SANBI hosts Public Health training in Bioinformatics

‘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 strengthen is genomic epidemiology, a field that combines pathogen genomics, bioinformatics and epidemiological 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 countries around Africa 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 last week attended a workshop on bioinformatics 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 national public health services. The training forms part of an ongoing partnership between Africa CDC and SANBI, and includes the naming of the Institute’s director, Professor Alan Christoffels, as a senior advisor to Africa CDC in August 2021.

A 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 made up of a host of laboratory specialists, data scientists and scientists from other disciplines, the group hailing from countries like Benin, Cameroon, the Ivory Coast,Kenya, Namibia, and Zambia.

Among the resources used in the workshops are Ilifu, a South African facility that offers infrastructure for big-data; and Galaxy Europe, the open-source web-based platform that, like Ilifu, allows for the analysis of large datasets, typically those usedin computational biological research.

The workshops seek to build on increased capacity in pathogen genomics around Africa, explains 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. But the data management coming out of these new-found technological capacity remains a challenge as public health facilities often lack the tools and skills to make sense of the information, says 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 explains. “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, adds 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,” he says. The delegates are equally optimistic about what they can 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,” says 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,” says 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, notes 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 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 says.