Covid: Africa new variants causing growing concern

Experts believe the emergence of new coronavirus variations in Africa have contributed to an increase in the number of cases in many countries on the continent.

There’s also concern that these variants can’t easily be tracked because the type of testing required to identify them isn’t available in most countries.

What’s happening to case numbers?
At least 40 countries have now seen a second wave of the pandemic, including all countries in the southern Africa region, says the Africa Centres for Disease Control (CDC).

“This new wave of infections is thought to be associated with the emergence of variants that are more transmissible.”
A new variant of the virus emerged in South Africa last year, and has contributed to record case numbers in the southern African region, according to the World Health Organisation (WHO).

Elsewhere in Africa, this variant has also been officially recorded in Botswana, Ghana, Kenya, Comoros and Zambia.
It’s highly likely to have reached other countries on the continent, but few have the capacity to carry out the specialised genomic sequencing required to detect coronavirus variants.

“Initial analysis indicates that the [South African] variant... may spread more readily between people,” according to the WHO. It doesn’t appear to cause more serious illness.
However, a new study shows the Oxford-AstraZeneca vaccine - the first to have arrived in South Africa - offers “minimal protection” against mild and moderate cases of Covid-19 arising from the new strain.

The study by the University of the Witwatersrand didn’t investigate the vaccine’s efficacy in preventing more serious infections.
In South Africa itself, daily new case numbers have started to fall significantly after a second peak.

And because there are many more cases in South Africa than anywhere else on the continent, this has resulted in an overall fall of 4 per cent in new cases across the continent over the past month, according to the CDC.

In Nigeria, scientists have also identified a new variant of the virus, although they say there is currently no evidence to indicate it is contributing to increased transmission.
However, cases in Nigeria have been on the rise since early December, and are only just starting to trend downwards.

Death rates rising
During the first stage of the pandemic, Africa’s overall fatality rates -the proportion of those with Covid who then die - were lower than those elsewhere in the world.
There were a number of theories put forward as to why that might be the case, such as the relatively younger population, and possible cross-immunity from other coronaviruses.

But the Africa CDC has now warned about rising fatality rates in the continent, saying of the 55 countries they monitor, 21 are now reporting fatality rates above the current global average of 2.2 per cent.

The fatality rate for Africa has crept up since July last year when it was 2.1 per cent - to 2.6 per cent in February this year.
It is worth pointing out that the global fatality rate has also come down since the start of the pandemic, which in itself would put more African countries above the global average.

And fatality rates are affected by how much testing is done - a country with low levels of testing will show a higher death rate because many non-fatal Covid cases are going undetected.

More importantly, data for deaths should be treated with caution, given the wide variations in how countries record them.
In South Africa, research into excess deaths - that’s the number of deaths in a certain period above what would normally be expected - shows that there were 83,918 between May 6 last year and January 5 this year.
The official death toll from Covid-19 since the start of the pandemic is currently at just under 45,000 deaths.

And South Africa was just one of eight countries on the continent that the BBC found in a recent investigation had adequate death registration systems.
So coronavirus deaths across Africa as a whole are likely to be under-recorded.

How much testing is done in Africa?
The WHO says testing in Africa is still low compared to other regions, and there’s also concern that irregular levels of testing over time may be masking the true spread of the virus.

There are wide variations in testing rates and while some countries have reduced testing, others have maintained or even increased it at different points during the pandemic.
Of the bigger countries, South Africa has been doing the most and Nigeria doing relatively few tests per capita, according to Our World in Data, a UK-based project which collates Covid-19 information.

However, in some countries, there are insufficient or no data available on testing to know how much is being done.
Tanzania, for example, stopped releasing data in May last year. President John Magufuli has been insisting the country is free from the virus.

The King’s Global Health Institute, which tracks the pandemic in sub-Saharan Africa, says testing activity in some countries also fell back after the first wave of the virus had subsided.

“Those countries that cut back on testing after the first wave will...have had less extensive and timely intelligence from surveillance,” it says.

South Africa coronavirus variant

What is the risk?
Coronavirus has been changing in ways that might help it escape some of the body’s immune system defences.
Scientists are working to update the Oxford-AstraZeneca vaccine, as research suggests it - and other coronavirus vaccines - may be less effective against the South Africa variant.
The ones being used now should still protect against severe illness, however.

What is the South Africa new variant?
All viruses, including the one that causes Covid-19, constantly mutate into new versions or variants.
These tiny genetic changes happen as the virus makes new copies of itself to spread and thrive.

Most are inconsequential, and a few can even be harmful to the virus’s survival, but some variants can make the virus more infectious or threatening to the host - humans.
There are now many thousands of variants of the pandemic virus circulating. But experts are concerned about the South African variant, also known as 501.V2 or B.1.351.

Is it more dangerous?
There is no evidence that the South Africa variant causes more serious illness for the vast majority of people who become infected.
As with the original version, the risk is highest for people who are elderly or have significant underlying health conditions.
But there are concerns it can spread more readily and vaccines may not work quite as well against it.

Some of the changes involve the virus’s spike protein - the part that gains the virus entry into human cells. It is also the bit that vaccines are designed around, which is why experts are concerned about these particular mutations.
The South African variant carries a mutation, called N501Y, that appears to make it more contagious or easy to spread.
Another mutation, called E484K, could help the virus dodge a person’s immune system and may affect how well coronavirus vaccines work.

Do vaccines work against the South Africa variant?
It is too soon to say for sure, or by how much, until more tests are completed, although it is extremely unlikely the mutations would render vaccines useless.
Scientists have tested the Pfizer Covid vaccine against N501Y and E484k mutations in the lab, using blood samples from vaccinated people.

In that study, vaccination appeared to work, but was slightly less effective.
Early results from Moderna suggest its vaccine is still effective against the South Africa variant, although the immune response may not be as strong or prolonged.