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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

Inaugural lecture: Prof Robert Bragg, Dept. of Microbial, Biochemical and Food Biotechnology
2006-05-17



Attending the inaugural lecture were in front from the left Prof Robert Bragg (lecturer at the Department of Microbial, Biochemical and Food Biotechnology) and Frederick Fourie (Rector and Vice-Chancellor).  At the back from the left were Prof James du Preez (Departmental Chairperson:  Department of Microbial, Biochemical and Food Biotechnology) and Prof Herman van Schalkwyk (Dean: Faculty of Natural and Agricultural Sciences). Photo: Stephen Collett
 

A summary of an inaugural lecture delivered by Prof Robert Bragg at the University of the Free State:

CONTROL OF INFECTIOUS AVIAN DISEASES – LESSONS FOR MAN?

Prof Robert R Bragg
Department of Microbial, Biochemical and Food Biotechnology
University of the Free State

“Many of the lessons learnt in disease control in poultry will have application on human medicine,” said Prof Robert Bragg, lecturer at the University of the Free State’s (UFS) Department of Microbial, Biochemical and Food Biotechnology during his inaugural lecture.

Prof Bragg said the development of vaccines remains the main stay of disease control in humans as well as in avian species.  Disease control can not rely on vaccination alone and other disease-control options must be examined.  

“With the increasing problems of antibiotic resistance, the use of disinfection and bio security are becoming more important,” he said.

“Avian influenza (AI) is an example of a disease which can spread from birds to humans.  Hopefully this virus will not develop human to human transmission,” said Prof Bragg.

According to Prof Bragg, South Africa is not on the migration route of water birds, which are the main transmitters of AI.  “This makes South Africa one of the countries less likely to get the disease,” he said.

If the AI virus does develop human to human transmission, it could make the 1918 flu pandemic pale into insignificance.  During the 1918 flu pandemic, the virus had a mortality rate of only 3%, yet more than 50 million people died.

Although the AI virus has not developed human-to-human transmission, all human cases have been related to direct contact with infected birds. The mortality rate in humans who have contracted this virus is 67%.

“Apart from the obvious fears for the human population, this virus is a very serious poultry pathogen and can cause 100% mortality in poultry populations.  Poultry meat and egg production is the staple protein source in most countries around the world. The virus is currently devastating the poultry industry world-wide,” said Prof Bragg.

Prof Bragg’s research activities on avian diseases started off with the investigation of diseases in poultry.  “The average life cycle of a broiler chicken is 42 days.  After this short time, they are slaughtered.  As a result of the short generation time in poultry, one can observe changes in microbial populations as a result of the use of vaccines, antibiotics and disinfectants,” said Prof Bragg.   

“Much of my research effort has been directed towards the control of infectious coryza in layers, which is caused by the bacterium Avibacterium paragallinarum.  This disease is a type of sinusitis in the layer chickens and can cause a drop in egg product of up to 40%,” said Prof Bragg.

The vaccines used around the world in an attempt to control this disease are all inactivated vaccines. One of the most important points is the selection of the correct strains of the bacterium to use in the vaccine.

Prof Bragg established that in South Africa, there are four different serovars of the bacterium and one of these, the serovar C-3 strain, was believed to be unique to Southern Africa. He also recently discovered this serovar for the first time in Israel, thus indicating that this serovar might have a wider distribution than originally believed.

Vaccines used in this country did not contain this serovar.  Prof Bragg established that the long term use of vaccines not containing the local South African strain resulted in a shift in the population distribution of the pathogen.

Prof Bragg’s research activities also include disease control in parrots and pigeons.   “One of the main research projects in my group is on the disease in parrots caused by the circovirus Beak and Feather Disease virus. This virus causes serious problems in the parrot breeding industry in this country. This virus is also threatening the highly endangered and endemic Cape Parrot,” said Prof Bragg.

Prof Bragg’s research group is currently working on the development of a DNA vaccine which will assist in the control of the disease, not only in the parrot breeding industry, but also to help the highly endangered Cape Parrot in its battle for survival.

“Not all of our research efforts are directed towards infectious coryza or the Beak and Feather Disease virus.  One of my Masters students is currently investigating the cell receptors involved in the binding of Newcastle Disease virus to cancerous cells and normal cells of humans. This work will also eventually lead to a possible treatment of cancer in humans and will assist with the development of a recombinant vaccine for Newcastle disease virus,” said Prof Bragg.

We are also currently investigating an “unknown” virus which causes disease problems in poultry in the Western Cape,” said Prof Bragg.
 
“Although disinfection has been extensively used in the poultry industry, it has only been done at the pre-placement stage. In other words, disinfectants are used before the birds are placed into the house. Once the birds are placed, all use of disinfectants stops,” said Prof Bragg.

“Disinfection and bio security can be seen as the ‘Cinderella’ of disease control in poultry.  This is also true for human medicine. One just has to look at the high numbers of people who die from hospital-acquired infections to realise that disinfection is not a concept which is really clear in human health care,” said Prof Bragg.

Much research has been done in the control of diseases through vaccination and through the use of antibiotics. “These pillars of disease control are, however, starting to crumble and more effort is needed on disinfection and bio security,” said Prof Bragg.

Prof Bragg has been working in close co-operation with a chemical manufacturing company in Stellenbosch to develop a unique disinfectant which his highly effective yet not toxic to the birds.

As a result of this unique product, he has developed the continual disinfection program for use in poultry. In this program the disinfectant is used throughout the production cycle of the birds. It is also used to ensure that there is excellent pre-placement disinfection.

“The program is extensively used for the control of infectious diseases in the parrot-breeding industry in South Africa and the product has been registered in 15 countries around the world with registration in the USA in the final process,” said Prof Bragg.

“Although the problem of plasmid mediated resistance to disinfectants is starting to rear its ugly head, this has allowed for the opening of a new research field which my group will hopefully exploit in the near future,” he said.

 

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