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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

“Breakthroughs depend on people believing in their own ideas”

2015-07-23

TED is a renowned international non-profit organisation dedicated to disseminating “ideas worth spreading” in the form compelling talks lasting up to 18 minutes.

Lerothodi Molete’s vision is to witness the youth of Bloemfontein emerge at the forefront of technological, scientific, and entrepreneurial innovations in both South Africa and the global arena.

Molete and Bonginkosi Leeuw are the organisers of TEDxUFS. Their duty is centered on inspiring people to believe in, and express, their ideas. These University of the Free State students have taken it upon themselves to inspire the youth to “push the boundaries of society.”

The second TEDxUFS event to be hosted by the university presents a unique opportunity for students, staff members, and the general public to mingle with influential speakers from across various disciplines.

Details of the event:

Date: Saturday 1 August 2015

Time: 08:00- 18:00

Venue: Albert Wessels Auditorium, Bloemfontein Campus

The keynote speakers include: Mmusi Maimane (Federal Leader: Democratic Alliance), Gareth Cliff (Radio personality: Cliff Central), Pieter Geldenhuys (Futurist), Brian Kally (Director: Arrow Logistics), Jonathan Jansen (Vice-Chancellor and Rector: UFS), Ricardo Peach (Director: Vrystaat Arts Festival, Pamela Nomvete (Former actor and writer), Gil Oved (Founder: Creative Counsel), Pepe Marais (CEO: Joe Public), Angelo Mockie (Senior Officer: Student Affairs and musician), Philippa Tumubweinee (Senior Lecturer in Architecture: UFS), and Melody Mentz (Psychology Senior Professor: UFS).

The reason behind the #AskWhy theme

"Why is a small word but it’s a quick, broad, sharp and abrupt one,” explains Leeuw. “It is the chosen word of the non-conformist, the defiant, and the visionary. It is a confrontational word. It challenges what is thought to be impossible.”

The ability to interrogate reality is what society and economies are built on. The absence of the fear to question encourages the capacity to progress.

Motivating young people to follow their dreams is the reason why the TEDxUFS team is persistent in their endeavours. Molete believes that, in order to change anything, people need to ask why.

Background of the innovation powerhouse called TED(x)

TED is a renowned international non-profit organisation dedicated to disseminating “ideas worth spreading” in the form compelling talks lasting up to 18 minutes.

In 1984, it was introduced as a conference exploring Technology, Entertainment, and Design. Three decades later, TED covers a wide variety of topics of global significance, reflecting the contemporary era in more than 100 languages.

TEDx events are under the TED umbrella. These events are organised independently, and create a platform for deliberating on local matters. The programme assists communities, organisations, and individuals to stimulate critical dialogue.

On 25 July 2014, the UFS hosted its inaugural TEDxUFS conference at the Odeion theatre on the Bloemfontein Campus, where eleven speakers addressed an audience of 150 people on interdisciplinary topics ranging from economics to entrepreneurship, technology, art, design, and theology.

This year, 200 seats will be available for innovative revolutionary individuals in search of inspiration.

Tickets are available at 0619284253 / 079 381 4126. Prices: R80 (Student/scholars) and R350 (Public/staff)

LINKS:

Lerothodi Molete- http://whoswho.co.za/lerothodi-molete-742022

Bonginkosi Leeuw- https://www.ted.com/tedx/events/10499

TEDxUFS- http://kovsielife.ufs.ac.za/templates/archive.aspx?news=276

Mmusi Maimane- http://whoswho.co.za/mmusi-maimane-44612

Garett Cliff- http://www.garethcliff.com/

Pieter Geldenhuys- http://pietergeldenhuys.com/

Brian Kally- https://za.linkedin.com/pub/brian-kally/4b/888/959

Jonathan Jansen- http://www.ufs.ac.za/adhoc-pages/rectorate/prof-(jd)-jonathan-jansen

Ricardo Peach- http://ricardopeach.com/

Pamela Nomvete- http://whoswho.co.za/pamela-nomvete-4789

Gil Ovid- https://za.linkedin.com/pub/gil-oved/3/910/892

Pepe Marais- http://joepublic.co.za/people

Angelo Mockie- https://za.linkedin.com/pub/angelo-mockie/27/56/302

PhilippaTumubweinee- http://natagri.ufs.ac.za/templates/staffmember.aspx?DCode=101&pid=zyNJm7KI%2b1k%3d

Melody Mentz- https://za.linkedin.com/in/melodymentz

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