(Published - 26 May 2020)
The South African National Bioinformatics Institute (SANBI) at the University of the Western Cape (UWC) was asked to play a leading role in the coordination of national research of infectious viruses like Covid-19. This enormous task forms part of a globally coordinated project in answer to a request from the Bill & Melinda Gates Foundation.
The director of the institute and the research chair of Bioinformatics and Health Genomics, Professor Alan Christoffels, says the role of the newly-established research coalition -PHA4GE - is to bring scientists and the government closer together. The aim is to unite public health practices with cutting edge genomics research and analysis.
Prof Christoffels speaks in his capacity as a leading roleplayer in this global coalition and public health alliance for Genomics Epidemiology.
Q: What is bioinformatics and health genomics and how is it resolving the Covid-19 crisis?
The term bioinformatics is actually a combination of two words, biology and informatics. What you have is an intersection of biology, computer science and IT. The other big term, health genomics is really asking how do we use information such as genetics or DNA to help us understand diseases and also to help medical practitioners try and provide a better solution when they're trying to treat people.
Q: Let’s talk about PHA4GE, a global scientific alliance, uniting genomics and public health. Will this speed up finding a vaccine for Covid-19?
It is interesting that when we first conceptualized this idea, it was way back in March 2019 when we hadn't even thought of the current pandemic.
If you actually step back and you ask yourself what happens when you go into a public hospital such as Tygerberg Hospital today and you go and have tests done? You'll find that the clinician will run tests which are sent off to a laboratory that is approved by the hospital. And so we are seeing laboratories in the public health space that are approved by hospitals and are doing a great job of running these very routine diagnostic tests. What we are now proposing is, what stops us from taking state public laboratories and stepping them up to be able to exploit that type of genetic testing and techniques. This might seem like a dream to some people, but because of the available technologies, we are looking at how we can globally assist public laboratories to ably assist with that kind of high-tech work.
Q: What would you say is the crux of the matter in aligning ourselves so that public laboratories are able to reach this point?
I’d say that it will probably be that we need IT skills – we need this very strange combination of biology and computer science, and we would need to be able to look at data. Can we then come alongside public laboratories and assist them with cutting-edge analytical skills to be able to make those methods available to the general public?
Q: Let’s talk about the long-term view. What would the benefits be?
In the long-term, these steps would save governments around the world huge amounts of cash, even though they might need a bit of seed funding in the beginning. I think the best example here is the old TB test. With the available new DNA technology, it can be fast-tracked to get right to the source of the problem, particularly when you're dealing with drug-resistant tuberculosis.
If we look at this particular case, one could also ask if it’s possible to use all of the genetic code for the bacteria that causes TB? Also, is it possible for us to look at that and then make a prediction, or try and say whether or not somebody is multidrug-resistant or not? To do that, we have to bring both the public health officials as well as the research scientists on board. You want to plan this strategy collectively, because the alternative is that we continue to do research within the university space without the knowledge being of service to the general public – which is at the heart of what we’re supposed to do.
Q: Tell us about your relationship with African institutions and institutions in different parts of the world. It looks like it's a very exciting project that could actually reshape medical or public medical practices in Africa, where they are most needed.
We have partners that have come on board that are probably at different stages of applying these cutting-edge techniques. And so, you are bringing people on board that are really wanting to contribute, both for their own countries, as well as recognising that if we can strengthen low and middle-income countries, we then strengthen the global public health space.
Therefore, I can bring on board my skills, and somebody else sitting in Sierra Leone can bring onboard theirs. What this means for us as the African continent is that we strengthen our public health systems, and by extension, we are partnering with people in America and Europe, for example. Once you start to combine these types of resources and skills, I think we actually have a way in which we can really start to set the agenda for trying to improve public health globally.
Q: Would you agree that if people work together, as they are in this particular programme, it's a lot easier to make faster progress because one researcher may notice something another researcher wouldn’t?
If we actually agree to come together and in fact strategize and plan, we can utilise our limited resources and find out where our strengths are. We can collectively decide that as of now, this is a priority globally.
But at the same time, we can hold each other accountable. For example, we still have problems with TB and malaria on the African continent. So if we all work together on a global platform like this, we can start to plan how we prioritise what is needed now, and we can put our hands together to assist in solving a problem. Let's also be frank. It can be quite a headache to try and manage people. So we're going to have to carefully manage the relationships as we build this global consortium, which is already approaching 100 people. But it's exciting. I think we're starting with something which should have happened a long time ago.