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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

UFS policies want to help all students

2005-03-09

The death of Hannes van Rensburg, a first-year student from the JBM Hertzog residence, this past weekend, placed various aspects of student life in the spotlight. Dr Natie Luyt, Dean: Student Affairs at the University of the Free State (UFS), and the Student Representative Council (SRC) of the UFS explain which policies are in place to counter these practices.

At all tertiary institutions there are rules and policies to guide students and provide direction for certain behaviour and practices. The same applies to the University of the Free State (UFS).

“At the beginning of the year the UFS provides every residence committee with a manual to establish a framework for meaningful and orderly relations within and among residences on the campus,” said Dr Natie Luyt.

However, it is one thing to set rules, but it is an impossible task to enforce all aspects thereof. Policies currently in place include an alcohol policy, a policy on the induction of first years and a policy on banned practices in residence orientation.

“The alcohol policy was compiled in cooperation with students and their input was constantly asked,” said Dr Luyt. We also liaise on a continuous basis with residences and senior students to encourage the responsible use of alcohol, especially around activities like intervarsities and Rag.

In the policy, recognition is given to the right and voluntary and informed choice of every individual to use alcohol on the UFS campus in a responsible way.

Guidelines for the use of alcohol on campus include among others the following:

Only authorised points of sale will be permitted on campus. In this case it is the various league halls in most of the male residences on campus.

Alcohol will only be made available during fixed times and is not permitted in residence rooms.

All alcohol-related functions are regulated and an application for a temporary alcohol license must be obtained from the Dean: Student Affairs.

The UFS obtained a liquor license in March 2004 which must be administered by senior leagues in various residences on campus. Normal liquor license conditions and the county’s liquor laws apply. Liquor can only be sold to members of the senior league (or special guests) and also to persons over the age of 18 years. Liquor may not be used in public (outside the senior league) or on campus.

The senior leagues may only be open three nights per week and within prescribed times. No liquor could be used in any other place than the senior league halls. Senior leagues could buy liquor from club monies generated by themselves.

The right of senior leagues to serve liquor was suspended by the Rector and Vice-Chancellor the UFS, Prof Frederick Fourie, on Monday 7 March 2005 – pending an investigation of the recent events on campus.

The policy on banned practices include among others that no swearing and shouting at first-years may take place, no first-year student may be targeted individually, no senior may enter the room of a first-year student without an invitation or permission from that first-year student and no senior under the influence of alcohol may have contact with first-year students.

The induction of first-year students takes place by means of three functions, namely an information function (the introduction to the various facets and possibilities of the university system), an induction function (the first-year student becomes involved in various campus and residence activities) and a development function (the first-year student is motivated to take charge of his development potential).

No first-year induction activity may commence before the residence committee’s contracting with the senior students is not completed. This meeting is attended by the residence head and all senior students. The induction policy, residence induction policy of first-year students and first-year rules are discussed.

The senior students sign an attendance list to show that he/she was informed about the policies. A senior who does not sign, may not be involved with any induction session with first-year students.

No physical contact is allowed during the conclusion of the first-year students’ official induction period. The induction of first-year students as full members of the residence is a prestige event, presented by the residence committee. No physical or degrading activities may take place.

The Dean: Student Affairs also has a daily meeting with the primarii of all the residences during the induction period. This helps to monitor the situation and counter any problem behaviour or tendencies.

“Enforced behaviour – where a senior student forces a first-year student to do something against his/her own free wil – is not allowed. Where there is any sign of this, it is met wortel en tak uitgeroei,” said Dr Luyt.

“In any group of people – whether it is a group of students or people at a workplace – there will always be those who will break the rules or those who would like to see how far they could push it.

The SRC, the UFS management and myself are and will stay committed to make each student’s life on this campus a school of learning and an experience which would be remembered for ever,” said Dr Luyt.

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