SOUTH AFRICA – The Africa CDC, through its Pathogen Genomics Initiative (Africa PGI), has conducted a series of hands-on bioinformatics training held at the University of the Western Cape, South Africa to support countries on the African continent to rapidly respond to disease outbreaks.

The Africa Pathogen Genomics Initiative aims to enhance disease surveillance and public health partnerships through integrated, cross-continent laboratory networks equipped with the tools, human resource capacity and data infrastructure to fully leverage critical genomic sequencing technologies.

Expanding access to surveillance tools, training the workforce to make use of sequencing facilities and streamlining the sharing of data aims to improve the use of genomics in the tracking of potential pandemic pathogens including viruses, bacteria, fungi and other organisms.

Subsequently, Africa CDC collaborated with the African Society for Laboratory Medicine and the South African National Bioinformatics Institute to launch the bioinformatics training to strengthen genomic sequencing capability which resulted in the sequencing of nearly 100,000 SARS-COV-2 genomes.

The training workshop is expected to create a network of experts within the African continent with the ability to collaborate in projects as well as share and exchange genomic data and data analytics resources to respond to the COVID-19 pandemic and future disease outbreaks.

The training offered focused on introduction to bioinformatics, data management, bioinformatics analysis, interpretation of genomic results as well as presentation of genomic data to inform public policy decision-making.

The 15 targeted participants from 11 African Union Member States that benefitted from the training workshop expertise and support include DRC, Egypt, Ethiopia, Ghana, Kenya, Nigeria, Morocco, Senegal, South Africa, Uganda and Zambia.

The training funded by an Africa CDC grant to the African Society for Laboratory Medicine will bolster workforce development in sequencing and bioinformatics which is key to developing a continental capacity that can deliver at speed, scale and quality in outbreak detection and response.

The bioinformatics training is the first of a range of data-intensive analytics support that is intended to meet the needs of genomic surveillance for COVID-19, other outbreaks and endemic diseases in Africa.

Furthermore, 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 to strengthen continental health security.

The established 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 the COVID-19 pandemic surveillance.

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