South Africa’s Omicron turnaround: From global travel ban to R1bn in genomic funding

In late November 2021, South African scientists identified a new COVID-19 variant, which the World Health Organisation named Omicron and, without wasting any time on rationality, declared a ‘variant of concern’. It was the discovery of Omicron that led to a near-global travel ban to and from South Africa, which left the local hospitality industry reeling, caused even more untold damage to many local businesses, and left South Africans abroad stranded. Eighteen months later, in a head-spinning turnaround, South Africa has achieved global recognition for its success in detecting and responding to Omicron and was rewarded for this achievement with over R1 billion in genomic funding, plus additional scientific talent. This was announced at the launch of the Abbott Pandemic Defense Coalition, which, supported by a new genomics facility at Stellenbosch University, is monitoring and responding to new pathogens to prevent disease outbreaks from becoming pandemics. Having worked on HIV/AIDS and TB for decades, Professor Tulio de Oliveira and his team are world leaders in genome sequencing. Professor De Oliveira has warned that climate change will lead to more epidemics in the future. He is also monitoring and responding to new pathogens to prevent disease outbreaks from becoming pandemics. This article is republished courtesy of Axess Health and Medbrief Africa. – Nadya Swart

SA’s viral hunt success bags big bucks.

South Africa has achieved global genomic surveillance ‘powerhouse’ status after the discovery of the highly infectious COVID Omicron variant, attracting over R1 billion in genomic funding – with more money plus additional scientific talent now flowing in.

That’s according to Professor Tulio de Oliveira, Director of the Centre for Epidemic Response and Innovation (CERI) – responsible for globally-innovative breakthroughs in detection and responses to HIV and TB – upon which South Africa’s COVID genomic response is built.

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He was speaking at the launch of the Abbott Pandemic Defense Coalition and state-of-the-art genomics facility launch at the Biomedical Research Institute of Stellenbosch University on the Tygerberg Hospital campus on Thursday, 20 April this year.

Mary Rodgers, Principal Scientist at Abbott, said the ‘defence coalition’ was a global monitoring and detection initiative aimed at preventing disease outbreaks from becoming pandemics.

Abbott is supporting the monitoring of and response to new pathogens at twenty sites on five continents while helping develop new diagnostics to limit disease spread – with the Stellenbosch University facility at the forefront.

“We support the labs and ensure they have reagents and protocols so they don’t have to do it. Or else they do it themselves, and we do the training, like here at the Tygerberg campus genomics facility of the Biomedical Research Institute,” Rodgers added.

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Unpacking just how the CERI and KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP, which he also directs) discovered the Omicron variant of COVID-19, De Oliveira said samples from one hundred geographically diverse clinics across the country were collected and brought to their laboratories to identify variants.

“If you have the same strain in 100 different places, then you know that something is spreading very fast. With all pathogens, we can find out within thirty-six hours whether it’s widespread or a false alarm. We’d done this dozens of times with Covid, looking for something unusual in the virus DNA,” he said.

Many of the defence coalition partners send their samples to be sequenced in South Africa, where the facilities were “exceptional”, Rodgers boasted.

De Oliveira’s group has worked for decades with HIV/AIDS and TB using the same methodology, rendering them world leaders in genome sequencing.

He explains, “If we see a cluster, we try and stop that spread. It’s not just about having the right equipment and working quickly. When you detect a new pathogen, you need to ensure you have the right diagnostics to prevent the spread. Because we detected Omicron so early, it didn’t cause much damage locally, though it caused half of all COVID deaths across the world. We got punished with travel bans for broadcasting its existence, something you’ll notice hasn’t happened since.”

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When CERI’s new cutting-edge laboratory was opened at Tygerberg last week, 25 scientists from all over the world attended, 20 of them from Africa. It’s one of ten similar facilities in the global genomic survey network and, according to Oliveira, the most advanced, best equipped, and largest on the continent. He said so far, R300 million had been invested in the facility, while a constant stream of top international scientists was either visiting to learn or moving back to South Africa to become part of the virus hunt project. One returning professor helped raise R50 million within the first three months of his return. So far, R1,2 billion has been invested in SA staff, facilities, and equipment to promote the project.

Asked what most kept him awake at night, De Oliveira said he “slept very well”, knowing that the global surveillance project was so well run and efficient.

“I’d easily put our SA team in the top five in the world. We have clinicians, computer scientists, lab technicians, and pathologists linked to all the data to understand the pandemic as it emerges. This allows me to sleep very well,” he said.

He said it was crucial to remain completely transparent. Despite the initial, counter-productive Omicron travel ban on South Africans, his team’s subsequent discovery of Omicron variants was widely publicised – “and nobody punished us for it”.

The COVID pandemic resulted in a huge leap in public awareness, understanding and behaviour, which would “benefit society next time around”.

“We continue to see scientists trying to explain things, even when it’s quiet, to help grow trust with the public. The relationship between the media and scientists is crucial. I devote a lot of time to it. It’s almost a mandate of scientists today to learn how to communicate with the media,” he added.

As an example, he cited the emergence of the Kraken COVID variant earlier this year, sparking some sensationalist coverage. Within hours’ serious scientists” had engaged with the media, giving nearly a dozen interviews. Within one or two days, the panic subsided.

Engaging with anti-vax groups and COVID harm denialists was a fool’s errand. The best way forward was publishing peer-reviewed solid scientific studies in the world’s top medical journals. (De Oliveira has notched up more than 250 publications, with many in Nature, Science and Lancet).

He singled out climate change as the most worrying development for viral and bacteriological diseases, citing the crushing Durban floods in April last year – for which the local authorities were totally unprepared, Malawi’s recent cholera outbreak leading to 100 000 cases and 3000 deaths and Paraguay’s lethal mosquito-driven chikungunya epidemic. Both were the worst outbreaks in the history of these two countries.

“It’s all driven by climate change and the rise in global temperatures. Unfortunately, that’s what will happen in the next few years. Epidemics will emerge much more often,” he warned. 

He described the pandemic defence coalition as “health insurance for the world”.

  • Over 90% of South Africans are now estimated to have developed antibodies to the COVID virus, either through vaccination or infection, with one in every 200 having succumbed to the disease (0,5%). 

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