Africa Defense Forum
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Staying One Step Ahead: Surveillance, Health Systems Key to COVID-19 Fight


As the latest wave of COVID-19 infections subsides across Africa, governments and public health experts are asking what’s next in the continent’s response to the global pandemic.

The answer is multifaceted. Here are a few of the issues Africa faces as it works to defeat COVID-19 over the coming months and years.

New Variants

With about 12% of COVID-19 tests returning positive results, the disease continues to spread steadily. That raises the possibility of developing new, potentially deadlier variants, according to Mark Ainsworth, head of data insights and analytics for United Kingdom-based asset manager Schroders.

“We can’t know if there is another variant down the road with the scale of advantage that delta has over previous variants, but it is absolutely a risk,” Ainsworth told Bloomberg.

So far, African researchers have identified two variants that the World Health Organization (WHO) considers worth watching. The eta variant was discovered in Nigeria in late 2020. The C.1.2. variant turned up in the Guateng province of South Africa during the now-waning delta wave.

The eta variant has spread across West Africa and is now the second-most common variant on the continent. C.1.2 accounts for a small number of cases across Southern Africa and the Democratic Republic of the Congo.

Could one of those variants rise to prominence as the delta variant loosens its grip? So far, experts have taken a wait-and-see approach.

Increased Testing and Surveillance

To stay ahead of any future variant outbreak, the Africa Centres for Disease Control and Prevention (Africa CDC) plans to expand testing across the continent in hopes of stopping a new wave before it gets out of control.

Africa CDC Director Dr. John Nkengasong has said the agency will increase testing using antigen-based rapid tests, which are simple to use and easy to transport to remote areas. Rapid tests are not as accurate as more complex laboratory-based PCR testing, but they can detect whether someone has been exposed to the virus and should go into isolation to prevent further spread.

PCR tests, which are more precise, can take several days to produce results. They will remain the standard test for people to take ahead of travel, Nkengasong said.

Expanded Gene Sequencing

Africa has a limited ability to identify COVID-19 variants based on their genetic code. Since the pandemic began in 2020, African laboratories performed just 1% of the 3 million genetic sequences around the world.

That’s likely to change, however, as the WHO, universities and private benefactors pour resources into expanding the continent’s sequencing abilities.

The continent is getting close to sequencing up to 50,000 genomes, five times the number that had been done at the beginning of 2021.

“There are several great success stories of countries that are well established, such as South Africa, Angola, Nigeria and Kenya, and countries that are catching up quickly, like Botswana,” said Dr. Tulio de Oliveira, director of the KwaZulu-Natal Research Innovation and Sequencing Platform and the Centre for Epidemic Response and Innovation (CERI), both based in South Africa.

CERI recently trained researchers from Malawi, who quickly produced their own results when they returned home. Researchers from Uganda also have learned new sequencing techniques at CERI to improve their capacity.

Genomic sequencing has been important for the COVID-19 response, according to de Oliveira.

“New variants are forming all the time, so genomic data has guided countries to make quick and informed public health decisions since the start of the pandemic,” he said.

Improved Health Systems

The demands of the COVID-19 pandemic have revealed the cracks in health systems across Africa. Nkengasong is urging countries to use the lessons learned during the pandemic to strengthen their public health systems to prepare for future epidemics or pandemics.

“I think that we all have recognized during this pandemic it is no longer a theoretical concept that we must invest in our health systems,” Nkengasong said. “They are the cornerstones for our economic growth and our won health security.”

Countries need to build their own versions of the Africa CDC to help them monitor and respond to disease outbreaks, Nkengasong said.

Building such capacity will mean developing a workforce of scientists and public health experts and an emergency operations system that can respond quickly to crises. On a continent of 1.3 billion people, that will require tripling the number of epidemiologists from the current 1,900 to 6,000.

“These are some of the key areas that are challenging countries, and we must invest in that space,” Nkengasong said.

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