University of the Western Cape: UWC Provides Continental Support for COVID-19 Surveillance

The Africa Centres for Disease Control and Prevention (Africa CDC), through its Pathogen Genomics Initiative (Africa PGI), has supported African countries during the past two years in responding to the COVID-19 pandemic. Strengthening genomic sequencing capability has resulted in the sequencing of nearly 100,000 SARS-COV-2 genomes. Cognisant of the scale-up of data generation capability, the Africa CDC, in partnership with the South African National Bioinformatics Institute (SANBI), has been designing data management protocols and tools for use in National Public Health Institutes.

On 23 May 2022, the Africa CDC, in partnership with the African Society for Laboratory Medicine (ASLM) and SANBI, launched the first in a series of hands-on bioinformatics training held at the University of the Western Cape (UWC), South Africa. The training workshop targeted 15 participants from 11 African Union (AU) Member States, DRC – Egypt, Ethiopia, Ghana, Kenya, Nigeria, Morocco, Senegal, South Africa, Uganda and Zambia. This workshop underpins the Africa CDC’s range of bioinformatics training to support countries in Africa to rapidly respond to disease outbreaks in general and develop a response to COVID-19 surveillance in particular. A vital ingredient of this course is the hands-on training offered by experienced bioinformatics scientists to participants who had acquired experience in generating Next-generation sequencing (NGS) data. A long-standing partnership between the Africa CDC and SANBI has provided the data management framework needed for the wealth of pathogen data being generated in response to COVID-19 pandemic surveillance.

The workshop is using ilifu, South Africa’s big data infrastructure for data-intensive research. ilifu is a node in the South African national data infrastructure which enables South African researchers to be leaders in the strategic science domains of astronomy and bioinformatics.

“Competency in public health bioinformatics is key in our effort to expand genomic surveillance in Africa. This training is critical in building the bioinformatics capacity in public health institutes to effectively utilise NGS data and inform decision making,” said Dr Yenew Kebede, Head: Division of Laboratory Systems and Networks at the Africa CDC. Professor Alan Christoffels, Director of SANBI, commented: “The training covers a range of topics from an introduction to bioinformatics, data management, bioinformatics analysis, and the interpretation of genomic results, to the presentation of genomic data to inform public policy decision-making. This training represents the first of a range of data-intensive analytics support intended to meet the needs of genomic surveillance for COVID-19, other outbreaks and endemic diseases in Africa”.

The participants are expected to put into practice the skills and knowledge gained from this training to respond to the COVID-19 pandemic and future disease outbreaks. Furthermore, the training workshop will create a network of experts within the continent with the ability to collaborate on projects as well as share and exchange genomic data and data analytics resources.

The training was funded by the Centers for Disease Control and Prevention (CDC) grant to the ASLM.