Q&A: The hunt for new COVID-19 variants

Dr Gabrielle Breugelmans is head of epidemiology at the Coalition for Epidemic Preparedness Innovations (CEPI), a global partnership launched in 2017 to develop vaccines to stop future epidemics. She explains how new COVID-19 variants are identified, and why strengthening this system could help reduce the impact of future pandemics.

  • 7 February 2022
  • 6 min read
  • by Linda Geddes
Two laboratory technicians at work. Photo by Pavel Danilyuk from Pexels
Two laboratory technicians at work. Photo by Pavel Danilyuk from Pexels


How are new variants of SARS CoV-2 identified and reported?

They are first detected by a laboratory with the capability to perform genomic sequencing, and then those sequences are shared with the scientific community. In the case of Omicron, there were suddenly a lot of infections in South Africa, which was different from before. Local labs in South Africa and Botswana were able to sequence samples of circulating virus, and realised that this might be something new, so they shared it globally with GISAID – a public repository, which originally stood for the Global Initiative on Sharing of Avian Influenza Data. Before COVID-19, a few laboratories would use it to share information about circulating variants of influenza, but now it has become the repository to go, with many labs that are involved in SARS-CoV-2 surveillance sharing its sequences there.

CEPI has been working closely with GISAID over the course of the pandemic to strengthen this influential database.

“When you look at the economics, investing in surveillance costs a fraction of what it would cost to contain a pandemic.”

What happens next?

Once a sequence has been uploaded, lots of different people with different areas of expertise, including CEPI, can start looking at it, and really teasing out whether this is a completely new variant, and if it contains specific mutations that might be of concern.

Because South Africa was so quick to share the sequence data for the Omicron variant, it meant that other countries were on the alert. It meant they could put the necessary health and social measures in place to, not control it – that wasn’t feasible in the end, because it is so transmissible – but to be prepared for it coming their way and limit its transmission.

Having a global repository like GISAID for such an amount of data also enables us to track the transmission of new variants such as Omicron from very, very early on. We saw it increasing very quickly in southern Africa, and then sequences popping up in in Europe, in North America, and so on. The speed at which it happened was phenomenal. Really, I've never seen anything like it before in my life.

How widespread is this surveillance network, and are some geographical regions better covered than others?

Most of the genomic sequencing is coming out of high-income countries, particularly the UK and the US, but also countries like France, Germany, Australia. We recognised this as a gap from very early on, because it creates some blind spots. For instance, Omicron is circulating globally, but if you don't have genomic sequencing capabilities in all countries, you don’t know what’s happening there.

Some of CEPI’s partners, such as the Bill & Melinda Gates Foundation and Wellcome, have created initiatives to try and increase genomic sequencing capabilities in sub-Saharan Africa and Asia, and already we’re starting to see more data being reported out of Africa – particularly from South Africa, Nigeria, Kenya and Senegal. So I think that's one “benefit” from the pandemic. The global collaboration and global sharing that has come out of it hasn’t happened before.

Could building this kind of surveillance capacity have any benefits beyond COVID-19?

Absolutely, but we need more than just additional surveillance and genome sequencing labs. More than 75% of emerging infectious diseases in humans originate from animals. Ideally, you want to capture those ‘spillover’ events, but you never know when, or why, they’re going to happen. So we need better surveys of wildlife and livestock to detect outbreaks of novel pathogens that could potentially become a global disaster – we call that our Disease X.

If you could capture those events very early on, it would reduce the chances of an outbreak leading to an epidemic. It would also buy us more time to develop necessary countermeasures, such as vaccines, supporting CEPI’s goal to develop a vaccine against future outbreak-causing pathogens in just 100 days. The ambition, known as the 100 Days Mission, is part of CEPI’s plan to minimise or even eradicate the risk of epidemics and pandemics of the future.

Achieving this will require close collaboration between people working on the veterinary and the human side of disease surveillance. We also need to go beyond traditional passive disease monitoring and implement artificial intelligence (AI) that can combine information about the influence of weather patterns, deforestation, urbanisation, etc. For example, we know in Australia and southeast Asia that when there has been a drought, this puts stress on bats, which means they need to travel further for food, meaning they may expel the viruses that they carry more widely. This could be very powerful, because if you could predict hotspots where spillover events are more likely to occur, you could improve local surveillance, rather than strengthening it everywhere, which would be more expensive.

Are there any ongoing initiatives to try and strengthen global disease surveillance?

CEPI’s partners are trying to put some of the necessary capabilities in place. For example, The Gates Foundation has provided funding to help set up the Pathogen Genomics Initiative, which aims to boost laboratory networks, disease surveillance and emergency response capacity in Africa and South Asia. The Rockefeller Foundation has a great interest in setting up a global early warning system, which would use AI to detect the signs of outbreaks and share that information globally. We’re also working with the new WHO Hub for Pandemic and Epidemic Intelligence, which is trying to improve data sharing and to develop technologies that would enable better decisions to be made about future threats.

We too have been leading on a programme to advance global surveillance and ensure this feeds into vaccine development. Over the past 18 months, we’ve worked with GISAID and a couple of UK health and science agencies to create a system that not only monitors new COVID-19 variants but also then tests to see if antibodies (part of the immune response generated following infection or vaccination) are still able to neutralise the strain. This information then gets shared with vaccine developers – and it’s this piecing together of real-time viral changes that is proving to be really influential for COVID-19 vaccine programmes.

Building on these collaborations, we are also speaking to our partners to advance efforts to create a dedicated alert system that could speed identification of and, in turn, vaccine development against a future Disease X, supporting the 100 Days Mission. I think that, because of COVID-19, people have come to understand the importance of surveillance, but usually, when a pandemic goes, so does the funding. It is important to keep surveillance up during the interpandemic periods – what we call ‘peacetime’ – because if you don’t, you will miss those early events. When you look at the economics, investing in surveillance costs a fraction of what it would cost to contain a pandemic.