Over the past several months Dr. Shirlee Wohl, in the Andersen Lab, spearheaded the development of an interactive WARN-ID genomic epidemiology training course focused on generating and analyzing SARS-CoV-2 data. WARN-ID partners from the African Centers of Excellence for Genomics of Infectious Diseases (ACEGID), The Broad Institute, and Scripps Research have a wealth of training and sequencing experience that they contributed to the development of the coursework, training resources, and materials for trainees to learn how to perform sequencing, bioinformatics, and analysis.
The 6-week training course launched on May 31st with 40 participants from 7 countries (Sierra Leone, Liberia, Senegal, Nigeria, Mexico, Jordan, and the US). Guided by live zoom sessions, pre-recorded lectures available via YouTube, virtual office hours, and the messaging app Slack, trainees receive ongoing support and troubleshooting help.
Now halfway through the course, trainees have been taught the theory behind genomic epidemiology and performed the amplicon-based SARS-CoV-2 sequencing protocol developed by Scripps Research and the Broad Institute. The next two weeks of the training will focus on the bioinformatics tools that convert raw sequence data generated using Illumina sequencing platforms (MiSeq or iSeq) into whole-genome assemblies. This includes performing genome assembly, sequence alignment, and variant identification. The training will conclude with a module focused on phylogenetic analysis, interpretation, and visualization methods to display the sequence data.
This incredible international training has been a highly collaborative effort across all WARN-ID sites. It’s been wonderful to see our partners come together to problem-solve and engage in lively discussion. We look forward to seeing the final results and continuing to support the sequencing efforts of trainees across the WARN-ID network.