17 July 2023 | Story Andre Damons | Photo Supplied
Jason Mwenda
Prof Jason Mwenda, from the World Health Organization Regional Office for Africa (WHO-AFRO), gives an overview of the roles and responsibilities of a World Health Organization Collaborating Centre (WHO CC).

The University of the Free State Next Generation Sequencing (UFS-NGS) Unit in the Faculty of Health Sciences recently held a successful Data and Bioinformatics Workshop on the UFS’s Bloemfontein Campus.

The week-long workshop, which took place from 3 to 7 July 2023, attracted participants from 13 local universities and organisations from across the country and Africa, including Cameroon, Ghana, Kenya, Lesotho, Malawi, Mali, Mozambique, Namibia, Zambia, and Zimbabwe. Other international participants came from the UK, Australia, and America. 

According to Prof Martin Nyaga, Associate Professor and Head of the UFS-NGS Unit, the emergence of the recent COVID-19 pandemic and epidemic diseases has emphasised the importance of bioinformatics as a critical tool for public health response and disease surveillance. 

He said it is increasingly important for experimental scientists to gain the bioinformatics skills required to analyse the large volumes of data produced by the next generation sequencers in order to inform public health policy and interventions as well as pandemic and epidemic preparedness.

Workshop equipped participants with foundational bioinformatics skills

“The workshop was designed to equip the participants with the necessary foundational bioinformatics skills required to analyse NGS data, focusing on three aspects: whole genome data, 16S/ITS metagenomics, and microbial metagenomics data. The workshop began by giving participants a basic understanding of the Linux command line functionality that was helpful as they navigated the various stages of NGS data analysis. The workshop combined both theoretical and practical sessions,” he added.

During the opening day, Prof Nyaga said the NGS Unit wants to evolve into a genomics hub in Africa, and it’s on the right path. The unit wants to be a specialist on pathogen genomics and shine in what they do best, he said.

Prof Jason Mwenda, from the World Health Organization Regional Office for Africa (WHO-AFRO), was one of the guest speakers, and gave an overview of the roles and responsibilities of a World Health Organization Collaborating Centre (WHO CC) on Vaccine Preventable Diseases (VPD) surveillance and pathogen genomics.

The UFS-NGS Unit is such a collaborating centre and is part of the VPD surveillance and Pathogens Genomics Cluster in the African region and will run till September 2024.

Prof Joyce Tsoka-Gwegweni, Vice-Dean for Research at the Faculty of Health Sciences, said the UFS-NGS is one of the signature units in the faculty and is one of the faculty’s prides, as it is a WHO CC. 

Workshop contributes to UFS and Health Sciences Faculty’s vision 

“The aim of this workshop is to fuel the researchers here with the necessary bioinformatics,” Prof Joyce Tsoka-Gwegweni said. “I am excited about the workshop for various reasons, because it’s not only about training, but for me in my role as Vice-Dean for research, the workshop is going to assist us with the vision of the UFS and the faculty, the vision of academic excellence. 

“I see this workshop contributing to Vision 130, in terms of the research capacity and development and also research collaboration and partnerships, as well as strengthening the research and promoting the culture of research, not only within the faculty but also within the institutions represented here.” 

She is also looking forward to the research output that might come from the workshop in terms of promoting and strengthening quality research projects, strong research collaborations, research articles, as well as highly competent researchers.

The course was aimed at individuals from a molecular biology background who are interested in bioinformatics and who work (or are planning to work) on genomic datasets. 

  • The UFS-NGS also hosted a five -day wet-lab workshop on the Illumina Viral Surveillance Panel (VSP) from 10 to 14 July 2023. The VSP provides a streamlined workflow that allows researchers and public health scientists to sequence 66 different high-risk viruses, including those of interest to the UFS-NGS Unit and its collaborating partners, such as rotavirus, norovirus, enteric adenovirus, astrovirus, sapovirus, rhinovirus, SARS-CoV-2, and respiratory syncytial virus, among many others. The VSP’s workflow integrates library preparation, target enrichment, sequencing, and data analysis. The workflow is intended to enrich whole viral genomes from total nucleic acid extraction. The DIPLOMICS-funded workshop was facilitated by SEPARATIONS’ field Application Specialists Marija Kvas and Charles Wairuri Kamau. Although the training was themed around VSP, the trainers took things back to basics, from the fundamentals of Next Generation Sequencing to the rigorous workflow that the VSP entails. The workshop was designed to have interactive talks, competitive fun quizzes on the Kahoot! Platform, and practical hands-on bench work for the VSP workflow. The workshop trained members of the UFS-NGS Unit and individuals from its collaborating partners from within South Africa, Malawi, Zambia, and Ghana.

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