Growing bioinformatics capacity in Africa

MORGAN MORRIS 00:07

Hi there. My name is Morgan Morris, and I’m here today to talk about work being done by public health organisations to improve capacity in genomics – ie the study of organisms’ genetics – in Africa. This as part of continent-wide efforts to stem the tide of especially but not exclusively infectious diseases. Welcome.

We’re going to talk specifically about pathogen genomics, which is the genetic sequencing of disease-causing pathogens. Why is this useful? Well, as we saw over Covid-19, it proved critical – if at times politically risky – for the surveillance of the disease across the world. We could monitor the rise of new variants, and in this way keep politicians and public health decision-makers updated and informed.

Advocates for pathogen genomics have long argued that we should be doing more of it in Africa. Why? Because they believe it could help change the narrative of infectious disease outbreaks and control on the continent. As the five authors, all affiliated with the Africa Centres for Disease Control and Prevention, noted in a 2021 Lancet paper, “Adding pathogen genomics tools to the existing strategies will be beneficial for early detection and prevention of zoonotic diseases before they jump to humans, improve outbreak management by rapidly identifying the causative agent, and facilitate the designing of diagnostics and preventive, therapeutic, and other countermeasures, while monitoring their effectiveness.” The Africa Centres for Disease Control and Prevention, by the way, is the autonomous public health arm of the African Union, or AU.

Elsewhere in the world, sequencing tools have become part and parcel of public health systems for the monitoring of disease outbreaks, observes Professor Alan Christoffels of the South African National Bioinformatics Institute at that country’s University of the Western Cape. As senior advisor to the Africa CDC’s Pathogen Genomics Initiative, Christoffels has helped to shape the unit’s genomics strategies, he says.

ALAN CHRISTOFFELS 02:10

Very crude attempts at doing disease surveillance have been shown in high-income countries where scientists have effectively used next-generation sequencing technologies in order to characterise pathogens to better understand what strains are circulating within a particular community. I think for us in Africa this has become an essential tool as part of our public health response, one that we have seen during the Covid pandemic, a capability that is growing steadily in a number of Africa countries.

MORGAN MORRIS 03:00

For his part, Christoffels believes that when it comes to genomics, parts of the richer world’s playbook can be applied to Africa. More than that, it’s essential.

ALAN CHRISTOFFELS 03:11:

Emerging and re-emerging infectious diseases continue to plague the African continent, in fact half of the deaths recorded in Africa are caused by infectious diseases, compared to about two percent in Europe. We clearly see the need to better manage our infectious diseases, and this is particularly essential if you want to detect pathogens early and in so doing use that information in order to mount a rapid public health response.

MORGAN MORRIS 03:45:

As Christoffels and the authors of the Lancet paper point out, COVID-19 allowed African countries to begin to put in place some of the capacity. Organisations like the Africa CDC and the World Health Organisation Regional Office for Africa were able to raise the funding to put in place, through initiatives like the African Pathogen Genomics & Bioinformatics Network, sequencing technologies – the equipment – and training. As a result, many more public health laboratories in Africa now have the ability to conduct their own sequencing.

However, running a genetic sequence means little without the means to decipher its results – the varied arrangements of the four-letter genetic alphabet, the A, C, G, and T that represent DNA’s base pairs. Reading these sequences and being able to report the results in a way that makes sense to non-technical public health officials, demand the hardware, software and skills of the field known as bioinformatics.

The next step then is to build the bioinformatics skills base, especially as Africa looks to apply pathogen genomics to diseases endemic to the continent. And here we’re talking about the likes of HIV, malaria, tuberculosis, cholera, Lassa Fever and even Ebola.

Among the institutions the Africa CDC has called on to help expand training is Christoffels’ South African National Bioinformatics Institute. Keeping up the training it has run over the past years, the latest instalment took place over two weeks at the end of June and beginning of July 2023.

PETER VAN HEUSDEN 05:20:

This is done with Africa CDC’s Institute for Pathogen Genomics. We have participants from public health labs in Southern and Eastern Africa. And these people are all involved in pathogen surveillance. Trying to see what infective agents are causing diseases in their countries.

MORGAN MORRIS 05:50:

Setting the scene is Peter van Heusden, a researcher at SANBI who has been leading such training sessions over the past years.

PETER VAN HEUSDEN 05:58

Now we are seeing people having DNA sequencing machines in many African countries, and the thing is then how to analyse the data. When it comes to analysing data, and that is called bioinformatics, there are some techniques that can be re-used between different pathogens. And one of the important things is the platforms. Once you get used to the platforms, whether it’s web-based things like Galaxy, or whether it’s command-line bioinformatics, the platforms are very similar between things. We are teaching them the different platforms and techniques for analysing pathogens. And what we mean by that is really trying to identify firstly the genotype of the pathogen, in other words, genetically speaking what type of pathogen are we dealing with here. With SARS-COV-2, we all got very familiar with Beta and Alpha and all of those kinds of things, and you can do similar analysis for other pathogens.

MORGAN MORRIS 07:05:

A key driver behind the ongoing training, says Van Heusden, is the ambition to expand on the growing network of African scientists able to work in both genomics and bioinformatics.

PETER VAN HEUSDEN 07:15:

We're not going to teach them the specifics of every kind of analysis, but we’re going to do two things. Firstly, we’re going to give them the exposure to understand what questions they need to ask, where to look for further information. And we’re also going to incorporate them into the network with the other people we had trained previously. You know, maybe somebody in Zambia wants to deal with something and maybe someone in Botswana can assist them. Or vice versa. So we’re ready to build the skills base on the continent so that we don’t need to send samples to Germany. Or even send data to Germany for analysis. Or the UK or something like that. So we can say, look, we have an expert in Eswatini who can provide you with some advice on that.

MORGAN MORRIS 08:06:

Tanzania is one of the countries hoping to tap into the full potential of next-generation sequencing as it combats diseases of interest like Dengue Fever. Which is why it is keen to expand its workforce through the Africa CDC training opportunities. Two of its lab scientists had attended previous training, and another two attended the course in June/July. One of these was Maria Kelly, based at her country’s National Public Health Laboratory. She in April this year published a paper on the molecular characterisation and phylogenetic analysis of Dengue Fever Viruses from three outbreaks in Tanzania between 2017 and 2019. While there is an uptick in bioinformatics work, the country still has some way to go, Kelly explains.

MARIA KELLY 08:53

We have a lot of new technology that involves a lot of bioinformatics work. At our institute, we don’t have any bioinformaticians. Even in the country, you can easily count the number of bioinformaticians there. But at this point of time, we have the instruments and we are required to sequence and do analysis. So for us it was very difficult so we had to learn by ourselves. Currently we are like two people – we tried to learn on our own, especially through online courses. But through this course we have managed to train more than four people.

MORGAN MORRIS 09:52

Ethiopia, likewise, is hoping to build on its genomics skills base and its application. His institution, explains Abel Negash of the Armauer Hansen Research Institute in Addis Ababa, was the first to generate sequences of SARS-CoV-2, the coronavirus responsible for the Covid-19 disease. While a lot of work in his country is now focused on tuberculosis and malaria, Negash also sees opportunities in his own research on the bacterium known as Streptococcus pneumoniae, a major cause of childhood morbidity and mortality across the globe. In Africa alone, streptococcus pneumonia is responsible for between one and four million cases a year. But it is the younger generation of scientists, especially, who are driving the interest in genetics in their country, Negash explains.

ABEL NEGASH 10:40

There is a great deal of interest. Our institution, because it is a research institution, we take students – we don’t give degrees but students come for research from the universities. The institution has about 60-80 postgraduate students who come to do research at the institution. And almost everyone is thinking of doing genomics – that’s what students propose, that’s what everyone is trying to do. There is interest, but there is a lack of trained manpower in terms of bioinformatics. We have one very good bioinformatician and other junior researchers with an interest in bioinformatics. Now I think the next thing is broadening this capacity – okay, we have a sequencer. Although we have a problem finding reagents, but that is being solved by support from collaborators from outside. The next thing is analysis of that sequenced data. And as I said, because there are many students who want to do genomics, and the analysis requires bioinformatics. So there is a need for training in bioinformatics.

MORGAN MORRIS 12:10

For one person in attendance, much of the course material was not new. Monica Mbabazi is a bioinformatics scientist with the Central Public Health Laboratories in Uganda. But as versed as Mbabazi is in bioinformatics, even she picked up a few new tricks – especially about Galaxy, the popular open-source web-based platform used by tens of thousands of scientists from across the globe to analyse large biomedical datasets.

MONICA MBABAZI 12:37:

It’s not new. Because on top of being an employee of CPHL, I’m also a bioinformatics student at Makerere University. So I’m pursuing a PhD in bioinformatics. And of course I’ve done some of these things before.

MORGAN MORRIS 12:54

So what have you learnt that is of use to you? So did you learn anything?

MONICA MBABAZI 12:58

You know, when you have knowledge of something and you go through, you’re polishing up what you already know. And then you can understand better. For example, I think I’ve used Galaxy before but I’ve noticed that I’ve not been exploring it to the full. I’ve noticed that with Galaxy you can do a lot. There are different packages for different organisms. You can create a workflow that you can actually share with other researchers, and you know, you can have some level of collaboration within Galaxy.

MORGAN MORRIS 13:39:

But drilling down to its foundation, the aim of pathogen genomics is ultimately to save lives. That is of key concern to Kabengele Siame, a biomedical scientist with the Tropical Diseases Research Centre in Zambia. Siame’s recent work looks at the use of genomics to track drug resistance and transmission patterns of tuberculosis in his country. He believes it can be applied to fill current information gaps and improve the diagnosis, surveillance and treatment of tuberculosis. And it comes with important economic benefits.

KABENGELE SIAME 14:12:

Some of the positives which have come out of the Covid pandemic is that it has afforded us an opportunity to start sequencing other pathogens for which we can actually do something about. These are big diseases like HIV, tuberculosis and even malaria. TB and tuberculosis, in particular, it takes quite a long time, months, to get drug sensitivity results so that the patient can be put on appropriate therapy. And so with this technology and this type of analysis, what was taking us even up to six months to get a result, we’re able to get a result in two weeks. That goes a long, long way in the sense that, one, the patient will likely get cured in the recommended time, and also simultaneously you are going to stop the spread of drug-resistant tuberculosis in the community. Which will be way more expensive to treat in any case. So even though sequencing can be seen as an expensive thing, when you look at it in a holistic manner, it is actually cheaper because you are saving on the spread of these extremely difficult-to-treat cases of tuberculosis in a shorter time. And the same thing goes for HIV.

MORGAN MORRIS 15:36:

Rolling out equipment and skills training may be a big step in the right direction, but organisations like the Africa CDC and the WHO AFRO recognise that individual nations will have to step up. They have to put in place the right policy frameworks and the infrastructure that will be essential for pathogen genomics to be fully incorporated into their public health systems.

“The emergence of SARS-CoV-2, including its variants of concern, crystalized the need for coherent country, regional and global genomic surveillance systems,” noted the World Health Organisation in its Global Genomic Surveillance Strategy for 2022-2032. It also pointed to the gains made over Covid-19, which it says “should be leveraged as a foundation to sustainably build genomic surveillance capacity”.

This is Morgan Morris on behalf of Nature Africa, thank you for listening.