MRCG Genomics Team leads Virtual Training Course on SARS-COV-2 Bioinformatics

A five-week virtual training on SARS-COV-2 bioinformatics for beginners was recently organised by Wellcome Connecting Science in collaboration with Covid-19 Genomics Global Training. The training was held locally across South America, Africa, and Asia from 1 November - 8 December 2022 and aimed to enhance SARS-CoV-2 bioinformatics capacity in low- and middle-income countries.
Scientific officer working in the Genomics Laboratory

The genomics core laboratory at the Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine (MRCG at LSHTM) hosted one of these classrooms with four local teaching assistants. There were 15 students across West Africa including Gambia, Senegal, Togo, Guinea, Ivory Coast, and Ghana. Students used the latest bioinformatics tools and resources to analyse SARS[NS1] -CoV-2 genomic data and gain an understanding of current technologies used to identify SARS-CoV-2 variants and lineages.

Led by Abdul Karim Sesay, the MRCG’s Genomics Core Strategic Platform has conducted impressive work on SARS-CoV-2 genome sequencing that has contributed significantly to The Gambia’s COVID-19 response. This includes close collaboration with the Gambian Ministry of Health and the National Public Health Laboratories, where he led the setup of the COVID-19 testing facilities as well as training for personnel. This increased capacity led to The Gambia being ranked 6th in the world for the percentage of SARS-CoV-2 samples sequenced relative to national cases.

In addition, the Genomics Platform has established strong collaborative links with West African institutions in the field of genomics, enabling others to identify circulating SARS-CoV-2 variants.

Martha Anita Demba, a Bioinformatician at MRCG at LSHTM and training assistant for the course said: “The training… was an opportunity for me to connect with different researchers from around the world and share my knowledge as a bioinformatician. I have learned a lot and formed valuable networks with some of the students.”

“Considering the huge amount of data generated through sequencing and the minute number of bioinformaticians available in the continent, I believe it is essential to conduct such training which will significantly aid in the speed and quality of research and pave a way for greater research opportunities”, she added.

Mariama Telly Diallo (MSc Molecular Biology and Population Genetics, Universite Cheikh Anta Diop) was a teaching assistant for the course. She said: “It was helpful for young researchers engaged in generating data in our setting. During this training, I realize there is a huge gap in bioinformatics in our research setting. I got the opportunity to share my bioinformatics knowledge with young African researchers, but also learnt a lot from this training which will be useful in my future endeavours.”

At the end of the training, participants were able to analyse viral genome sequences and interpret genomic data obtained by high-throughput sequencing. Participants were also able to use the command line to analyse viral next-generation sequencing (NGS) data, quality control of sequences, reference mapping and de novo assembly of viral genomes, pathogen identification from metagenomics data, and creating phylogenetic trees.

Charles Mensah, a Ghanaian bioinformatician said: “SARS-CoV-2B4B 2022 was such an insightful step-by-step beginner guide to bioinformatics for all. I highly recommend this training for all who would like to have a comprehensive and tailored taste of bioinformatics.”

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