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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

Sites of memory. Sites of trauma. Sites of healing.
2015-04-01

Judge Albie Sachs – human rights activist and co-creator of South Africa’s constitution – presented the first Vice Chancellor’s Lecture on Trauma, Memory, and Representations of the Past on 26 March 2015 on the Bloemfontein Campus.

His lecture, ‘Sites of memory, sites of conscience’, forms part of a series of lectures that will focus on how the creative arts represent trauma and memory – and how these representations may ultimately pave the way to healing historical wounds. This series is incorporated into the five-year research project, led by Prof Pumla Gobodo-Madikizela, and funded by the Mellon Foundation.

Sites of memory and conscience – and healing

“Deep in solitary confinement, I read in the Bible: ‘the lion lay down with the lamb … swords will be beaten into ploughshares.’” And with these opening words, Judge Sachs took the audience on a wistful journey to the places in our country that ache from the past but are reaching for a better future at the same time.

Some of the sites of memory and conscience Judge Sachs discussed included the Apartheid Museum, Liliesleaf, District Six Museum, and the Red Location Museum. But perhaps most powerful of them all is Robben Island.

Robben Island

“The strength of Robben Island,” Judge Sachs said, “comes from its isolation. Its quietness speaks”. Former prisoners of the island now accompany visitors on their tours of the site, retelling their personal experiences. It was found that, the quieter the ex-prisoners imparted their stories, “the gentler and softer their memories; the more powerful the impact,” Judge Sachs remarked. Instead of anger and denouncement, this reverence provides a space for visitors’ own emotions to emerge. This intense and powerful site has become a living memory elevated into a place of healing.

After Judge Sachs visited the National Women’s Memorial in Bloemfontein some years ago, he came to an acute realisation as he read the stories, experienced the grief, and saw the small relics that imprisoned commandoes from Ceylon and St Helena sculpted. “It’s so like us,” he thought, “our people on Robben Island making a saxophone out of seaweed, our people carving little things. It was so like us. It was another form of inhumanity to human beings in another period.”

The Constitutional Court

The Constitutional Court next to the Old Fort Prison is also a profound site of trauma and healing. Bricks from the awaiting trial lock-up were built into the court chambers. “We don’t suppress it, we don’t say let’s move on. We acknowledge the pain of the past. We live in it, but we are not trapped in it. We South Africans are capable of transcending, of getting beyond it,” Judge Sachs said.

Transforming swords into ploughshares

Judge Sachs had great praise for Prof Gobodo-Madikizela’s research project on Trauma, Memory, and Representations of the Past. “You convert and transform the very swords, the very instruments, the very metal in our country. In a sense, you almost transform the very people and thoughts and dreams and fears and terrors into the ploughshares; into positivity.”

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