Africa Expands Its Genomic Research Capacity to Fight COVID-19

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In the fight against COVID-19, public health leaders say increasing Africa’s capacity for genomic surveillance is a key part of understanding the enemy and defeating it.

If hospitals and health workers are the front line of the fight against the pandemic, laboratories and genetic researchers are the intelligence officers, analyzing the incoming data and predicting the virus’s next move so public health systems can be ready.

When the pandemic began in early 2020, African health systems quickly found themselves drastically underequipped and understaffed to confront a virus that moves quickly and mutates rapidly.

Genomic surveillance uses powerful computers and other tools to analyze the genetic material found within samples of the COVID-19 virus. The process can spot subtle differences in the genetic makeup, alerting scientists to the presence of potentially harmful new variants in the population.

Genomic surveillance is in part a numbers game: The more samples researchers collect and sequence, the more likely health workers can stop outbreaks before they start.

When the pandemic began, Africa had only a handful of laboratories capable of doing genomic research. One of those, the African Centre of Excellence for Genomics of Infectious Diseases in Ede, Nigeria, detected the first case of COVID-19 in Sub-Saharan Africa in March 2020.

Nearly two years later, Africa still faces a shortage of trained lab workers and adequate technical capacity to do genomic surveillance.

To overcome the shortages, the Africa Centres for Disease Control and Prevention (Africa CDC) and the Africa regional office of the World Health Organization (WHO) are building a continental system of laboratories that can track the COVID-19 virus, identify its shifting genetics and help health workers keep it in check.

Along with those labs, both agencies have launched community surveillance programs designed to expand testing beyond hospitals to locate pockets of infection and react quickly to keep them from expanding. The data collected by those tests will feed into the genomic surveillance system.

In October 2020, the Africa CDC received $100 million to expand pathogen genomic research on the continent over the next four years. The WHO is spending $4.5 million to create a new Centre for Excellence in Genomic Testing in Cape Town, South Africa.

The Africa CDC established its Institute for Pathogen Genomics in 2019, months before COVID-19 was first identified in China. The institute was created to support national public health institutes with sequencing work.

At a meeting in Dakar, Senegal, in early November, the Africa CDC certified representatives from 16 countries to perform genomic surveillance.

“We have improved rapidly the number of countries that are able to do the genomic sequencing of the virus,” Dr. John Nkengasong, director of the Africa CDC, wrote in an article in the journal Cell.

Other researchers are training in pathogen genomics at South Africa’s Centre for Epidemic Response and Innovation (CERI) in Durban. Dr. Rene Essomba, head of the genomic unit of Cameroon’s Ministry of Health, is among the researchers trained by CERI.

“Before, we used to send our samples abroad in other countries to do sequencing,” Essomba said in an interview with CERI. “Now, we will start making our own genome sequences. It will increase the turn-around time so that we can have real-time surveillance of variants in Cameroon.”

The work to expand Africa’s genomic surveillance is paying off. Early in the pandemic, the continent sequenced 5,000 COVID-19 samples from 23 countries. As of mid-November, that number had grown to more than 53,600 samples from 53 countries.

That’s still about 1% of all sequences worldwide, but it is growing. South Africa remains the dominant force, producing 43% of those sequences.

The WHO estimates that because disease outbreaks cost Africa $800 billion in lost productivity each year, the drive to expand Africa’s genomic surveillance goes beyond COVID-19.

The same labs will be able to provide crucial knowledge about any of the 140 disease outbreaks the continent experiences in a year, from anthrax and chikungunya to measles and Rift Valley fever, according to Africa CDC expert Dr. Seth Inzaule. Genomics research helped break the West African Ebola outbreak in 2014-16.

“The COVID-19 pandemic has revealed that Africa needs a new public health order to be resilient, to adapt, and to cope with 21st century disease threats,” Nkengasong said during a recent press briefing.