How Africa could protect the world from new pathogens

Sophisticated genomic surveillance lab aims to keep one step ahead of outbreaks with effective tests, treatments and vaccines

By Ben Farmer, 3 May 2023

Genomic surveillance has been focused on Covid-19, but as the pandemic fades, other pathogens are being studied CREDIT: Shelley Christians/REUTERS

Prof Tulio de Oliveira is clearly proud of the impression his gleaming new Cape Town laboratory makes on academic visitors from Europe, America and beyond.

'To see the faces of the Americans, the Australians, the British, the Germans, the Swedes, when they arrive here,' he smiles.

'They are just completely surprised. They don't expect that kind of lab,' he says.

Built inside a recently-opened Stellenbosch University research complex, the new Centre for Epidemic Response and Innovation (CERI) lab is a centrepiece in a rapidly growing network of genomic surveillance centres across Africa.

'It's awesome,' enthuses one visiting scientist from Berlin. 'This building is so great. I have seen a lot of labs, but this is really, really nice. The entire atmosphere. And equipment-wise, you are so well-equipped.'

The lab's sleek sequencing machines can quickly read the DNA code, or genomes, of scores of samples of viruses and other germs at once.

Monitoring and comparing pathogens' genomes came under the spotlight during the Covid pandemic when the world's epidemiologists hunted for new variations and mutations which might make the coronavirus more infectious, more harmful, or negate vaccines.

Researchers from the lab have recently been studying cholera sequences from Malawi, which has been hit by its worst outbreak of the disease in decades CREDIT: Thoko Chikondi/AP

Yet this research is not new to Africa, which has been at the forefront of genomic surveillance for years, says Prof de Oliveira. His new lab and others around the continent will mean African nations remain at the cutting edge, he believes. Indeed the continent has to be in the lead, he says, because the world stands at the dawn of an age of epidemics and many of the factors likely to cause them to emerge can be found in Africa.

'Why [these labs] have to be located in Africa is because that's where the new pathogens, a lot of them, emerge and we should identify them quickly so vaccines, therapeutics and diagnostics can be developed,' he explained to the Telegraph.

'So it's in the interest of the globe that these facilities, and the network, work in Africa because we can protect not only Africa, but the globe from new pathogens.'

Africa's expertise in genomic surveillance came to widespread attention during the pandemic, when South African labs discovered and analysed important variants, including beta and omicrom.

'A lot of people got surprised about that,' he recalls, 'but they failed to understand this is built on decades of experience dealing with epidemics and pathogens and also very large investment, such as this building.'

International health donors have been pouring large sums into building a genomic surveillance network in African in the past few years. CERI and African Centre of Excellence for Genomics of Infectious Diseases (ACEGID) in Nigeria are the continent's main facilities, but there are another eight regional labs and increasingly individual countries have the resources to carry out their own sequencing.

An ‘age of epidemics’

Genomic surveillance has been focused in the past three years on Covid-19, but as the pandemic fades, other pathogens are being studied.

Scientists in South Africa have for example for years been sequencing and tracking HIV and tuberculosis variants so that they can tailor treatment effectively.

That gets to the heart of what Prof de Oliveira says are the three benefits of genomic surveillance.

Firstly, by tracking the changing genomes and genes of known pathogens, they can ensure that tests, treatments and vaccines remain effective.

Secondly, the lab can help virus hunters quickly identify and track new emerging infections, such as the coronavirus, or ones that have re-emerged.

For example researchers from the lab have recently been studying cholera sequences from Malawi, which has been hit by its worst outbreak of the disease in decades. The lab has also tracked Zika and Chikungunya outbreaks in South America.

Finally CERI will play a leading role in an ambitious new consortium, known as CLIMADE, aiming to thwart climate-amplified diseases and epidemics. Shifting weather patterns and climate change are increasing the range and potency of many infectious diseases.

The consortium will analyse weather data, the environment and viral sequences to warn when conditions are ripe for a disease outbreak. If an outbreak is identified, they can track its evolution and help contain its spread.

Climate change is driving the spread of mosquito-borne dengue, chikungunya and Zika into new areas CREDIT: Edgar Su/REUTERS

Climate change is driving the spread of mosquito-borne dengue, chikungunya and Zika into new areas, the World Health Organization (WHO) warned this week.

Several countries in the Americas have reported an increase in cases and that pattern might repeat in the northern hemisphere.

'I really believe that you are just entering the age of epidemics here,' says Prof de Oliveira.

'We have destroyed a lot of the environment, animals are in much closer contact than before, we are having more extreme climate events, we are having very high mobility and travel, and we have large urbanised pockets with high population density.'

Part of the lab's role is to spread expertise across Africa. Scientists from across the continent regularly attend for training.

Quickly identifying pathogens will be key, he says, before local outbreaks become epidemics or even pandemics.

He said: 'I know that everyone wants to forget about the Covid pandemic, but the best way is not to forget, but to learn from that exercise and make sure that places like this have enough scientific and financial support to quickly identify and characterise these pathogens before they become of global concern.'

News date: 2023-05-03