FIVE YEARS ON: HOW COVID WAS THE CATALYST FOR AFRICA’S GENOMIC REVOLUTION

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Summary of Nature Africa photos: CERI

When the COVID-19 pandemic struck in early 2020, the world braced for an unknown threat, with widespread fears that Africa would struggle to cope with the crisis. Instead, the continent mounted a robust scientific response, leveraging existing expertise in infectious disease research.

Among those at the forefront was Tulio de Oliveira, a genomicist in South Africa whose work played a key role in tracking the evolution of the virus. Five years on, reflecting on the lessons and progress made, he says it is evident that Africa’s contributions to global public health have been substantial and far-reaching.

In late 2020, amidst a deadly second wave in South Africa, De Oliveira and his team at the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) identified the variant later designated as Beta, which carried mutations that increased transmissibility and potentially reduced vaccine efficacy.

The discovery was made possible by an already-robust genomic surveillance infrastructure, built over years to combat HIV and tuberculosis. De Oliveira recalls receiving a tip-off from doctors in the Eastern Cape province, where an unusual surge in cases was observed.

Within days, his team sequenced the virus and confirmed the presence of significant mutations. Recognising the global implications, he immediately sought an emergency meeting with the World Health Organization (WHO), leading to international recognition of the Beta variant.

Despite the scientific importance of the discovery, South Africa faced an international backlash.

“Instead of sending vaccines and diagnostics, countries imposed restrictions,” De Oliveira recalls. Disproportionate travel bans or restrictions were imposed by Australia, Brazil, Canada, the European Union, India, Japan, New Zealand, Saudia Arabia, UAE, UK, and US.

The same scenario played out a year later when his team, now based at both KRISP and the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University, identified Omicron. This time, however, detection was even faster – his team sequenced the variant and informed the world within 72 hours.

The backlash was expected, but De Oliveira remains steadfast in his belief that transparency is crucial. “We knew the repercussions, but we also knew that rapid data-sharing was necessary to control the virus,” he explains. Thanks to this approach, South Africa was able to prepare for Omicron, with minimal restrictions and lower death rates than in previous waves.

Beyond national efforts, De Oliveira’s work catalysed a shift in Africa’s scientific standing. South Africa was the second country in the world, after the United Kingdom, to launch a national genomic surveillance programme for SARS-CoV-2. Through partnerships with 42 African nations, his team coordinated datasharing efforts that resulted in groundbreaking publications1,2.

“We built a culture of collaboration, not competition,” he says. “We have trained over 660 African scientists in genomic surveillance and data analysis. This wasn’t just about COVID-19; it was about building a future in which Africa is at the forefront of global health security.”

The pandemic provided a blueprint for future epidemic preparedness. One of the most significant breakthroughs, De Oliveira explains, was the shift towards real-time data-sharing through platforms like the Global Initiative on Sharing All Influenza Data (GISAID). This enabled scientists around the world to track viral evolution, and develop diagnostics and vaccines, at an unprecedented pace.

But he warns that the gains are fragile. “There’s a real risk of dismantling the genomic surveillance systems we built. Maintaining these capabilities is crucial, not just for COVID-19, but for emerging threats like Mpox, Marburg and climate-amplified epidemics.”

To help sustain these advances, De Oliveira and his colleagues launched the Climate Amplified Diseases and Epidemics (CLIMADE) initiative. The partnership, spanning 40 African countries, is aimed at predicting and mitigating outbreaks fuelled by climate change.

The Genomic Surveillance Unit (GSU) of the Wellcome Sanger Institute also partnered with CERI, marking a major step in equitable global health collaboration. This collaboration will expand genomic research, bolster training programmes, and ensure that discoveries benefit all regions of the world. “This partnership is not about dependency,” De Oliveira stresses. “It’s about equitable exchange – leveraging Africa’s expertise and infrastructure while collaborating with global institutions. The days of African scientists being seen as mere participants in global research are over.”

Challenges remain, including the rise of vaccine nationalism, misinformation and funding cuts. De Oliveira has been vocal about these issues, arguing in the New York Times that global health leaders could learn from Africa’s coordinated, community-driven approach to disease surveillance.

Yet, his commitment to scientific transparency and innovation has never wavered. “This is not about individual recognition. It’s about building something greater – an Africa that leads in science, that protects its people, and that contributes meaningfully to global health,” he says.

References:

1 - Wilkinson, E. et al, Science 374, 423-431(2021).

2 - Tegally, H. et al, Science 378, eabq5358 (2022).

CERI Sequencing Core in Stellenbosch Univ.

KRISP team at UKZN inspecting a flow cell.