Covid-19: How Africa’s top scientists have tracked emerging variants, ensuring we’re not left behind

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  • Scientists and public health officials in Africa have played a crucial role in identifying new variants of the SARS-CoV-2 virus.
  • A new paper explains how this has helped to ensure Africa isn't left behind in the response to the pandemic.
  • The slow rollout of the vaccines in many African countries, however, can lead to more worrying variants, they caution.

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

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.

*For more Covid-19 research, science and news, click here. You can also sign up for our Daily Dose newsletter here.

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