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27 September 2022 | Story André Damons | Photo Charl Devenish
Prof Martin Nyanga
Prof Martin Nyaga, Associate Professor in the UFS-NGS Unit and Director of the WHO Collaborating Centre (WHO CC), says the UFS researchers – through the Division of Virology/NHLS and the UFS-NGS Unit – were involved in the major publication as part of the NGS-SA consortium from the study design phase, ethics applications, and throughout the study.

Researchers from the University of the Free State (UFS) Next Generation Sequencing (UFS-NGS) Unit and Division of Virology/ National Health Laboratory Service (NHLS) were part of a major publication featuring hundreds of authors from Africa who did research on the evolution of SARS-CoV-2.

The scientific publication in the journal Science (impact factor 47.728) featured more than 300 scientists and public health officials from Africa and abroad, who worked together to look into the evolution of SARS-CoV-2, the viral agent causing COVID-19. It was the first collaborative study of this nature conducted in Africa during the COVID-19 global pandemic. The publication became available online on 15 September this year. 

According to a press release by the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University and the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at the University of KwaZulu-Natal (UKZN), this was the largest consortium of African scientists and public health institutions working together to support data-driven COVID-19 response in Africa. This collaboration was led by two labs (CERI and KRISP) and the Network for Genomic Surveillance in South Africa (NGS-SA) consortium, of which the UFS-NGS Unit and Division of Virology are founding members, in close coordination with the Africa CDC, WHO/AFRO and 300 other institutions across the continent.

It is an awesome feeling

Prof Martin Nyaga, Associate Professor in the UFS-NGS Unit and Director of the WHO Collaborating Centre (WHO CC), says the UFS researchers – through the Division of Virology/NHLS (coordinated by Prof Dominique Goedhals and Mr Philip Armand Bester) and also the UFS-NGS Unit (Prof Nyaga, Dr Peter Mwangi, Mr Milton Mogotsi, and Mr Emmanuel Ogunbayo) – were involved as part of the NGS-SA consortium from the study design phase, ethics applications, and throughout the study, processing the SARS-CoV-2 positive samples for whole-genome sequencing, thus generating significant sequence data of the SARS-CoV-2 variants circulating in South Africa.

“It is an awesome feeling to be part of the solution in resolving the COVID-19 pandemic by providing data that would track variants in real time and data used to implement prophylactic solutions, such as vaccine development, against a virus that was a global threat,” says Prof Nyaga. 

According to him, the utility of next-generation sequencing technologies in understanding genomics of diseases was clearly demonstrated in this study and will assist in addressing future diseases/pandemics. These genomic studies provide deeper insights regarding diseases, and they will provide timely solutions to solving diseases affecting the Mother Continent.

UFS Free State variants study

Prof Nyaga says their Free State variants study, which was also recently published in the journal Frontiers in Virology, performed analysis of samples from patients who tested positive for SARS-CoV-2 throughout all the COVID-19 waves. “We aimed to determine whether the variants driving the epidemic waves at the national level were also driving the epidemic waves at the local level, in the context of the Free State province. The data further indicates that SARS-CoV-2 variants driving the epidemic waves in the Free State at the local level correlated with the ones driving the epidemic waves at the national level. Findings from this study highlight the importance of continued genomic surveillance and monitoring of the circulating SARS-CoV-2 variants to inform public health efforts and ensure adequate control of the ongoing pandemic. 

“Our data has been incorporated into the analyses of the bigger continent-wide collaboration on genomics surveillance to determine how the majority of COVID-19 variants were introduced into Africa, which has now been published in the journal Science,” says Prof Nyaga.  
The publication highlights that sustained investment in diagnostics and genomic surveillance in Africa was needed to not only help combat SARS-CoV-2 on the continent, but to establish a platform to address the emerging, re-emerging, endemic infectious disease threats, such as Ebola, HIV/Aids, TB, malaria, and enteric disease-causing viruses.

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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