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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

Statement on protest at the UFS

2005-03-04

Following a protest by student and non-student organisations today, the management of the University of the Free State (UFS) would like to place the following facts on record:

1. There is a well-documented process underway to further transform the UFS. At the official opening of the UFS on 4 February 2005 , the Rector and Vice-chancellor, Prof Frederick Fourie, announced that the UFS would draft a comprehensive Transformation Plan to guide the next phase of transformation at the institution.

The UFS appeals to student formations, staff associations, trade unions and other role-players to make a constructive input into this Transformation Plan.

The UFS management has been - and always will be - willing to engage with role-players and is prepared to do so even after today’s protest.

2. There is thus no regulation or policy prescription which separates students in hostels according to race.

The reality is that students exercise their freedom of choice as to which hostel they wish to be placed in. This was agreed upon by black and white students in 1997/8.

However, the unintended consequence and practice of this hostel placement policy has been that students themselves have tended to choose to stay in hostels which have over time become black hostels and white hostels.

This is a matter of concern for the management of the UFS as such a situation does not promote interaction across language, cultural and socio-economic groupings of students.

This matter is receiving attention and an intensive consultative process, which will include students, will be launched to review this policy.

The management is convinced that such interaction will enhance the learning experience of all students and sensitise them to the reality of a multicultural South Africa and a multicultural world.

3. No student organisation has been banned from operating at any of the three campuses of the UFS.

In the past few weeks, SASCO, the Young Communist League and the ANC Youth League (ANCYL) have held meetings on all three campuses, namely the Qwaqwa campus, the Vista campus and the main campus.

There are also regular interactions between top management and the leadership of SASCO and the ANCYL on campus.

In fact, the UFS upholds the right of students and staff to associate freely and to organise themselves as they see fit.

The UFS also upholds the rights of staff and students to engage in legal and peaceful protests.

The management however remains committed to discussing issues that affect staff and students in a constructive manner and appeals to student organisations in this case to engage with management.

4. The issues of registration, fees, debt and financial aid are continually monitored, and interventions to assist students are made regularly. To assist as far as possible those academically deserving students who face financial difficulties, the UFS management has put in place a structure called the Monitoring committee that includes management and student representatives.

The purpose of the Monitoring Committee is to review the cases of individual students to determine how best they can be assisted.

This applies to the Qwaqwa campus, the Vista campus and the main campus.

It is generally the case that students who perform academically will not have any difficulty in obtaining financial assistance. However, according to the requirements of National Student Financial Scheme, students who perform poorly will have difficulty in obtaining such assistance.

5. With regard to student governance, the process to institute an inclusive Central Student Representative Council (SRC), on which all three campuses will be equitably represented, was launched in July 2004, and a preliminary constitution has just been drafted. At the same time an inclusive process to review certain elements of the constitution of the main campus SRC was initiated at the end of 2004. This process, which includes all relevant student organisations and structures, is planned to produce an outcome within the next couple of months.

6. There is no policy at the UFS that is based on racism or that discriminates on the basis of the race of students and staff.

As part of the building of a new institutional culture within the broader transformation process, the UFS management is determined to eradicate all elements of racism that may occur on its campuses, and has already instituted inclusive forums on campus to discuss the issue of values and principles for a non-racial university.

Issued by: Mr Anton Fisher
Director: Strategic Communication
Cell: 072 207 8334
Tel: (051) 401-2749
4 March 2005

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