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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 and Mexico forge links
2006-03-30

Some of the guests attending the signing of the memorandum of agreement were in front from the left Prof Wijnand Swart (Chairperson: Centre for Plant Health Management at the UFS), His Excellency Mauricio de Maria y Campos (Ambassador of Mexico in Southern Africa), Prof Magda Fourie (Vice-Rector: Academic Planning at the UFS) and Dr José Sergio Barrales Domínguez (Rector of the University of Chapingo in Mexico).
Photo: Stephen Collett

UFS and Mexico forge links
The Centre for Plant Health Management (CePHMa) in the Department of Plant Sciences at the University of the Free State (UFS) is presenting its first international conference.  The conference started yesterday and will run until tomorrow (Friday 31 March 2006) on the Main Campus in Bloemfontein. 

The conference is the first on cactus pear (or prickly pear) in South Africa since 1995.  It coincides with 2006 being declared as International Year of Deserts and Desertification by the United Nations General Assembly. 

During the opening session of the conference yesterday a memorandum of understanding (MOU) was signed between CePHMa and the University of Chapingo (Universidad Autonoma Chapingo) in Mexico.  The signing ceremony was attended by the Ambassador of Mexico in Southern Africa, His Excellency Mauricio de Maria y Campos, the Rector of the University of Chapingo, Dr José Sergio Barrales Domínguez, and the Vice-Rector: Academic Planning of the UFS, Prof Magda Fourie, amongst other important dignitaries. 

“South Africa and Mexico have a lot in common where agricultural practices in semi-arid areas and the role of the cactus pear are concerned,” said Prof Wijnand Swart, Chairperson of CePHMa at the opening of the conference.

He said that the MOU is the result of negotiations between CePHMa and the Ambassador of Mexico in Southern Africa over the past 12 months.

“The MOU facilitates the negotiation of international cooperative academic initiatives between the two institutions.  This entails the exchange of students and staff members of the UFS, curriculum development, research and community service,” said Prof Swart.

“During the next two days, various areas of interest will be discussed.  This includes perspectives from commercial cactus pear farmers in South Africa, the health management of cactus pear orchards, selection of new cultivars of cactus pear, and the nutritional and medicinal value of the crop,” said Prof Swart.

In his welcoming message Prof Swart explained that in recent years there has been increased interest in the cactus pear for the important role it can play in sustainable agricultural systems in marginal areas of the world.  These plants have developed phenological and physiological adaptations to sustain their development in adverse environments. 

“The cactus pear can serve as a life saving crop to both humans and animals living in marginal regions by providing a highly digestible source of energy, water, minerals and protein,” said Prof Swart. 

“In an age when global warming and its negative impact on earth’s climate has become an everyday subject of discussion, the exploitation of salt and drought tolerant crops will undoubtedly have many socio-economic benefits to communities inhabiting semi-arid regions,” said Prof Swart.

“Plantations of cactus pear grown for fruit, forage and vegetable production, as well as for natural red dye produced from the cactus scale insect known as cochineal have, over the last two decades, been established in many countries in South America, Europe, Asia and Africa.  The crop and its products have not only become important in international markets, but also in local markets across the globe,” said Prof Swart. 

Detailed discussions on the implementation of the MOU will take place between CePHMa and the University of Chapingo after the conference. 

Media release
Issued by: Lacea Loader
Media Representative
Tel:   (051) 401-2584
Cell:  083 645 2454
E-mail:  loaderl.stg@mail.uovs.ac.za
30 March 2006

 

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