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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 student makes breakthrough in the application of nanorobots
2005-04-21

A student from the University of the Free State (UFS) has made a ground-breaking discovery in the field of microbiology by uncovering a series of new compounds that may in future be used to lubricate man-made nanorobots.

Mr Olihile Sebolai, a full-time student at the UFS’s Department of Microbial- Biochemical and Food Biotechnology, made this discovery while working on his M Sc-study on yeast.

With this discovery Mr Sebolai will also be awarded six prestigious prizes during this week’s autumn graduation ceremony at the UFS.  This university has recognised this exceptional achievement as a build-up to the celebration of national Science and Technology week next month.     

Mr Sebolai’s dissertation on the yeast genus Saccharomycopsis Schionning has been published in an accredited international journal of repute. 

“Words cannot describe how excited I am. I never expected to receive such recognition for my studies.  I am humbled by all of this,” said Mr Sebolai.

The Lipid Biotechnology Group at the UFS recently discovered that some yeasts produce their own water-propelled capsules in which they are transported.  These capsules have different shapes and resemble among others miniature flying saucers, hats with razor sharp brims etc.  “In order to function properly, parts of the capsules are oiled with prehistoric lubricants – lubricants that are produced by yeasts and that probably existed for many millions of years as yeasts developed,” said Mr Sebolai.  

According to Mr Sebolai these capsules are so small that approximately 300 can be fitted into the full-stop at the end of a sentence and are therefore invisible to the naked eye.

“With my studies I discovered many new compounds that resemble these prehistoric lubricants.  These lubricants may in future be used to lubricate man-made nanorobots and are similar in size compared to yeast capsules,” said Mr Sebolai.  The nanorobots are used to perform tasks in places that are invisible to the naked eye and could one day be used, among others, to clean up human arteries.

Mr Sebolai has been interested in the subject of Micro technology since he was at RT Mokgopa High School in Thaba ‘Nchu.  “I was specifically interested in the many possible applications the subject has – in the industry, as well as in medicine,” said Mr Sebolai. 

His next goal is to successfully complete his Ph D-degree.

The prizes that will be awarded to Mr Sebolai this week include:

Best Magister student at the UFS (Senate medal and prize);

Best Magister student in the Faculty of Natural and Agricultural Science and Dean’s medal at the same faculty;

The Andries Brink – Sasol-prize for the best M Sc dissertation in Microbiology;

The JP van der Walt prize for best M Sc dissertation in yeast science;

The Chris Small prize for an outstanding Master’s dissertation; and

Honorary colours awarded by the UFS Student Representative Council

Media release

Issued by:                     Lacea Loader

                                    Media Representative

                                    Tel:  (051) 401-2584

                                    Cell:  083 645 2454

                                    E-mail:  loaderl.stg@mail.uovs.ac.za

20 April 2005

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