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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

SAMWOP creates space for sharing research
2016-12-06

Description: SAMWOP Tags: SAMWOP 

Dr Kristina Riedel, Head of the UFS Department of
Linguistics and Language Practice; middle:
Prof Nancy Kula, of the University of Essex; back:
from left, Dr Elias Malete, lecturer at the UFS
Department of Linguistics and Language Practice,
Prof Andy Chebanne, from the University of Botswana;
and Lesoetsa Motsamai, from the University of Stellenbosch,
at the SAMWOP workshop on 24 November 2016.
Photo: Rulanzen Martin

“The Southern African Microlinguistics Workshop (SAMWOP) creates space for sharing the latest research, networking and building stronger collaboration amongst linguists.”

This is what Dr Kristina Riedel, Head of the Department of Linguistics and Language Practice at the University of the Free State (UFS), said of the 5th SAMWOP hosted by her department. The workshop, hosted from 24 to 26 November 2016, also provided linguists who work on theory and language description in South Africa, the opportunity to network. “As a free conference it is very important, particularly for students and junior scholars.”

International delegates attend workshop

Participants at the workshop were from eight countries including the US, Botswana, Mozambique, Brazil and the UK. Prof Nancy Kula (University of Essex, UK), who was recently appointed as research associate to the department, presented jointly with Xiaoxi Liu, work on depressor effects (consonants which lower tones) in Bantu languages. Other presenters discussed Bantu languages, Khoisan languages and Afrikaans.

Microlinguistics analyses language and sound

“Microlinguistics focuses on analysing language data that deals with language sounds, structures and meaning, rather than language in society,” Dr Riedel said. “The range and diversity of the research on African languages presented at SAMWOP5 were a true highlight. There is a need for more research into African languages and SAMWOP presents the opportunity to scholars in the field to share their work, including in the accredited open-access proceedings.

“We are happy that we were able to hold a very successful and well-attended workshop despite the disruptions to the academic calendar this year,” the professor said.

The Linguistics Society of Southern Africa supported the cause in the form of a grant with additional support from the Office of Dean of Humanities at the UFS.

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