Covid-19 Genomic Surveillance in Africa: One Year On

10th September 2021

The genomic surveillance network set up across Africa to sequence coronavirus variants, in part with help from the Quadram Institute, has published a vital analysis of how the pandemic spread across the continent in the journal Science

The spread of the COVID-19 pandemic in Africa has been outlined using genomic surveillance, providing insights into how the virus entered and spread across the continent, and how new variants of concern emerged.

The findings drawn from 33 countries over the past year have today been published in the journal Science, and show that unless we ensure that Africa is not left behind in the global pandemic response, it could become a breeding ground for new variants of the virus. And that threatens further waves of the pandemic across the globe.

Genomic surveillance involves sequencing the genetic code of the virus, and using naturally occurring minor changes in the genome to trace how different lines, or variants, spread. As soon as the gravity of the pandemic was realised, scientist across the globe started genomic sequencing samples, sharing this data internationally to try to keep tabs on its spread from its origins in Wuhan, China.

The first COVID-19 cases were detected in Africa in late February 2020, and within a month almost every country was affected. From the outset, African laboratories started rapid genomic sequencing to help in tracing outbreaks and points of transmission, and identifying the emergence of new variants.

Other scientists across the world supported these efforts, especially where there were potential gaps in the surveillance net. Researchers from the Quadram Institute in the UK contributed material, equipment and their experience as part of the COVID-19 Genomics UK Consortium.

For example, they helped to train scientists from Zimbabwe’s National Microbiology Reference Laboratory to do their first genome sequencing ever and analyse their own data.

Professor Rob Kingsley said: “We were already working with scientists at NMRL to study typhoid fever in Zimbabwe and we used this close working relationship to rapidly pivot in response to the Covid-19 emergency. Our Zimbabwe colleagues continue to strive to apply the most recent technologies to address the ongoing epidemic.”

Over the next 12 months thousands more COVID-19 genomic sequences were read and uploaded to international databases. Now, in a paper published today in the journal Science, the researchers are able to present a dynamic view of how COVID-19 spread across Africa, and the lessons we must learn from this genomic data to prevent the future waves of the pandemic.

The dataset shows that there were many different introductions of the virus into Africa, and that 64% of these came from Europe. The introductions came to a halt in April 2020, coinciding with the complete halt in air travel. The pandemic then entered a new phase characterised by low levels of within-country movements and occasional between neighbouring countries, reflecting how trade continued to some extent during country lockdowns.

The second wave of the pandemic that broke across the world in late 2020 was clearly shown in the genomic data, with half of the sequences coming in the first 10 weeks of 2021. This second wave was more severe in Africa, in part because of the emergence of Variants of Concern (VOCs) that are more transmissible and/or cause more severe symptoms.

Genomic surveillance is crucial in identifying these variants. The current study clearly maps the emergence and spread of the “Beta” variant (B.1.351), originally detected in South Africa. Following its emergence in the Eastern Cape, it spread extensively within South Africa and then into neighbouring Botswana and Mozambique and then further to Zambia. By March 2021,

Beta had become dominant across Southern African countries as well as the overseas territories of Mayotte and Réunion. The apparently unimpeded spread of the Beta variant shows that current land border controls are ineffective at controlling the virus. The genomic surveillance analysis not only shows how rapidly new variants spread across Africa, but also how they are exported, mainly to Europe and Asia, making the second wave of the pandemic more severe globally, not just in Africa.

It’s vital that we learn the lessons highlighted in this study to prevent more pandemic waves driven by other variants. Other variants have also been identified and are rising in frequency in the areas they were detected. Genomic surveillance has shown its value in identifying and tracking these, and the collaborations and networks now established in Africa will be needed to catch future variants as they emerge. Whilst this surveillance network is wide, it is thinly stretched and there are gaps. Supply problems and a lack of support leads to a lag between sampling and obtaining data, preventing a rapid public health response. This is being addressed; one of the  main outcomes of this work has been to strengthen collaboration across African countries through training and data sharing in a timely manner.

But of biggest concern is the slow rollout of vaccines across much of Africa. This creates an environment that allows the virus to mutate and evolve, which left unchecked will inevitably lead to the emergence of new Variants of Concern, potentially even more transmissible than Beta, perhaps even able to escape the effects of current vaccines. The evidence from this year of genomic surveillance in Africa is clear: No-one is safe until everyone is safe.


Reference: A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa, Eduan Wilkinson, Marta Giovanetti, Houriiyah Tegall, James E. San et al was published by Science on Thursday 9th September at 19:00 UK BST, 2pm US ET


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