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13 September 2024 | Story André Damons | Photo André Damons
Prof Martin Nyaga – Associate Professor and Head of the University of the Free State (UFS) Next Generation Sequencing Unit (UFS-NGS) – recently obtained a B3 rating from the National Research Foundation (NRF).

Prof Martin Nyaga – Associate Professor and Head of the University of the Free State (UFS) Next Generation Sequencing (NGS) Unit – recently obtained an NRF B3 rating from the National Research Foundation (NRF), which is not only testament to his research prowess, but also demonstrates his unwavering commitment to academic excellence.

Prof Nyaga made a significant improvement from his previous NRF Y2 rating (categorised as a promising young researcher). His new B3 rating is assigned to a researcher who enjoys considerable international recognition by their peers for the high quality and impact of their recent research output.

“It is an incredibly thrilling experience to attain the esteemed NRF rating in the B category. Accomplishing the NRF B3 rating satiates an enormous sense of being appreciated and acknowledged individually and as an academic at the UFS. This acknowledgement emphasises the high quality of the research that I do and provides immense motivation to continue mentoring upcoming and emerging researchers in the field of molecular virology,” says Prof Nyaga.

Research output

According to him, this recognition serves as motivation to become an NRF A-rated researcher in the next rating cycle. “I am optimistic that I can meet the minimum threshold to be among the highly esteemed NRF A-rated researchers who are internationally recognised as leading scholars in their field of specialisation for their high-quality research and wide impact.”

Prof Nyaga, who is affiliated to the Division of Virology within the Faculty of Health Sciences, has an exponential trajectory in research output dissemination in reputable international conference presentations and scientific/medical journals such as Nature, Nature Medicine, Nature Communications, and Science, among other quantile 1 journals, with significant citations (3 337 times, h-index 20 and i-10 index 32). He has demonstrated unwavering commitment to academic excellence and has made significant strides within his niche research area of whole genome sequencing and metagenomics of enteric and respiratory viruses. He has not only successfully collaborated with eminent researchers both within and outside the university and globally, but his interdisciplinary research approach has led to groundbreaking studies that address complex issues from multiple perspectives.

Prof Nyaga has applied his expertise to address real-world challenges. One notable example is his involvement in community-based projects and public outreach and education. He has organised and participated in various workshops, seminars, and public lectures aimed at disseminating knowledge and raising awareness about important issues in the field of enteric and respiratory pathogen genomics. His efforts have strengthened the ties between the UFS and the broader community, enhancing the impact and visibility of the institution.

Support by the UFS

“Achieving this rating not only required self-driven research-enhancement discipline, networking, and implementation of novel concepts to enhance my NRF research rating from Y to B, but I also received substantial support from my affiliate institution, especially the Faculty of Health Sciences and the Directorate of Research and Development (DRD).”

“The UFS has put in place amazing policies and career development strategies to ensure that focused Y-rated researchers have the opportunity to become established researchers within one rating cycle of five years – a reality that I immensely thank God for enabling me to attain,” says Prof Nyaga.

These programmes include, among others, the Transforming the Professoriate Mentoring Programme, where he was part of the first cohort of members recruited in 2019.

Prof Nyaga, who has supervised/co-supervised seven PhDs and more than 20 master’s and honours postgraduates to graduation, also serves in various leadership roles, including Chairman for the Africa Centres for Disease Control and Prevention (ACDC) Pathogen Genomics Initiative (PGI), Vaccine-Preventable Diseases (VPD) Focus Group (FG), and Director of the WHO Collaborating Centre for VPD Surveillance and Pathogen Genomics. His ability to instigate and inspire as the team lead and his strategic vision for the UFS-NGS Unit are key factors in the successful execution of numerous initiatives. He is a strong advocate for diversity, equity, and inclusion, and his efforts have created a more inclusive and welcoming environment for his peers and students from diverse backgrounds.

Future

He plans to undertake future research that has an impact on the national health systems and to establish himself as an international leader in his niche research area. “I hope to create a vibrant association between research and national development goals and to have a transformative effect on my area of research in a way that can influence policy by addressing national and international challenges within global knowledge innovation,” says Prof Nyaga.

His continuing research involves the use of next generation sequencing to decipher the viral component of the respiratory and enteric milieu and accentuate the critical need to define the complete spectrum of disease-causing viruses. Several previously known and unknown viruses have been detected, including viruses with previously unrecognised tropism.

Additionally, whole genome sequencing of important respiratory viruses, such as the respiratory syncytial virus (RSV) (as part of the respiratory niche) and rotavirus (as part of the enteric niche), is being performed simultaneously for different countries, including South Africa, Zambia, Rwanda, Kenya, Cameroon, Mozambique, and Malawi, to enhance the genomic surveillance of specific respiratory and enteric viruses of interest.

The overall goal is to identify novel pathogens responsible for human viral diseases and to create a flexible and highly effective system for the rapid identification and analysis of emerging or re-emerging agents. This will serve four purposes: (i) improve preparedness for outbreaks, (ii) characterise new viruses, (iii) identify additional new pathogenic viruses, and (iv) provide new understanding of the human respiratory and enteric virome.

“Viruses that appear to be relevant will be prioritised to elucidate specific targets for rapid diagnostics using panels developed from the antigenic sites of the generated genomes, and immune mechanisms used to develop antiviral interventions such as drugs and vaccines,” explains Prof Nyaga.

Prof Vasu Reddy, Deputy Vice-Chancellor: Research and Internationalisation, commented: “The rating bears testimony to the incredibly important and impactful work that Prof Nyaga is undertaking. The solid international footprint of his publications and their citations also confirm the relevance and currency of his cutting-edge work. The UFS is extremely proud of this signal achievement, and we wish him well with his work in the years ahead.”

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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