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The new Omicron variant: What we know and don’t know

01 December 2021 | Story André Damons | Photo Charl Devenish

Prof Burt read more — 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

UV vestig hom afgelope eeu as leier op verskeie terreine

2004-05-11

Michelle O'Connor - Volksblad - 11 Mei 2004

Ondank terugslae nou 'n 'gesonde volwassene'

HOEWEL die Universiteit van die Vrystaat (UV) vanjaar sy eeufees vier en met 23 000 studente die grootste universiteit in die sentrale deel van die land is, was dié instelling se geboorte glad nie maklik nie. MICHELÉ O'CONNOR het met prof. Frederick Fourie, rektor, oor die nederige begin van dié instelling gesels.

DIE behoefte aan 'n eie universiteit in die Vrystaat het reeds in 1855, kort ná die stigting van Grey-kollege, kop uitgesteek.

Grey se manne het hulleself teen 1890 begin voorberei om die intermediêre B.A.-eksamens af te lê. Dié eksamen het hulle toegang gegee tot die tweede jaar van 'n B.A.-graad aan die destydse University of the Cape Good Hope, nou die Universiteit van Kaapstad.

"Presidente F.W. Reitz en M.T. Steyn het destyds albei die stigting van 'n universiteit hier bepleit. Die grootste rede was sodat die seuns van die Vrystaat nie weggestuur word nie.

"Dié twee se droom is op 28 Januarie 1904 bewaarheid toe ses studente hulle onder dr. Johannes Bril, as hoof/rektor van Grey-kollege, vir die graad B.A. ingeskryf het. Dié graad is aanvanklik deur die Kaapse universiteit toegeken.

"Net die klassieke tale soos Latyns en Grieks, die moderne tale, Nederlands, Duits en Engels, filosofie, geskiedenis, wiskunde, fisika, chemie, plant- en dierkunde is aanvanklik aangebied.

"Die UV se geboue het gegroei van 'n klein tweevertrek-geboutjie wat nou naby Huis Abraham Fischer staan, en verblyf in die Grey-kollege se seunskoshuis," sê Fourie.

Volgens hom is die universiteit se eerste raad en senaat tussen 1904 en 1920 saamgestel. Die eerste dosente is aangestel en die eerste geboue opgerig. "Dié tyd was egter baie moeilik.

"Die instelling het teen 1920 net 100 studente gehad en was geldelik in die knyp. Daar was geen vaste rektor nie en geen vooruitgang nie. Vrystaatse kinders is steeds na ander universiteite gestuur.

"Ds. J.D. Kestell, rektor van 1920 tot 1927, het egter dié instelling finaal gevestig.

"Hy het self studente van oor die hele Vrystaat gewerf en geld by onder meer kerke en banke ingesamel. Kestell het selfs Engelse ouers oortuig om hul kinders na die Greyuniversiteitskollege (GUK) te stuur en teen 1927 het dié instelling met 400 studente gespog.

"In die tydperk tussen 1927 en 1950 het die GUK weer verskeie terugslae beleef.

"In dié tyd was dit onder meer die Groot Depressie en die Tweede Wêreldoorlog. Die armblanke-vraagstuk het regstreeks op studente en dosente ingewerk en die politieke onderstrominge van dié tyd het die instelling ontwrig.

"Die GUK het egter oorleef en die Universiteitskollege van die Oranje-Vrystaat (UKOVS) is in 1935 gebore," sê Fourie.

Hy sê in dié tyd is verskeie fakulteite gevestig en teen 1950 het die UKOVS met 1 000 studente gespog.

Teen 1950 het dit 'n onafhanklike universiteit geword en die naam is verander na die Universiteit van die OranjeVrystaat (UOVS).

Dié tydperk is gekenmerk deur Afrikaner- en blanke selfvertroue en heerskappy. Studentegetalle het tot 7 000 in 1975 gegroei en heelwat vooruitgang het in dié tyd plaasgevind.

"Tussen 1976 en 1989 sukkel dieuniversiteit weer met onder meer ekonomiese krisisse, die land se politieke onstabiliteit en word die UOVS geï soleer.

"Een ligpunt in dié tyd is die toelating van die eerste swart studente, die nuwe Sasol-biblioteek en die fakulteit teologie wat die lig sien.

"Tussen 1990 en vanjaar het die UOVS verskeie op- en afdraandes beleef. Die universiteit doen nie net die eerste stappe van transformasie nie, maar begin ook aan 'n beleid van multikulturaliteit werk.

"Die UOVS se naam verander in 1996 na die Universiteit van die Vrystaat/University of the Free State en in 2001 word die Sotho-vertaling bygevoeg.

"Geldelike druk en probleme neem drasties toe en personeel word gerasionaliseer.

"Teen 2000 begin die UV met 'n draaistrategie en studentegetalle neem tot meer as 23 000 toe," sê Fourie.

Hy sê die UV het die afgelope eeu nie net verskeie terugslae oorleef nie, maar homself ook op verskeie gebiede as 'n leier gevestig.

Die universiteit behaal sy eie geldelike mikpunte, neem 'n nuwe taalbeleid van veeltaligheid aan en herbelê in personeel.

Die instelling inkorporeer die kampusse van die Vista- en Qwaqwa-universiteit en groei internasionaal.

Die UV vestig ook fondamente van 'n institusionele kultuur van verdraagsaamheid, geregtigheid en diversiteit.

"Die baba het in die afgelope eeu 'n gesonde volwassene geword."

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