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01 December 2021 | Story André Damons | Photo Charl Devenish
Prof Felicity Burt, expert in arbovirology in the Division of Virology at the University of the Free State (UFS) and the National Health Laboratory Service (NHLS).

Even though not much is yet known about the new COVID-19 variant, Omicron, the presence of a high number of mutations – more than 30 – in the spike protein of the variant raises concern. 

This is according to Prof Felicity Burt, expert in arbovirology in the Division of Virology at the University of the Free State (UFS) and the National Health Laboratory Service (NHLS). According to her, although Omicron is highly transmissible, further epidemiological data is required to determine if it is more transmissible than the Delta variant.

On Friday 26 November, the World Health Organisation (WHO) declared the new variant, B.1.1.529, a variant of concern (VOC) and assigned it the name Omicron. This assignation was based on advice from the Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE), an independent group of experts responsible for monitoring and evaluating emerging variants. The following are considered when categorising a newly identified variant – are there mutations (changes in the viral genes) that are known, or that have the potential, to affect the characteristics of the virus, such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; is there significant community transmission or increasing prevalence in multiple countries over time; are the public health and social measures effective against the variant.

With each new variant, the public health concerns are dependent on the transmissibility of the variant, the ability of the virus to escape immunity from natural infection or from vaccination, and the severity of illness caused by the variant or any change in clinical presentation. In addition, the ability of current diagnostic assays to adequately detect the variant and effectiveness of public health and social measures, must be considered.

We know, we don’t know 

Answers are derived from existing epidemiological data, laboratory research, and theoretical considerations. Although we can make some predictions based on the mutations identified and the location of these mutations, the epidemiological data and laboratory research are essential to answer with certainty, and this can take some time. The presence of a high number of mutations – more than 30 – in the spike protein of Omicron, raises concern. What do we know and what don’t we know?

“What we don’t know is whether these mutations have changed the severity of disease caused by the virus. We do know that the diagnostic PCR tests currently used in South Africa are not compromised by the presence of these mutations, and in fact, one of the molecular assays commonly used to target three regions of the virus, can be used as a rapid biomarker to detect the variant. Although sequencing of the genome is used as confirmation, this assay provides a useful rapid biomarker that can be used to detect the presence of the variant; subsequently, PCR results have shown that the variant is likely already present in most provinces in the country,” says Prof Burt, who currently holds an NRF-DST South African Research Chair in vector-borne and zoonotic pathogens research. 

There is also preliminary epidemiological evidence that reinfections are occurring. According to her, the occurrence of reinfections suggests some degree of immune escape; however, we do not know the extent of immune escape or the contribution of waning immunity towards reinfections. “Laboratory tests, in which the live virus is tested against samples from both recovered and vaccinated people, are required to confirm whether existing antibodies can neutralise the variant. The tests for neutralising antibodies require specialised facilities and is dependent on culturing the virus. 
“These tests are already underway in the country and should provide more information in the coming weeks. 

Neutralising antibody tests, although time consuming, are relatively easy to perform compared to tests to determine the role played by other arms of the immune response.”

Vaccines still best option to fight COVID-19

Prof Burt, who has worked on viral haemorrhagic fevers and arboviruses at the National Institute for Communicable Diseases (NICD), says it is known that vaccines are highly effective in reducing the severity of disease and fatalities in individuals infected with other variants, such as Beta and Delta, despite mutations in critical regions of the spike gene in the variants. 

The epidemiological data acquired from cases and the results of laboratory tests for neutralising capability will contribute towards understanding the effectiveness of the vaccine against Omicron. The questions regarding severity of the disease and level of protection from previous infection and vaccines are priority areas to understand the impact of this variant. The early identification of the variant and the initiation of vital research and data analysis highlight the importance of genomic surveillance.

Cases of Omicron have already been confirmed in Israel, the United Kingdom, Europe, Australia, and Africa. Travel restrictions have previously been shown to be ineffective in stopping the geographical spread of new variants, merely delaying the inevitable, and at significant cost to economies. “We know with certainty that vaccination has reduced the severity of illness and death with previous variants; even in the face of reduced neutralising ability, there was sufficient protection to save lives,” says Prof Burt.  

She concluded, “Globally, the impact of vaccination is evident in countries experiencing fourth waves, with a reduced number of deaths compared to previous waves. Many decisions in life are based on a risk assessment and consideration of the pros and cons. Vaccines save lives. Vaccines definitely boost waning immune responses from natural infection.” 

“This is certainly not the time to reject the vaccine based on perceived risks from inaccurate social media spreading harmful disinformation compared to the known risks associated with contracting COVID-19 and the known protection against severe disease afforded by the vaccines.”

News Archive

Publication on indigenous knowledge systems
2005-10-21

 

 

Dr Otsile Ntsoane (acting Director: IKS, Department of Science and Technology) and Prof Philip Nel (Director:  Africa Studies at the UFS and guest editor of the publication) at the launch of the publication

UFS launches most comprehensive publication on indigenous knowledge systems
A unique collection of essays on Indigenous Knowledge Systems (IKS) was launched yesterday (20 October 2005) by the University of the Free State’s (UFS) Programme of Africa Studies.

The essays are published as a special edition of INDILINGA, the African Journal for Indigenous Knowledge Systems and is an outcome of the colloquium on Indigenous Knowledge Systems that was presented last year by the UFS Director of Africa Studies in cooperation with the National Research Council.

“The amount and diversity of materials on IKS brought together under one cover is unique as there are no other South African publications of this magnitude on this issue.  It contains papers of international experts on IKS such as Prof Fritz Wallner from Austria and Prof Gayatri Spivak, foremost postcolonial theorist from India,” said Prof Philip Nel, Director of Africa Studies and guest editor of the publication.

“The publication is a rich source field for students and scholars to exploit because most of the sources quoted in the articles are recent, fresh and relevant.  The contributors are largely people responsible for managing, fostering and studying IKS in a responsible manner,” said Prof Nel.

“An added value of the publication is the inclusion of the policy document on IKS that was adopted by Cabinet in November 2004,” said Prof Nel.


“Millions of people in South Africa are faced with the painful choice of abandoning their heritage.  In this choice, the study and management of IKS has a major role to play; on the one hand, to encourage as much assimilation of traditional knowledge as possible into the modern systems, and on the other hand to provide a “language” and a “grammar” for indigenous people through which they can access modernity,” said Prof Nel.

The IKS debate involves questions of African identity, protection of indigenous communities and practices, political aspects as well as the scientific integrity of the enterprise. 

The publication displays the range of burning questions that have to be resolved in this field such as mainstreaming IKS in academic debate and practice, recognition and protection of the knowledge holders, bio-prospecting and bio-piracy, bio and ethnic healing, lack of textbooks and field manuals, etc and will prove worthwhile for future researchers.

 “One of the main reasons for publishing this volume is the fact that IKS should be studied not only to provide a sense of pride in the past, or  to engender respect for indigenous peoples, but also to enable people in indigenous mind sets to make a better transition into the world of science and technology,” said Prof Nel.

The guest speaker at the launch was Dr Otsile Ntsoane, acting Director of IKS at the Department of Science and Technology.  In his speech Dr Ntsoane stressed the symbolic and concrete value of the publication.  “The publication can have a great social impact and the research results can contribute to chancing the economic landscape of South Africa,” he said.

The publication can be purchased at R150 per copy.  For more information, Ms Steffi Cawood, Programme Coordinator for Africa Studies at the UFS can be contacted at (051) 401-2614.

Media release
Issued by:Lacea Loader
Media Representative
Tel:   (051) 401-2584
Cell:  083 645 2454
E-mail:  loaderl.stg@mail.uovs.ac.za
21 October 2005
 

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