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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

UFS hosts the first Southern African Young Scientists Summer Programme
2012-11-26

The University of the Free State is to host the first Southern African Young Scientists Summer Programme (SA-YSSP) from 1 December 2012 to 28 February 2013. 

This will form part of an annual three-month education, academic training and research capacity-building programme jointly organised by the National Research Foundation (NRF), the Department of Science and Technology (DST), and the International Institute for Applied Systems Analysis (IIASA), based in Austria.
 
The NRF, as the National Member Organisation (NMO), in collaboration with DST, has developed a novel and innovative initiative with IIASA to establish the SA-YSSP. This programme was officially launched by the Minister of Science and Technology during November 2011.
 
IIASA is an international research organisation that conducts policy-oriented scientific research in the three global problem areas of energy and climate change, food and water and poverty and equity (www.iiasa.ac.at). South Africa’s engagements with IIASA, and specifically with regard to the SA-YSSP, relate primarily to the DST’s Ten-Year Innovation Plan.
 
Aligned with the YSSP model that is presented by IIASA in Austria annually, the SA-YSSP offers scientific seminars covering themes in both the social and natural sciences. These seminars often have policy dimensions and aim to broaden the participants’ perspectives and strengthen their analytical and modelling skills, further enriching a demanding academic and research programme (www.ufs.ac.za/sa-yssp).
 
Keynote lectures are to be delivered by national and international leaders in their respective research fields, partly drawn from IIASA’s widespread network of alumni and collaborators, as well as from the NRF’s extensive international networks of excellence.
 
The programme is to be enhanced with specific field trips and cultural and heritage excursions that will involve networking with locally based research programmes. Supervisory teams of both IIASA and South African experts will guide a cohort of competitively selected South African and international advanced Ph.D candidates.
 
The programme will be opened on 2 December 2012 at the Centenary Complex by the Minister of Science and Technology, Mr Derek Hanekom, the Director/CEO of IIASA, Prof Pavel Kabat and the Vice-Chancellor and Rector of the UFS, Prof Jonathan Jansen. They will be joined by a number of Nobel Prize Laureates and luminaries representing the government, the diplomatic sector and Higher Education.
 
The programme is directed by a multidisciplinary team at the UFS that includes:
Prof Aldo Stroebel and Prof Neil Roos (Co-Directors)
Prof André Roodt (Dean of SA-YSSP)
Prof Martin Ntwaeaborwa and Dr Henriëtte van den Berg (Deputy-Deans of SA-YSSP)
Dr Priscilla Mensah and Dr Sonja Loots (Strategic Managers)

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