14 deaths on Wednesday, according to Nigeria Centre for Disease Control, with Lagos alone having 476 cases. The number of cases in the country passed 110,000 on Monday.
Parents there told CNN they are concerned about the decision to send children back to school.
Brenda Uphopho, a festival director from Lagos, said she opted to keep her nine-year-old son at home.
South Africa, which has the highest numbers of cases in Africa and has been dealing with a new virulent strain of the virus, delayed reopening schools by a further two weeks.
"Given the pressure experienced by the health system in the past few weeks, occasioned by increased COVID-19 infections which has led to the second wave, the Council of Education.. has taken the decision to delay the reopening of both public and private schools," Deputy Minister of Basic Education, Reginah Mhaule, MP said in a statement.
South Africa registered 12,710 new cases on Wednesday, bringing the total number of infections to nearly 1.4 million. 566 died from the virus, with another 839 fatalities the day before, according to John Hopkins University data.
In Malawi, hospitals have been 'overwhelmed' with patients and empty beds are scarce. Medical supplies including ventilators have also been in short supply.
Chakwera declared a state national disaster on January 12 in all 28 districts of Malawi in response to the recent spike.
He has since called for support from donors, including the United Nations.
But there has been criticism over the government's handling of the virus. A recent report by Oxfam indicates that the previous government -- which lost power last June following a presidential election rerun -- used 80% of the funds raised for the Covid-19 fight on allowances. The charity warned the current government against repeating the same mistakes.
Onjezani Kenani, a campaigner who has been calling on the government to equip the hospitals with medical supplies and personal protective equipment, asked for donations to assist hospitals through a Facebook post on January 15.
"Friends I prefer action," he said. "We can be pointing out things our government is not doing right, but the fact is that the people are suffering out there and some are dying. As the government does its part, you and I can chime in and do ours."
"I am calling for donations so that we can buy oxygen pressure regulators - they enable oxygen cylinders to deliver oxygen to patients," said Kenani, whose fund has raised $100,000 so far.
"I therefore applaud the efforts of private citizens who are already running capital campaigns to raise money to go towards these needs," said president Chakwera, acknowledging the effort. "I would like to call on private sector companies to follow this example and practice their corporate social responsibility in this critical hour.
Source: CNN