University of the Western Cape: Data management a pillar of stopping a pandemic or other disease outbreaks

‘Pandemic preparedness’ has become a mantra as countries and global public health organisations take stock of the weaknesses that Covid-19 exposed in public health systems.

One area that organisations like the Africa Centres for Disease Control and Prevention (Africa CDC) – the public health arm of the African Union – has been particularly eager to beef up is bioinformatics capacity, a field that, among other things, brings together pathogen genomics and the management of such data.

The ability to, for instance, sequence the genetic make-up of a disease-causing organism – like SARS-CoV-2, the virus behind the COVID-19 disease – was sorely lacking in many African countries at the start of the pandemic. So too, was the ability to manage and analyse the data coming out of these exercises.

With this in mind, 16 delegates from 15 African countries attended a workshop on bioinformatics last week hosted by the South African National Bioinformatics Institute (SANBI) at the University of the Western Cape.

This workshop is the second hosted by SANBI in collaboration with the Africa CDC and the Africa Pathogen Genomics Initiative (Africa PGI), part of a training programme directed at those working in African public health services.

The training forms part of an ongoing partnership between Africa CDC and SANBI, an arrangement that includes naming the institute’s director, Professor Alan Christoffels, as a senior advisor to Africa CDC in August 2021.

The first bioinformatics training session was hosted by SANBI in May this year.

The most recent workshop was titled, ‘Specialised Training Workshop on Bioinformatics Analysis for Pathogen Genomic Surveillance’.

The delegates were a host of lab technicians, data scientists and scientists from other disciplines, hailing from countries like Benin, Cameroon, the Ivory Coast, Kenya, Namibia, and Zambia.


Delegates Dr Francis Jaryan (right) of the National Public Health Institute of Liberia and Mr Alhagie Papa Sey of the National Public Health Laboratories in Gambia were among those to attend the training.
Among the resources used in the workshops are Ilufu, the South African facility that offers infrastructure for big-data; and Galaxy Europe, the open-source web-based platform that, like Ilufu, allows for the analysis of large datasets, typically those used in computational biological research.

The workshops sought to build on increased capacity in pathogen genomics around Africa, explained Peter van Heusden, the SANBI researcher who leads the training. So, for instance, use of next-generation sequencing (NGS) – or ‘bulk’ sequencing – was accelerated during COVID-19.

SANBI researcher Peter van Heusden takes delegates
through some powerful bioinformatics tools.

But the data management coming out of this new-found technological capacity remains a challenge as public health facilities often lack the tools and skills to make sense of the information, said Van Heusden. Samples and data had previously been sent elsewhere in the world for analysis, with little skills development in Africa.

“We’re covering SARS-CoV-2 sequence analysis, but we’re also talking about the whole data flow,” he explained. “We want to do more than getting the sequence data out because we really want to understand the epidemiology or spread of a disease, and there’s interest in diseases beyond COVID-19.”

One aim of the training is to help African labs become autonomous in both generating and the analysis of genomic data, said Van Heusden. That requires a systems approach – a journey to make sure that the data management software used by laboratories, for instance, can speak to the software used by public health ministries.

“The African continent is on this journey, but it’s not just a journey of technical things, but also of people, of skills, of a workforce,” added Van Heusden.

The delegates were equally optimistic about what they could achieve with their new skills. “I wanted to get more hands-on experience on different bioinformatics platforms, so that we can solve problems that we have with infectious diseases in my country,” said Ms Mary Chege of the Institute of Primate Research in Kenya. “The training was intense, but I think I’ve learnt so much.”

“Bioinformatics has definitely become a need in our laboratories over COVID,” said Ms Gugu Maphalala, chief medical laboratory technologist of the Eswatini National Blood Transfusion Services. “We discovered that we need more information about a disease, to be able to for instance give guidance to the Ministry of Health in our country.”

While the training initially focused on COVID-19 genomics, the idea is to simply use the disease as a springboard, noted Van Heusden. These technologies can be applied to tracking and stopping not just the next global pandemic, but also local disease outbreaks like Ebola in Uganda and measles in Zimbabwe, as has recently occurred.

“We want to give people a broad understanding of the field, so that we can later refine the technology for the disease burden of where they are,” he said.