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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 to investigate implementation of quality-monitoring system for SA food industry

2006-02-07

Some of the guests who attended the workshop were from the left Prof James du Preez (Chairperson: Department of Biotechnology at the UFS); Prof Lodewyk Kock (Head: South African Fryer Oil Initiative (SAFOI) at the UFS)); Mrs Ina Wilken (Chairperson: South African National Consumer Union (SANCU)); Prof Herman van Schalkwyk (Dean: Faculty of Natural and Agricultural Sciences at the UFS) and Mr Joe Hanekom (Managing Director of Agri Inspec).
Photo: Stephen Collet

UFS to investigate implementation of quality-monitoring system for SA food industry

The University of the Free State (UFS) will be investigating the implementation of a quality-monitoring service for the South African food industry.

This was decided during a workshop to discuss the external quality monitoring in the edible oil industry of South Africa, which was recently held at the UFS.

Major role players in the fast-food sector like Nando's, Spur, Captain
Dorego's, King Pie Holdings, Black Steer Holdings, etc and various oil
distributors like Felda Bridge Africa, Refill Oils, PSS Oils and Ilanga Oils attended
the workshop. Also present was Mrs Ina Wilken, Chairperson of the South African National Consumer Union (SANCU) and key-note speaker of this workshop. She represented the consumer.

These role players all pledged their support to the implementation of this quality- monitoring system for the whole food industry.

The decision to implement this system follows the various malpractices reported in the press and on TV concerning food adulteration (eg the recent Sudan Red Scare), misrepresentation (eg olive oil scandal exposed in 2001) and the misuse of edible frying oils by the fast-food sector.

“One of the basic rights of consumers is the right to safe food. Consumers must be protected against foods and food production processes which are hazardous to their health. Sufficient guarantee of the safety of all food products and food production processes should be implemented. It does not help to have adequate food standards and legislation and there is no manpower to do the necessary investigation or monitoring,” said Mrs Wilken.

The South African Fryer Oil Initiative (SAFOI), under the auspices of the UFS Department of Microbial, Biochemical and Food Biotechnology, currently monitors edible oils in the food industry and makes a seal of quality available to food distributors.

“Last week’s decision to implement the quality-monitoring system implies that we will now be involving also other departments in the UFS Faculty of Natural and Agricultural Sciences who are involved in various aspects of the food chain in an endeavor to implement this quality monitoring system,” said Prof Herman van Schalkwyk, Dean: Faculty of Natural and Agricultural Sciences at the UFS and one of the main speakers at the workshop.

Prof van Schalkwyk said that the main aim of such a system will be to improve the competitiveness of the South African food industry. “It is clear that the role players attending the workshop are serious about consumer service and that they agree that fraudulent practice should be monitored and corrected as far as possible. Although some of the food outlets have the capacity to monitor the quality of their food, it may not seem to the consumer that this is an objective process. The proposed external monitoring system would counteract this perception amongst consumers,” said Prof van Schalkwyk.

The workshop was also attended by representatives from SAFOI and Agri Inspec, a forensic investigation company collaborating with inter-state and government structures to combat fraud and international trade irregularities.

Agri Inspec has been working closely with SAFOI for a number of years to test the content of edible oils and fats. “Extensive monitoring and control actions have been executed in the edible oil industry during the past four years to ensure that the content and labeling of oil products are correct. Four years ago almost 90% of the samples taken indicated that the content differed from what is indicated on the label. This has changed and the test results currently show that 90% of the products tested are in order. However, to maintain this quality standard, it is necessary that quality monitoring and educational campaigns are continuously performed,” said Mr Joe Hanekom, Managing Director of Agri Inspec.

“The seal of quality presented by SAFOI should also be extended to include all the smaller oil containers used by households,” Mrs Wilken said.

The SAFOI seal of quality is currently displayed mainly on some oil brands packed in bigger 20 liter containers, which include sunflower oil, cottonseed oil, palm oil etc which are used by restaurants and fast food outlets. “Any oil type is eligible to display the seal when meeting certain standards of authenticity. In order to display the seal, the distributor must send a sample of each oil batch they receive from the manufacturer to SAFOI for testing for authenticity, ie that the container’s content matches the oil type described on the label. This is again double checked by Agri Inspec, which also draws samples countrywide from these certified brands from the end-user (restaurant or fast food outlets). If in breach, the seal must be removed from the faulty containers,” said Prof Lodewyk Kock, Head of SAFOI.

“It should however be taken into account that oils without a seal of quality from the UFS can still be of high quality and authentic. Other external laboratories equipped to perform effective authenticity tests may also be used in this respect,” said Prof Kock.

“It is also important to realise that any oil type of quality such as sunflower oil, cottonseed oil, palm oil etc can be used with great success in well controlled frying processes,” he said.

Further discussions will also be held with the Department of Health, the SA National Consumer Union and Agri Inspec to determine priority areas and to develop the most effective low-cost monitoring system.

More information on the UFS oil seal of quality and oil use can be obtained at www.uovs.ac.za/myoilguide

Media release
Issued by: Lacea Loader
Media Representative
Tel: (051) 401-2584
Cell: 083 645 2454
E-mail: loaderl.stg@mail.uovs.ac.za
6 February 2006

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