Organized by Centre for Epidemic Response and Innovation (CERI), Stellenbosch University and the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at University of KwaZulu-Natal in partnership with the Abbott Pandemic Defense Coalition (APDC) & Rockefeller Pandemic Preparedness Institute (PPI).

Workshop dates: 3 September – 17 September 2022

8 Countries attending the workshop:  Brazil, Botswana, Colombia, Democratic Republic of Congo, Kenya, Senegal, South Africa and Uganda.

Background on the workshop: The Africa Genomics Fellowship short term training program funded by the Rockefeller Foundation and we have already hosted over 100 scientists at CERI, KRISP, ACEGID, and ILRI. We have expanded this program in South Africa with CERI and KRISP with the The Abbott Pandemic Defense Coalition to also host fellows from other regions in the world.

This workshop we have fellows from Africa and Latin America for the hands-on NGS training on Oxford Nanopore Technologies (ONT) and Illumina sequencing. The Latin American fellows will be trained together with African fellows at the state-of-the-art KRISP labs at UKZN, 4-16 Sept 2022.

We are also working on the expansion of this training and fellowship program to south and east Asia, so the Global South can work together to expand capacity in genomics and bioinformatics.

Summary program of the workshop:

Day 1 to Day 5 –  Working hands-on the laboratory to sequence SARS-CoV-2 and other pathogens

  • Hands on cDNA synthesis and amplification 
  • Hands on DNA quantification and normalization 
  • Hands on Library preparation and sequencing
  • Saturday and Sunday (Day 6-7) is a rest day for us but a working day for the DNA sequencer (36h of sequencing)

Day 8 to Day 10: BioinformaticsAnalysis

  • QC of sequences •Submitting data to GISAID 
  • Bioinformatics 2 (base calling)
  • Bioinformatics 3 (Genome Assembly)
  • Bioinformatics 4: Variant and Lineage detection 

Day 11 –  Group presentations and interactive case studies discussion in Africa and the globe.

  • Public database for genomic surveillance, dissemination of genomics surveillance findings to policymakers and the public.

Day 12 to 13 – Data interpretation and Open discussion and next step for Member States•

  • In the last days, we will wrap up and try to understand WHY,  HOW and WHAT to do to set up a quick response genomics surveillance for epidemic response & investigation.