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28 March 2023 | Story André Damons and Engela Duvenage | Photo Charl Devenish
Prof Martin Nyaga, an Associate Professor and Head of the Next Generation Sequencing (UFS-NGS) Unit at the University of the Free State (UFS), is taking a leading role in the future of genomic surveillance as a public health tool in Africa.

As chair of the Africa Centre for Communicable and Preventable Diseases (Africa CDC) working groups on Vaccine Preventable Diseases (VPD), Prof Martin Nyaga, an Associate Professor and Head of the Next Generation Sequencing (UFS-NGS) Unit at the University of the Free State (UFS), is taking a leading role in the future of genomic surveillance as a public health tool in Africa.

The VPD Working Group of the Africa Pathogen Genomics Initiative (Africa PGI) – a unit of the Africa CDC – is one of four such expert focus groups (malaria, foodborne diseases, and antimicrobial resistant organisms, being the focus of the others) whose insights are informing the work of the Africa PGI of the Africa CDC. Its mandate is to develop a roadmap that will enhance the use of genomic surveillance tools in the fight against VPD such as measles, polio, rotavirus, cholera, typhoid fever, malaria and Ebola.

Prof Nyaga, who is also a medical virologist, has chaired the working group since 2022. 

Combat vaccine preventable diseases

“Thirty million cases of children suffering from VPD are reported in Africa every year. Around 500 000 children still die each year because of such illnesses. The VPD working focus group is helping to combat these diseases by among other initiatives, identifying the important and priority vaccine preventable diseases use cases and identifying the key stakeholders in Africa.

“It also providing technical advice on wet- and dry-lab genomics infrastructure to track, genotype and analyse data in real time to avert the rapid transmission and spread of these diseases from human to human," says Prof Nyaga, who is also the Director of the World Health Organisation (WHO) Collaborative Centre for VPD Surveillance and Pathogen Genomics in South Africa. 

According to him, in the recent past and in the post-COVID-19 pandemic peak era, there has been a rapid increase in the previously almost eradicated VPDs such as polio and measles that have recorded upsurges of more than 400-500% in some regions. At present, multiple African countries including Malawi, Mozambique, Zambia, Kenya and even South Africa are fighting the worst ever cholera outbreak, yet cholera is a disease that can be prevented by using vaccines. “While it is not definite to say that the roadmap will end these diseases, it will certainly utilise genomics science to expedite the tracking, diagnosis and improving existing vaccine candidates to drastically lower the burden of disease as it happened with SARS-CoV-2 tracking using genomics, where the impact was swift and effective,” he says. 

Roadmap to enhance implementation of genomics surveillance

The VPD roadmap document is expected to be finalised by the end of May 2023, to further guide the work of the Africa PGI and the Africa CDC. It will also provide a framework for individual countries, regions, funders, partners, and key stakeholders on how they can include the genomics of multi-pathogen and priority diseases and other use cases into existing policy and routine disease surveillance systems. 

Prof Nyaga says the roadmap is the expert document that the VPD focus group is working on to enhance informed implementation of genomics surveillance in Africa, coordinated by the Africa PGI of the Africa CDC.

Genomic surveillance an important public health tool

He believes genome surveillance can play an important role to track disease behaviours in Africa. This includes the introduction of new virulent or resistant variants and/or strain genotypes and understanding whether existing therapeutic solutions such as vaccines and antimicrobial drugs will work to fight them. 

“The use of genomic surveillance as an important public health tool came to the fore during the COVID-19 pandemic, when it was used to screen for new variants and outbreaks, and to control and manage its spread. Researchers from Africa rose to prominence by being the first to note the Beta and Omicron variants of the SARS-CoV-2 virus that causes COVID-19.”

Prof Nyaga and other researchers from the UFS have also contributed valuable research and advice pertaining to government policy about COVID-19 variants in South Africa. The UFS-NGS unit is part of the NGS-SA network and has recently collaboratively published in Science, Nature and Nature Medicine about insights drawn from genomic surveillance as the SARS-CoV-2 evolved, leading to discovery of new variants and escalation of rollout of vaccines in Africa from an informed perspective. 

More countries can now do Next Generation Sequencing

Before the COVID-19 pandemic, fewer than 10 of the 55 African Union (AU) member states could do NGS work on own soil – South Africa being one of them. Today, around 40 African countries can on a molecular level monitor the pandemic, detect, and track emerging SARS-CoV-2 variants. This is among others thanks to the efforts of the Africa PGI unit, working closely with the World Health Organisation Africa Regional Office for Africa (WHO/AFRO) and other partners, to provide appropriate hardware, software, and training to countries in different regions amid the pandemic. The Africa PGI was launched in 2019, and with the outbreak of COVID-19 was ideally placed to strengthen the roll-out of genomic surveillance tools across the continent.

“It is a great honour, not just to be a member of this VPD working group, but also for being given the privilege to lead it and engage other UFS scholars and eminent African researchers to be part of it. This opportunity has placed the UFS in the continental map of providing health solutions for Africa through the mandate of the AU and Africa CDC,” says Prof Nyaga.

Among the researchers from across Africa serving on the VPD Working Group are also Dr James Ndirangu, a public health researcher and Programme Director, Division of Public Health, UFS; Dr Peter Mwangi, a postdoctoral fellow of the UFS-NGS Unit, as well as a former UFS alumnus; Dr Saheed Sabiu of the Durban University of Technology’s Department of Biotechnology and Food Science. Others are Prof Charles Muyanja (Department of Food Technology and Nutrition, Makerere University, Uganda); Dr San Emmanuel James (KRISP/CERI, South Africa); Dr Tresor Kabeya (Institut national de recherché biomedicale (INRB), Democratic Republic of Congo); Dr Sanni Osman, (Federal Medical Centre Birnin Kebbi, Nigeria); Dr Daniel Mugendi (Embu Level V Hospital, Kenya) and; Dr Aquillah Kanzi, (Africa Society for Laboratory Medicine (ASML), South Africa. From the Africa CDC PGI, the Senior Technical officer for this programme is Dr Francis Chikuse and the Programme Lead is Dr Sofonias Tessema.  

News Archive

SASOL TRAC laboratory launched at UFS Qwaqwa Campus
2006-05-08

Some of the guests attending the launch of the Sasol TRAC Laboratory at the University of the Free State's (UFS) Qwaqwa Campus were from the left Prof Peter Mbati (Principal of the Qwaqwa Campus), Mrs Zimbini Zwane ( Communications Manager of Sasol Infrachem), Prof Gerhardt  de Klerk (Dean : UFS Faculty of the Humanities), Prof Fred Hugo
 Director of TRAC SA) and Prof Jack van der Linde (Director of RIEP at the UFS).

SASOL TRAC laboratory launched at UFS Qwaqwa Campus

The Research Institute for Education Planning (RIEP) of the University of the Free State (UFS) today unveiled the Sasol TRAC Laboratory at its Qwaqwa campus.

The laboratory will be used to help grade 10, 11 and 12 learners and educators from the Qwaqwa region to conduct the experiments from the physical sciences outcome-based curriculum.

“The Sasol TRAC Laboratory introduces learners not only to the latest technology used by engineers and other scientists in practice but also to stimulate the learner’s interest in the field of science in such a way that more of them will enter into science related careers,” says Mr Cobus van Breda, Co-ordinator of the TRAC Free State Regional Centre.

According to Mr van Breda the newly established Sasol TRAC Laboratory will enable RIEP to train learners and their educators in Physical Sciences.  The laboratory will consist of six work stations equipped with computers and electronic sensors.

“Learners from the Qwaqwa region will visit the Sasol TRAC Laboratory on regular basis to conduct experiments based on the curriculum.  Data will be collected with electronic apparatus and presented as graphs on the computer so that results can be analysed and interpreted,” says Mr van Breda.

“There is a serious shortage of suitable qualified teachers in maths and science in the Qwaqwa region.  Many schools in the region are not yet part of the RIEP project and are in dire need of assistance.  A large number of these schools are in remote areas not reached regularly by intervention programmes,” says Prof Peter Mbati, Principal of the UFS Qwaqwa Campus.

“The establishment of the Sasol TRAC Laboratory at the Qwaqwa Campus provides us the opportunity to engage with our community and assist in the development and training of these vital education subjects.  We are pleased that Sasol agreed to fund the project,” says Prof Mbati.

Students from the Qwaqwa Campus will also benefit from the TRAC programme.   “Some promising students will also undergo further training and become assistants for the TRAC programme,” says Prof Mbati. 

“Nurturing science and mathematical skills is of great importance in growing our national economy. Annually, Sasol invests more than R50 million in supporting mathematical and science education in South Africa. Our primary aim is to increase the number of learners gaining access to tertiary education in the science fields. Therefore, our Corporate Social Investment (CSI) education interventions at secondary school level focus on educator development and direct learner interventions such as the Sasol TRAC Laboratory,” explains Ms Pamilla Mudhray, CSI and SHARP manager at Sasol.

According to Ms Mudhray the implementation of the National Curriculum Statement for physical sciences in the further education and training (FET) phase from 2006, under resourced schools will need greater access to the tools and equipment necessary to teach the syllabus and fulfil the ideals of the curriculum.

TRAC South Africa is a national non-profit programme focused on supporting and expanding science, mathematics and technology education in secondary schools. The programme was first introduced to South Africa in 1994. In 2005, RIEP established the TRAC Free State regional centre on the UFS Main Campus in Bloemfontein.

Media release
Issued by: Lacea Loader
Media Representative
Tel:   (051) 401-2584
Cell:  083 645 2454
E-mail:  loaderl.stg@mail.uovs.ac.za
5 May 2006

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