IBADAN – Five African countries have now confirmed cases of the SARS-CoV-2 501Y.V2 variant, which first appeared in South Africa, and there is concern that the variant is circulating undetected elsewhere on the continent. The Gambia and Nigeria have seen cases of the variant B.1.1.7, first identified in the United Kingdom, said WHO’s African Regional Director today, Dr. Matshidiso Moeti, at a press briefing.

Meanwhile, Africa CDC Director, Dr John Nkengasong, called for a “common approach” to COVID testing to oil the wings of international air travel – and halt the wave of new travel restrictions that countries have been imposing based on people’s national origin or the origins of flights – including people and flights arriving to Europe and the United States from South Africa.

Researchers now believe the variants may be both more infectious but also more deadly than the COVID virus strains that were prevalent until just recently. Researchers also fear the variants could also elude COVID tests and be more resilient to vaccines just being rolled out now – although many unknowns remain.

The countries where 501Y.V2 is circulating include: Botswana, Ghana, Kenya and Zambia, as well as South Africa. Beyond Africa, the variant has been confirmed in 24 countries globally. And there’s concern, it is circulating undetected in other countries in Africa,” Moeti told the press briefing.

“We are seeing more and more cases of variants and 501Y.V2, which was first identified in South Africa now, cropping up in other countries,” Moeti said. “The evidence suggests that these variants are more transmissible and emerging evidence indicates that the UK variant may cause more severe illness than other common strains, although more research needs to be done.”

These variants in conjunction with “the aftermath of year-end gatherings”, Moeti said, “risk powering a perfect storm and driving up Africa’s second wave and overwhelming health facilities”.

The continent saw a 50% rise in infections between 29 December 2020 and 25 January 2021, when compared with the previous four weeks, while deaths doubled.  Last week, more than 6,200 deaths were reported across Africa, said the WHO.The past week saw a small dip in cases in South Africa, but 22 other countries continued to see numbers surge.

Existing COVID-19 vaccines remain effective against the variants, Moeti said. But Professor Tulio de Oliveira, of the University of KwaZuku-Natal, South Africa, noted that these or other emerging variants may likely require individuals receiving booster doses of the vaccine.

WHO’s African Region is meanwhile setting up a new surveillance network with Africa CDC to track the spread of the virus mutations and variants across Africa and beyond, Moeti added.

“The variant which was first detected in South Africa has spread quickly beyond Africa and so what’s keeping me awake at night right now is that it’s very likely circulating in a number of African countries,” said Moeti. “Africa is at a crossroads. We must stick to our guns and double down on the tactics we know work so well. That is mask wearing, handwashing and safe social distancing. Countless lives depend on it.”

WHO’s African CDC Calls for Common COVID Testing Approach For International Travel

Dr John Nkengasong issued his call for a rethink of travel policies after several foreign countries, including the United States, are considering or have already banned flights originating from South Africa. Travel restrictions aiming to limit the importation of variants should be based upon a systematic testing policy – and not geographic or national origins, said Nkengasong.

“We should not be banning people because of their geographical origin, but we should be encouraging people to travel with negative tests and facilitate the testing process so that people can travel with a negative test,” Nkengasong said.

“If I were to go to Kenya and I show up at the airport with a valid negative test, I pose no threat to the country of Kenya, and that way so you shouldn’t just ban me because I’m coming from a certain country. They should be looking at that test, is your test valid,” Nkengasong added.

Up until now, the World Health Organization has resisted recommending pre-travel COVID testing, ostensibly due to fears that it would put an unnecessary onus on poor countries.

In fact, however, many of the poorest African and Asian countries have been requiring pre-flight COVID tests for all incoming passengers – which are paid for privately. Some counties, such as the Democratic Republic of Congo, also demand arrivals briefly quarantine until a post-flight test is completed as well, paid privately as well.

Paradoxically, it is wealthier European and American countries that first issued a rash of orders banning passengers of certain nationalities or flights from certain destinations as a result of variant scares – although more developed countries, most recently Switzerland on Wednesday, have adopted testing requirements.

Senegal’s Pasteur Institute – At Center Of New Genetic Surveillance Network

At the outset of the pandemic, most countries in Africa lacked adequate testing capacity for COVID-19 but this was gradually surmounted as new testing facilities were added.

Now, however, the identification of new variants of the virus will require more advanced capacities for gene sequencing that several countries in Africa have yet to obtain.

To address this vacuum, the Africa CDC, the WHO and member countries have created a network that enables existing labs with gene sequencing capabilities to collect samples from countries that lack such.

One of the labs in the network is the Dakar-based Institut Pasteur de Dakar in Senegal. Its CEO, Dr Amadou Sall, said in addition to providing gene sequencing services for Senegal, the institute is now supporting other countries, Cameroon and Equatorial Guinea notably. Others include Mali, Burkina Faso Guinea-Bissau, Côte d’Ivoire, Niger, Verde, and of course, Guinea.

“With the partnership we have with Africa CDC and WHO, we have the possibility of sequencing 500 genomes per week. And we’re trying to increase this capacity and to make these capacities available in different countries,” Sall said.

Key to the success of COVID-19 genomic surveillance in Africa, Sall said, will be the willingness and openness of African countries to share information.

“We need to be able to share information data and the Pasteur Institute is at the center of a global platform and we’re able to share information; to exchange information rapidly, if countries are willing to do so,” he said.

Knowing When to Raise the Alarm

While noting that identification of new variants is a significant feat, genomic experts warned that alarm should not be raised every time a new strain is identified.

Professor de Oliveira, who heads the KwaZulu-Natal Research and Innovation Sequencing Platform, said attention is raised when new strains are being confirmed in increasing numbers of cases with the new variant and not when just one case has been confirmed.

Describing the impacts that variants have on the epidemiology of the pandemic in South Africa, Oliveira said in some regions, the new variant has become the prominent type. But beyond this, he said South Africa is also worried about the variants from elsewhere getting into the country and circulating among its populations.

“Today, we just reported the first important case of the B.1.1.7, the variant of concern that is circulating in the UK. And it’s quite common that in addition to our main variant that is dominating, we’re going to still have introductions of new lineages,” Oliveira said.

“And in the case they begin to spread very fast, then we will communicate it and then highlight that could be a variant of concern.”

He said that while no one can know for sure about the possibility of third or fourth waves of the pandemic in Africa, the variants are highlighting the need for the entire world to globally control the transmission of  SARS-CoV-2 as a global community.

“We have to really decrease transmission to avoid the next waves and more worry that emergence of new variants of concern will transmit too fast or evade immune response,” he said.

“The appearance of these variants in the African continent, but also in South America and Europe really means that more than ever, it is the time that we don’t leave any continent behind, especially on vaccination,” Oliveira said.

Silver Lining In Cloud – Variants Also Impetus For Cooperation

But within Africa itself, Sall said the various SARS-CoV-2 variants constitute a new impetus for cooperation between countries, to be able to track and measure the circulation of the virus, and to enhance diagnostic capacities that he said will soon be available across Africa.

“The new variants are the object of a very thorough study, and the path of our countries is very clear: obtain maximum information and adapt the strategy to contain the transmission,” he said.

Moeti enjoined countries and individuals to strive to overcome COVID-19 fatigue and return to the fundamental actions that have been found to be effective against these variants. These measures, she said, need much more emphasis that news that the virus is much more transmissible.

“The vaccine is a tool that’s going to make a huge difference all over the world,” she said.

But she reminded that “having a corner of the world not protected, the way the world’s economies and peoples are connected, will have negative economic impact even in those countries that managed to vaccinate the entire population. We really are all in it together, and we have to work to support each other to overcome this global crisis.”

Image Credits: Paul Adepoju/HealthPolicyWatch, Africa CDC.