Training Workshop on SARS-CoV-2 Genome Sequencing and Bioinformatics

Organized by Africa CDC, the Centre for Epidemic Response and Innovation (CERI) and the African Society for Laboratory Medicine (ASLM) at Stellenbosch Institute for Advanced Study (STIAS), Stellenbosch University in South Africa.

Workshop dates: 1st November – 12th November 2021

  • 17 African Union Member Countries attending the workshop: Angola, Botswana, Democratic Republic of Congo, Ethiopia, Kenya, Lesotho, Mauritius, Mozambique, Rwanda, Sao Tome, South Africa, Sudan, Tanzania, Uganda, Union of Comoros, Zambia, Zimbabwe.
Participants of the workshop at the garden at STIAS.

Background on the workshop: To maximize the benefit of genomics surveillance in the continental efforts to contain COVID-19, Africa CDC jointly with partners has supported various institutions in the continent to serve as both in-country and regional reference sites for SARS-CoV-2 sequencing. However, sufficient hands-on training was not provided due to lockdowns and travel restrictions.

The Africa CDC and the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University in South Africa are organizing a two-week hands-on training on the genomic surveillance of SARS-CoV-2. The training will be part of the Genomics Africa Fellowship program with the Rockefeller Foundation and will include laboratory methods for SARS-CoV-2 sequencing and the analysis of the sequence data, from raw read data to variant analyses and data uploading on the GISAID platform. The training workshop aims at establishing the best laboratory and analytical practices for the fifteen participating African Countries.

Summary program of the workshop:

Day 1 and Day 2 –  Introductory session on Genomic Surveillance and group study of four settings that implemented genomics surveillance and its application to the own African setting

Participants studying global genomics surveillance activities.

Day 3 –  Group presentations and interactive case studies discussion in Africa and the globe.

Day 4 – Public database for genomic surveillance, dissemination of genomics surveillance findings to policymakers and the public.

Keynote Presentation: Genomic surveillance of SARS-CoV-2 and other pathogens in Brazil  – By Dr. Marta Giovanetti, FioCruz, Brazil.

Day 5 to Day 9 – Working in the temporary laboratory to sequence SARS-CoV-2:

  • Hands on cDNA synthesis and amplification groups 
  • Hands on DNA quantification and normalization 
  • Hands on Library preparation and sequencing
  • Hands on SARS-CoV-2 Bioinformatics Analysis 
  • Sunday (Day 7) is a rest day for us but a working day for the DNA sequencer (36h of sequencing)
Teaching at the ‘Clean room’ for reagent preparation.

Day 10 & Day 11: BioinformaticsAnalysis

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

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

  • In the last day, 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.