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01 April 2021 | Story Andre Damons | Photo istock
The Easter weekend runs the risk of being a major catalyst for the third wave and people’s behaviour will be the primary driver of transmission for the third wave.

Similar trends as during the festive season of 2020 – when the behaviour of people was driving COVID-19 transmissions and played a role in the second wave – have emerged due to the Easter holidays, and may contribute to a third wave. 
“This means that we can already anticipate gatherings and a higher rate of travel during the next three weeks. As a result of this as well as non-adherence to the non-pharmaceutical interventions, we can anticipate this event to serve as a catalyst for transmission.” 

“If nothing is done to prevent this, it is anticipated that the Free State will see a steady increase and a potential third wave between 17 April and 26 June,” says Herkulaas Combrink, the interim Director of the UFS Initiatives for Digital Futures and PhD candidate in Computer Science at the University of Pretoria (UP).

The Easter weekend runs the risk of being a major catalyst for the third wave

According to him, the vulnerability and population density dynamics in each province, the behaviour of people, and the social norms between communities must be taken into consideration to contextualise the impact of Easter on disease transmission – especially when looking at SARS-CoV-2.

For the Free State, the Easter weekend runs the risk of being a major catalyst that will lead up to the third wave, says Combrink. “If no interventions are put in place and people do not adhere to non-pharmaceutical interventions to mitigate the spread of the disease, then we will see a steady climb and increase in cases up until that time. This means that the behaviour of people will be the primary driver of transmission for the third wave.”

Reducing the severity of the third wave

According to Combrink, who is involved in risk communication and vaccine analytics with other members of the UFS, we may be able to reduce the severity of the third wave if the variant remains the same and the vaccination roll-out plan is in full effect. It will also help if the correct number of people are vaccinated, the general population adheres to PPE and mitigation strategies, and people practise the appropriate behaviour as indicated in all official COVID-19 communication, including the UFS COVID-19 information page.  

According to Prof Felicity Burt and Dr Sabeehah Vawda, both virology experts in the UFS Division of Virology, the current vaccination programme is aimed at reducing the severity of the disease among health-care workers. Prevention of further waves of infection through vaccination will require sufficient coverage to induce at least 70% herd immunity in the country. Currently, no country has achieved that level of herd immunity through vaccine programmes – this is the long-term goal of vaccination. 

“Irrespective of the government’s vaccination programmes and schedules and a virus that may mutate and perhaps become more virulent, the fundamental ways to protect yourself remain unchanged, namely social distancing, wearing of masks, and regular hand washing. People need to realise that this ‘new normal’ is going to be with us for a while and remains the best defence against all SARS-CoV-2 viruses and even provides protection against other respiratory pathogens.”

Vaccines and mutations

The exact frequency of mutations differs between different types of viruses, but generally, SARS-CoV-2 is known to have a slower ‘mutation rate’ than other RNA viruses because of its built-in ‘proofreading’ enzyme. The true mutation rate of a virus is difficult to measure, as the majority of mutations will be lethal to the virus. Irrespective, very few have actually resulted in clinical impact. 

“This highlights the rather gradual process of mutation, so vaccines should remain effective or at least partially effective in the near future, as they elicit antibodies that target different parts of the virus. Continuous surveillance of SARS-CoV-2 is necessary and ongoing to monitor for changes that may impact vaccines and diagnostic tests,” the experts say.

According to Prof Burt and Dr Vawda, scientists are continuously monitoring the situation to detect if the current vaccines would remain effective and to try to adjust them accordingly. How or when the virus will mutate in a clinically significant way is unknown, so at this point, the current vaccines have been shown to be effective against severe disease and hence have application in reducing significant disease. 

“There remains a lot unknown about the extent of protection and the duration of protection, and it is obviously hoped that the vaccine’s immune response in the human body would be able to provide at least some protection or decrease the possibility of severe disease even against potentially newer variants.”

News Archive

Newly operational sequencing unit in genomics at UFS
2016-09-09

Description: Next Generation Sequencing  Tags: Next Generation Sequencing

Dr Martin Nyaga and his research assistant,
Tshidiso Mogotsi in the Next Generation
Sequencing Laboratory.
Photo: Charl Devenish

The Next Generation Sequencing (NGS) unit at the UFS was established as an interdisciplinary facility under the Directorate for Research Development, Faculty of Health Sciences and Faculty of Natural and Agricultural Sciences.

The aim of the NGS facility is to aid internal and external investigators undertaking studies on Deoxyribonucleic acid (DNA) sequencing, assembly and bioinformatics approaches using the more advanced Illumina MiSeq NGS platform.

The NGS unit became operational in 2016 and is managed by Dr Martin Nyaga and administered through the office of the Dean, Faculty of Health Sciences, under the leadership of Prof Gert Van Zyl. Dr Nyaga has vast experience in microbial genomics, having done his PhD in Molecular Virology.

He has worked and collaborated with globally recognised centres of excellence in Prokaryotic and Eukaryotic genomics, namely the J. Craig Venter Institute and the Laboratory of Viral Metagenomics, Rega Institute, among others.

The unit has undertaken several projects and successfully generated data on bacterial, viral and human genomes. Currently, work is ongoing on bacterial and fungal metagenomics studies through 16S rRNA sequencing.

In addition, the unit is also working on plasmid/insert sequencing and whole genome sequencing of animal and human rotaviruses. The unit has capacity to undertake other kinds of panels like the HLA, Pan-cancer and Tumor 15 sequencing, among others.

Several investigators from the UFS including but not limited to Prof Felicity Burt, Prof Wijnand Swart, Dr Frans O’Neil, Dr Trudi O'Neill, Dr Charlotte Boucher, Dr Marieka Gryzenhout and Dr Kamaldeen Baba are actively in collaboration with the NGS unit.

The unit has also invested in other specialised equipment such as the M220 Focused-ultrasonicator (Covaris), 2100 Bioanalyzer system (Agilent) and the real-time PCR cycler, the Rotor-Gene Q (Qiagen), which both the UFS and external investigators can use for their research.

Investigators working on molecular and related studies are encouraged to engage with Dr Nyaga on how they would like to approach their genomics projects at the UFS NGS unit. 

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