Africa's total reported death toll from Covid-19 was approaching 100 000 on Thursday, a fraction of those reported on other continents but rising fast as a second wave of infections overwhelms hospitals.

The continent's reported deaths, at 99 800, compare favourably with North America, which has registered more than half a million, and Europe, which is approaching 900 000, a Reuters tally shows.

But deaths are rising sharply across Africa, driven by its southern region, especially economic powerhouse South Africa, which accounts for nearly half. South Africa was ravaged by a second wave caused by a more contagious variant that has jammed up casualty wards.

"The increased number (of infections) has led to many severe cases and some of the countries really found it quite difficult to cope," Richard Mihigo, coordinator of the immunisation programme at the World Health Organization's Africa office, told Reuters.

"We have seen some countries getting to their limit in terms of oxygen supply, which has got a really negative impact in terms of case management for severe cases."

Mihigo said the rise in deaths was pronounced in countries near South Africa like Zimbabwe, Mozambique and Malawi, raising the possibility that the 501Y.V2 variant identified in South Africa late last year had spread through the southern Africa region - although more genomic sequencing needs to be carried out to prove that.

International aid group Doctors Without Borders (MSF) this month called for urgent vaccine distributions in southern Africa to counter the spread of the new variant, as most African countries have lagged richer Western nations in launching mass vaccination programmes.

Reuters data show Africa's case fatality rate is now at around 2.6%, higher than the global average of 2.3%, and marginally up on the 2.4% rate after the first wave of infections - which at the time compared favourably with other continents.

Experts caution against reading too much into the data - the real toll may be much higher or lower. For instance, South Africa's excess deaths - deaths considered over-and-above the normal rate - during the pandemic have reached over 137 000, almost three times its official Covid-19 death toll.

Then again, in some cases Africa's low testing rates could inflate its true case fatality rate (CFR), said Professor Francisca Mutapi, an infectious disease expert at the University of Edinburgh.

"If deaths being registered as Covid-19 deaths are not necessarily contingent on a positive test ... as is the case in South Africa, then this can drive up CFR," she said.

Even with these caveats acknowledged, African countries look like they are struggling with Covid-19 more than last year.

"Are we counting all the deaths on the continent? No ... but most people on the continent do know somebody who has died of Covid during this second wave," Africa CDC director John Nkengasong told reporters last week.

"Hospitals are being overwhelmed due to health systems that are fragile."