University of the Free State | UFS | Universities | Next Generation Sequencing Unit

UFS researchers contribute to roadmap for genomic disease surveillance 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.