Africa has stepped up its surveillance of emerging variants of the Covid-19 virus, and a detailed paper shows how the work of hundreds of scientists and public health officials from the continent is ensuring that Africa does not get left behind in the global response to the pandemic.
According to a paper published in the journal Science in September, when the Covid pandemic started, Africa was initially left behind due to its fragile health and scientific infrastructure, and diagnostics and reagents being hoarded by developed countries. As a result, Africa is the world's least vaccinated continent.
But a mammoth effort – involving 112 African and 25 international organisations, in close collaboration with the Africa Centres for Disease Control and Prevention (Africa CDC) and the World Health Organisation (WHO) – soon closed this gap. Together, they worked to create detailed analyses of the variants and lineages in Africa.
Genomic surveillance, which has been crucial to identify these variants and control outbreaks, took place in 33 African countries and two overseas territories. Without these networks in place, we would arguably be in a much worse situation.
Using advanced tech in Africa
Even when sampling was limited, the team of African scientists identified many of the variants of concern (VOCs) and variants of interest (VOIs) that are being transmitted across the world, such as the Beta variant which dominated South Africa’s second wave of infections.
“We are deeply committed to using the most advanced technologies in Africa to trace and combat the virus,” co-author of the paper, Professor Tulio de Oliveira, said in a news release by Stellenbosch University.
De Oliveira is a bioinformatician and director of the genomics surveillance lab KRISP (KwaZulu-Natal Research Innovation and Sequencing Platform).
He previously told Health24: “In South Africa, we were fortunate to identify [the Beta variant] quickly, otherwise we would have ended up with a more severe second wave because we wouldn't have been able to respond.”
Huge network in SA
Vaccines should be effective against new variant
Vaccines should be effective against the new C.1.2 COVID-19 variant. This is according to KRISP Director, Túlio de Oliveira. He says its mutational profile is similar to that of the Beta variant. Courtesy #DStv403
KRISP is the principal investigative institute for the network of genomic surveillance in SA, but it is part of a collaborative network comprising a handful of institutes, including the National Health Laboratory Service, the National Institute of Communicable Diseases, the University of Cape Town, Stellenbosch University and the University of the Free State.
“One of the things we showed, and one of the reasons South African science is being praised – not only nationally by our ministers and by the president, but internationally by scientists and funders – is because we have shown that by working together, we can do much more than by working independently,” said de Oliveira.
Collaboration a 'fulfilling' experience
De Oliveira dubbed the network of collaborations as a “very fulfilling” experience.
“Not only did we manage to share and analyse our African data together, the collaboration also involved complete sharing of knowledge, with all analysis scripts shared and hundreds of hours of capacity building in analysis and data generation so that genomics can be decentralised and performed in real time in Africa,” he said.
According to Dr John Nkengasong, director of the Africa CDC, strengthening genomic surveillance systems across the continent is critical for early detection and control of disease outbreaks.
“The [Africa CDC Institute Institute] is very proud of this collaborative work and will continue to coordinate collaboration among public health, academic and research institutions to strengthen pathogen genomics and bioinformatics capacity in Africa,” he said.
Gayle Smith, a former administrator with the US Agency for International Development, said in September 2020 that Africa was doing “a lot of things right the rest of the world isn’t”, AP reported.
Delta variant a 'wake-up call'
Currently, there are 40 000 African genomes available in GISAID, a global science initiative that provides genomic data of the Covid virus.
The highly transmissible Delta variant which is dominating infections in multiple countries, including South Africa, is a “wake-up call and underlines the importance of genomic information”, said Dr Matshidiso Moeti, WHO regional director for Africa. Moeti added that it underscores the importance of African scientists having the necessary resources to analyse the evolution of the virus.
“Without this analysis, variants can spread undetected on the continent and across the globe. This will prolong the acute phase of the Covid-19 pandemic, not just in Africa, but worldwide,” she said.
Stopping the evolution of the virus
Importantly, the authors point to the slow rollout of vaccines in most African countries, suggesting that it “creates an environment in which the virus can replicate and evolve".
This, in turn, can lead to additional VOCs with higher transmissibility than the Delta variant, and that escape vaccine-induced protection, for example, and further derail the global fight against Covid.
“If the virus keeps evolving on the African continent, this will become a global problem. It is our moral duty to try to protect Africa and the world,” said de Oliveira.
ASPEN Pharmacare is in talks to make Johnson & Johnson’s coronavirus shot under licence in South Africa, at what would be the continent’s first major independent distribution base for a global vaccine against COVID-19, the company has announced.
News of the talks coincided with the suspension of heavily criticised shipments to Europe from Africa of the same shot, which is already being made under contract and packaged by Aspen but distributed by J&J.
WHO Director-General Tedros Adhanom Ghebreyesus said last month he was “stunned” by that arrangement, since Europe has very high inoculation rates while less than 3% of Africa’s adults in Africa have been vaccinated.
Aspen CEO Stephen Saad told Reuters it was now seeking a far bigger deal with J&J that would allow it to make, market and sell the vaccine under licence for the whole of Africa, along the lines of the model used by India’s Serum Institute.
“At the moment we contract manufacture for J&J. So that’s what we do. We take it, they release it,” Saad said in an interview.
“…But a licence would be different. We would then sell to the end-customer. And then we have a brand. And then we also have control over where our product goes” and overpricing.
“…At the moment, J&J could take all the product we make because it’s their product, and sell it …wherever they choose to. We have no say in that.”
J&J did not immediately respond to an email from Reuters seeking comment.
In an online briefing, African Union (AU) coronavirus envoy Strive Masiyiwa said the arrangement whereby J&J was sending shots finished in Africa to Europe was halted following interventions by South African President Cyril Ramaphosa and European Commission President Ursula von der Leyen.
The fewer than 20 million doses shipped so far would be returned. “All the vaccines produced at Aspen will stay in Africa and will be distributed to Africa,” Masiyiwa said.
Africa aims to vaccinate 60% of its adult population by 2022.
But by August, just 10% of the doses that the COVAX vaccine-sharing programme, co-run by the World Health Organization, had forecast it would ship there by that time had been delivered, according to the AU.
Masiyiwa said the talks between J&J and Aspen also came as a result of the South African President requesting that the arrangement between them be changed.
Aspen is looking to expand its annual vaccine production capacity from around 300 million doses to about 450 million by February 2022.
Saad said it was too early to say whether some of that would be reserved for production under licence, though from October onwards, all of the J&J vaccine doses being packaged at its plant would go to African countries.
J&J has contracts to supply 31 million doses of vaccine to South Africa and at least 220 million to the rest of Africa.
The new arrangement would be “like (India’s) Serum where they get the licenses to manufacture. It’s not a foreign model,” Saad said of the licensing talks.
EGYPT is ramping up production of the Sinovac coronavirus vaccine as it aims to become a hub for vaccine exports to Africa and protect its own population of more than 100 million from a fourth wave of infections.
The government is preparing new facilities that it says could produce several million vaccine doses daily and is also in talks with an unspecified European vaccine producer.
“We are currently in discussions with other companies because it is important to us that we diversify our sources, and hopefully soon we will announce our partnership with a European company,” said Dr Heba Wali, president of the state-run Holding Company for Biological Products and Vaccines (VACSERA).
Wali, speaking at VACSERA’s headquarters, said one million doses of the VACSERA-Sinovac jab had already been distributed within Egypt.
In recent months, Egypt has also received shipments of vaccines made by Sinopharm, AstraZeneca, Sputnik, Sinovac and Johnson & Johnson.
Nearly 7.5 million people in Egypt had received at least one dose of a vaccine, Health Minister Hala Zayed said last week as she announced a push to accelerate jabs.
A fourth wave of COVID-19 infections is expected to peak in late September after a lull in infections, according to Zayed.
A new VACSERA facility outside Cairo aims to begin production in November and have a capacity of 1 billion vaccines per year.
“We aim to not only be self-sufficient regarding the vaccine, but we hope to export it to our brothers in African countries and the entire region,” Prime Minister Mostafa Madbouly said in a statement on Monday.
Wali said that Egypt’s Chinese partners had overseen the local production lines, and she dismissed doubts about the Sinovac shot’s efficacy, citing its approval by the World Health Organization.
“However, with the appearance of new strains of the virus, companies always study their vaccines and their effectiveness with these new strains, and if any company confirms that it is ineffective, they will (further) develop their vaccine.”
On Tuesday, Egypt reported 263 new cases, bringing its total to 288,162, including 16,727 deaths. Officials and experts say the real number is far higher but not reflected in government figures because of low testing rates and the exclusion of private lab results.
KENYA’S oxygen production firm Hewatele is doubling production this year to keep up with surging demand from hospitals that are treating critically ill COVID-19 patients, the company said.
Demand for the commodity has more than doubled to 880 tonnes from 410 tonnes before the pandemic, the ministry of health said, causing a steep shortage due to lack of installed capacity.
The East African nation is confronting a severe fourth wave of COVID-19 infections that is putting pressure on health facilities.
“This country doesn’t have capacity to put 2,000 patients under high flow oxygen at the same time. We need to do something urgently,” said Bernard Olayo, founder of the company.
Hewatele plans to invest $3.5 million to double production to two tonnes a day by year-end, Olayo said.
The firm produces oxygen by the chemical method, using a naturally occurring salt to separate nitrogen from the air.
“It (chemical method) has limitations because you can’t produce a lot of oxygen,” Olayo said.
To resolve that issue, Hewatele will invest another $15 million next year to build an air separation unit to produce liquid oxygen, which will lead to a ten-fold output increase to 20 tonnes per day, he said.
Kenya has only one such plant, which belongs to industrial gases firm BOC, said Olayo, who was inspired to produce oxygen for hospitals by his experience as a young government doctor in the west of the country two decades ago.
“Children would die of pneumonia, not because we didn’t know what to do, but because we didn’t have oxygen,” he said.
Hewatele’s expansion is being financed by a combination of debt and equity from international financiers, he said.
But the process will not be easy since the pandemic has driven up demand for oxygen and for components used by oxygen plants.
“Getting oxygen compressors is very difficult,” Olayo said.
Hewatele, which supplies 200 hospitals with oxygen, has three production plants around the country to help keep costs down. Still, a litre of liquid oxygen costs 120-150 Kenyan shillings, compared with 10 shillings internationally.
“The demand far outstrips the supply,” said Olayo.