Photographer: Julia Koblitz on Unsplash
Cementing its reputation as a respected training hub for anything bioinformatics in Africa, UWC’s South African National Bioinformatics Institute (SANBI) will, over the first two weeks of March 2024, host 18 trainees from public health laboratories and research facilities from around the continent – with an urgent focus on cholera.
The 10-day programme, Bioinformatics for Genomic Epidemiology, is a collaboration between SANBI and the NGS Academy – focused on training in next-generation sequencing (NGS) – of the Computational Biology Division (CBIO) at the University of Cape Town.
The training will be run by lead bioinformatics trainer at SANBI, Peter van Heusden, SANBI postdoctoral researchers Dr Tracey Calvert-Joshua and Dr Nasr Eshibona, SANBI alumnus John Juma of Kenya’s International Livestock Research Institute (ILRI), and George Githinji of the Kenya Medical Research Institute (KEMRI).
The programme will be divided into two parts, explained Van Heusden. The first week will focus on fundamental bioinformatics, looking at programming, the management and analysis of data, as well as introductions to some of the most commonly used genomics databases like International Nucleotide Sequence Database Collaboration (INSDC) and the Global Initiative on Sharing All Influenza Data (GISAID).
“This is one more step towards building a capable network of African public health pathogen bioinformatics practitioners,” said Van Heusden, alluding to the growing repertoire of training programmes that SANBI has hosted before, but especially since the COVID-19 outbreak. “We want to build on our previous training and move the participants to a more advanced level.”
A guiding principle at SANBI is highlighting the invaluable role that bioinformatics can play in the monitoring and management of disease outbreaks. In the wake of recent headline incidents, the second week of the programme will zero in on cholera outbreaks.
Of the 29 countries that reported cholera outbreaks in 2023, 16 were from the African Region, including South Africa, reported the World Health Organisation (WHO). According to the European Centre for Disease Prevention and Control, over 950,000 cholera cases, including 5518 deaths, were reported worldwide in 2023.
“Our ‘capstone’ project at the end of the two weeks will be analysing and characterising an outbreak of cholera,” said Van Heusden. To this end, the trainees will look at data taken from Haiti's real-world 2010-onwards outbreak, building a picture of how the outbreak unfolded and how the responsible bacterial strains changed over time.
Training the next generation of bioinformatics-savvy technicians and researchers aligns with the work that SANBI and others are doing on the development of the African Pathogen Data Sharing and Archive Platform, or AGARI. This platform is being piloted for real time pathogen genomics data management, sharing and exchange in Africa.
One current area of focus is the negotiation and drawing up of continental data governance protocols.
Cementing its reputation as a respected training hub for anything bioinformatics in Africa, UWC’s South African National Bioinformatics Institute (SANBI) will, over the first two weeks of March 2024, host 18 trainees from public health laboratories and research facilities from around the continent – with an urgent focus on cholera.
The 10-day programme, Bioinformatics for Genomic Epidemiology, is a collaboration between SANBI and the NGS Academy – focused on training in next-generation sequencing (NGS) – of the Computational Biology Division (CBIO) at the University of Cape Town.
The training will be run by lead bioinformatics trainer at SANBI, Peter van Heusden, SANBI postdoctoral researchers Dr Tracey Calvert-Joshua and Dr Nasr Eshibona, SANBI alumnus John Juma of Kenya’s International Livestock Research Institute (ILRI), and George Githinji of the Kenya Medical Research Institute (KEMRI).
The programme will be divided into two parts, explained Van Heusden. The first week will focus on fundamental bioinformatics, looking at programming, the management and analysis of data, as well as introductions to some of the most commonly used genomics databases like International Nucleotide Sequence Database Collaboration (INSDC) and the Global Initiative on Sharing All Influenza Data (GISAID).
“This is one more step towards building a capable network of African public health pathogen bioinformatics practitioners,” said Van Heusden, alluding to the growing repertoire of training programmes that SANBI has hosted before, but especially since the COVID-19 outbreak. “We want to build on our previous training and move the participants to a more advanced level.”
A guiding principle at SANBI is highlighting the invaluable role that bioinformatics can play in the monitoring and management of disease outbreaks. In the wake of recent headline incidents, the second week of the programme will zero in on cholera outbreaks.
Of the 29 countries that reported cholera outbreaks in 2023, 16 were from the African Region, including South Africa, reported the World Health Organisation (WHO). According to the European Centre for Disease Prevention and Control, over 950,000 cholera cases, including 5518 deaths, were reported worldwide in 2023.
“Our ‘capstone’ project at the end of the two weeks will be analysing and characterising an outbreak of cholera,” said Van Heusden. To this end, the trainees will look at data taken from Haiti's real-world 2010-onwards outbreak, building a picture of how the outbreak unfolded and how the responsible bacterial strains changed over time.
Training the next generation of bioinformatics-savvy technicians and researchers aligns with the work that SANBI and others are doing on the development of the African Pathogen Data Sharing and Archive Platform, or AGARI. This platform is being piloted for real time pathogen genomics data management, sharing and exchange in Africa.
One current area of focus is the negotiation and drawing up of continental data governance protocols.
