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

Organized by Africa CDC jointly with The Centre for Epidemic Response and Innovation (CERI) at KRISP, Nelson R Mandela School of Medicine, Durban, South Africa. 23 August 2021 – 04 September 2021

To maximize the benefit of genomics surveillance in the continental efforts to contain COVID-19, Africa CDC jointly with CERI have supported various institutions in the continent to serve as both in-country and regional reference sites for SARS-CoV-2 sequencing. This training will be delivered to scientists from Uganda and Cameroon public health institutes that have received Illumina equipment and reagents to increase SARS-CoV-2 sequencing in their countries.

 The Africa CDC and the Centre for Epidemic Response and Innovation (CERI) in South Africa are organizing a two-week hands-on training on the genomic surveillance of SARS-CoV-2. This is the second Illumina training at CERI in 2021 and we expect to deliver at least another 4 workshops in 2021.

The training will include laboratory methods for SARS-CoV-2 sequencing and the analysis of the sequence data, from raw read data to variant analyses and phylogenetic inference. The training workshop aims at establishing good laboratory and analytical practices for the participating African Union Member States. 

Course overview 

The goal of this course is to teach DNA sequencing using the Illlumina Miseq platform. The course will start with an introduction to Illumina technology and devices, with the goal of covering end to end workflows for the preparation and analysis of SARS-CoV-2 specimens using whole-genome sequencing approaches. Daily activities at the workshop will include individual and group hands-on training exercises, supplementary lectures and practical sessions on genomic and bioinformatic techniques. The hands-on laboratory sessions will focus on the preparation of sequencing libraries for SARS-CoV-2 whole-genome sequencing with particular emphasis on how to improve the efficiency of viral NGS by undertaking variations in library preparation techniques and optimization approaches.

Participants will also gain practical experience in bioinformatics analysis and interpretation of SARS-CoV-2 sequence data. These include reference mapping, viral genome assembly, comparative viral genomics and data interpretation and downstream applications in public health contexts. There will be lectures and demonstrations of the potential applications of NGS in public health, limitations and pitfalls of the techniques and clinical case studies and on the ongoing SARS-CoV-2 pandemic.

Objectives and expected outcomes

The purpose of this training is to provide intensive hands-on training for 20 Africa Union Member States on SARS-CoV-2 sequencing and data analyses and to sequence at least 200 COVID-19 cases from the participating countries as part of the workshop, Member states will be welcome to send samples beforehand, as we found that sequencing their own samples is not only motivating but allow a real work experience. At the end of the workshop participants will have a profound knowledge of SARS-CoV-2 sequencing and computational methods as well as insight on its application to inform the SARS-CoV-2 outbreak response. In addition, the lectures, videos and instruction manual will be shared with participants to promote open science and open sharing of knowledge. 

Target audience

This course is directed towards scientists or lab technicians from Uganda and Cameroon experienced in molecular biology and are not well versed in the sequencing and analysis of SARS-CoV-2. Previous experience in molecular techniques including RT-PCR testing or sequencing of SARS-CoV-2 is mandatory. Knowledge of Illumina sequencing technology is desirable but not essential. This is a targeted training that is designed to support the Member States to expand SARS-CoV-2 genome surveillance.

Learning Outcomes 

After this training, trainees should be able to:
• Prepare libraries for Illumina sequencing
• Run Illumina devices and assess sequencing performance during a run
• Understand the basics of Illumina data handling and analysis
• Analyze and interpret Illumina whole genome data
• Generate reports for MOH and public health officials