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Variants, vaccines, and virology – are we protected?

01 February 2021 | Story Prof Felicity Burt, Prof Dominique Goedhals & Dr Sabeehah Vawda | Photo istock

Opinion article by Prof Felicity Burt, Prof Dominique Goedhals, and Dr Sabeehah Vawda, Division of Virology, Faculty of Health Sciences, University of the Free State and National Health Laboratory Service, Bloemfontein.

As we optimistically embarked on a new year with hopes of seeing an end to the global pandemic, masks, and social restrictions, our news channels were consumed with stories about virus variants and vaccine roll-out. What do these variants mean and will the vaccines protect against the changes that have emerged in the virus and save us from the new normal?

The news of a ‘mutated’ virus most likely conjures movie-like images of an invisible, indestructible enemy causing massive disruption. The reality is fortunately much less dramatic, as these changes are actually expected. Just to reiterate, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has an RNA genome that codes for all the proteins which the virus produces. The exact details of how the virus replicates and produces new progeny, although of interest, are beyond the scope of this article. It is sufficient at this point to merely acknowledge that, during replication, the mechanism employed by viruses with an RNA genome allows for the introduction of mutations in the genes that code for the viral proteins. This is expected to occur and there is substantial evidence that the SARS-CoV-2 viral genes have evolved and adapted globally. Some mutations are silent, in other words, they do not change the viral proteins. However, in some instances the changes can affect the proteins encoded by the virus. If these changes occur in regions of the protein responsible for binding to the cell receptors that facilitate entry of the virus into the cell, or in regions of the protein that induce an immune response, the virus may show new characteristics, such as more successful transmission or escape from an existing immune response.

Second wave of infections

South Africa and the United Kingdom are probably the two countries globally that have methodically sequenced the largest number of SARS-CoV-2 viruses isolated from patients. This technique allows the determination of the complete genome of each isolate and subsequent comparison, using bioinformatic software specifically designed to compare and identify changes and mutations in the nucleotide sequences. As we are all now aware, scientists in these two countries have identified virus variants with an accumulation of mutations and deletions occurring in the gene that encodes for the viral spike protein associated with binding to cell receptors and inducing protective immune responses. These variants have now become the predominant lineages circulating within local communities.

In December 2020, scientists in South Africa revealed the presence of a variant of concern (VOC), now referred to as 501Y.V2. Sequence data confirmed that this variant initially emerged in October 2020, and by January 2021 it was present in multiple provinces in the country and is considered to be responsible for a significant number of cases occurring in the second wave of infections in the country. A second VOC reported by scientists in the United Kingdom in December 2020, (202012/01) likely emerged during September 2020. A third VOC has been reported from Brazil and is simply known as variant P1. To date, variant 501Y.V2 has been reported from at least 23 countries. VOC 202012/01 has been reported in at least 60 countries, and although the cases were initially associated with travellers, there is an increasing number of clusters of cases occurring in people with no history of travel. The United States, Israel, and India currently have the highest number of cases associated with this variant outside of the UK, keeping in mind that at the rate at which the pandemic unfolds, these statistics quickly become outdated. In contrast, variant P1 has only been reported from Brazil, and outside of Brazil it has been associated with travellers in a small number of countries.

Immune responses

Changes in viral proteins may or may not influence certain characteristics of a viral infection. Current epidemiological data and modelling have all suggested that the VOC circulating in South Africa and the UK are more transmissible than previous lineages of the SARS-CoV-2. Despite the increased transmissibility, to date the severity of illness and the proportion of severe disease in different age groups appear to be unaffected by the changes in the protein. The increased transmissibility has increased the burden on the public and private health systems, emphasising the importance of rolling out a vaccine to healthcare workers and persons at increased risk of severe illness.

The changes in the spike protein responsible for inducing immune responses have sparked research studies to determine whether the vaccines will be able to protect against the new variants. It must be remembered that there are two arms to the immune response with complex interactions, and that natural protection will likely be a combination of responses. However, the presence of antibodies that neutralise the virus, in other words, block it from entering cells, and the ability of these neutralising antibodies to block new variants from entering the cells, can be investigated in the laboratory. Although the exact responses required for protection are not fully understood and will require studies that take more time to complete, an indication of neutralising capacity provides some information with regard to the potential efficacy of the vaccine against variants. What we currently know from laboratory research is that there is a reduction in the ability of antibody from people previously infected during the first wave of cases to neutralise the new variant circulating in South Africa. This reduction varied among the cohort of samples tested, but overall, there was a weaker neutralising capability. Similar results were demonstrated using pseudoviruses representing the variant virus. Studies looking at antibodies in people who have been vaccinated show similar reductions in neutralisation. The answer is unfortunately not clear at this stage, with many pieces of the puzzle still to be determined. The reduced capacity to neutralise in a laboratory was not what we wanted to hear, but it must be remembered that vaccines induce a broad immune response and not only neutralise antibody, and hence there are other components to the immune response that will likely contribute to protection. Nonetheless, even a reduced immune response will contribute towards vaccine-induced herd immunity and saving lives by preventing severe disease.

Vaccine trials

In addition to the vaccines currently in use, results were released from clinical trials using vaccines from Novavax and Johnson & Johnson. Although a lower efficacy was shown among the South African population compared to results obtained in the UK, the efficacy was still in the region of 57% to 60%, which is certainly encouraging in view of the new variant circulating. The differences observed illustrate the importance of conducting vaccine trials in local populations. An efficacy of 60% will still contribute towards herd immunity and the prevention of severe disease, emphasising the importance of a rapid roll-out and hopefully a high uptake of the vaccine. Vaccination will not only protect the vaccinee but should contribute to minimising the risk of further variants emerging.

The roll-out of vaccine, further research on immune responses in vaccinated communities, epidemiological data, and sequence data will all contribute towards monitoring the evolution of the outbreak. Flu vaccines are modified annually and if the COVID-19 vaccine needs to be modified, manufacturers have the capability to do this, and some have already started this process.

Additional waves of infection are predicted to occur until herd immunity can be achieved. Whether the current variants will be responsible for the next wave is not possible to predict, and continued research analysing the gene sequences of future isolates will play an important role in determining how the virus is evolving.

In the interim, until we have sufficient vaccine-induced herd immunity to provide protection, non-pharmaceutical interventions and human behaviour will continue to play the important role of minimising new infections. To quote CS Lewis: “You can’t go back and change the beginning, but you can start where you are and change the ending.”

News Archive

Eye tracker device a first in Africa

2013-07-31

31 July 2013

Keeping an eye on empowerment

"If we can see what you see, we can think what you think."

Eye-tracking used to be one of those fabulous science-fiction inventions, along with Superman-like bionic ability. Could you really use the movement of your eyes to read people's minds? Or drive your car? Or transfix your enemy with a laser-beam?

Well, actually, yes, you can (apart, perhaps, from the laser beam… ). An eye tracker is not something from science fiction; it actually exists, and is widely used around the world for a number of purposes.

Simply put, an eye tracker is a device for measuring eye positions and eye movement. Its most obvious use is in marketing, to find out what people are looking at (when they see an advertisement, for instance, or when they are wandering along a supermarket aisle). The eye tracker measures where people look first, what attracts their attention, and what they look at the longest. It is used extensively in developed countries to predict consumer behaviour, based on what – literally – catches the eye.

On a more serious level, psychologists, therapists and educators can also use this device for a number of applications, such as analysis and education. And – most excitingly – eye tracking can be used by disabled people to use a computer and thereby operate a number of devices and machines. Impaired or disabled people can use eye tracking to get a whole new lease on life.

In South Africa and other developing countries, however, eye tracking is not widely used. Even though off-the-shelf webcams and open-source software can be obtained extremely cheaply, they are complex to use and the quality cannot be guaranteed. Specialist high-quality eye-tracking devices have to be imported, and they are extremely expensive – or rather – they used to be. Not anymore.

The Department of Computer Science and Informatics (CSI) at the University of the Free State has succeeded in developing a high-quality eye tracker at a fraction of the cost of the imported devices. Along with the hardware, the department has also developed specialised software for a number of applications. These would be useful for graphic designers, marketers, analysts, cognitive psychologists, language specialists, ophthalmologists, radiographers, occupational and speech therapists, and people with disabilities. In the not-too-distant future, even fleet owners and drivers would be able to use this technology.

"The research team at CSI has many years of eye-tracking experience," says team leader Prof Pieter Blignaut, "both with the technical aspect as well as the practical aspect. We also provide a multi-dimensional service to clients that includes the equipment, training and support. We even provide feedback to users.

"We have a basic desktop model available that can be used for research, and can be adapted so that people can interact with a computer. It will be possible in future to design a device that would be able to operate a wheelchair. We are working on a model incorporated into a pair of glasses which will provide gaze analysis for people in their natural surroundings, for instance when driving a vehicle.

"Up till now, the imported models have been too expensive," he continues. "But with our system, the technology is now within reach for anyone who needs it. This could lead to economic expansion and job creation."

The University of the Free State is the first manufacturer of eye-tracking devices in Africa, and Blignaut hopes that the project will contribute to nation-building and empowerment.

"The biggest advantage is that we now have a local manufacturer providing a quality product with local training and support."

In an eye-tracking device, a tiny infra-red light shines on the eye and causes a reflection which is picked up by a high-resolution camera. Every eye movement causes a change in the reflection, which is then mapped. Infra-red light is not harmful to the eye and is not even noticed. Eye movement is then completely natural.

Based on eye movements, a researcher can study cognitive patterns, driver behaviour, attention spans, even thinking patterns. A disabled person could use their eye-movements to interact with a computer, with future technology (still in development) that would enable that computer to control a wheelchair or operate machinery.

The UFS recently initiated the foundation of an eye-tracking interest group for South Africa (ETSA) and sponsor a biennial-eye tracking conference. Their website can be found at www.eyetrackingsa.co.za.

“Eye tracking is an amazing tool for empowerment and development in Africa, “ says Blignaut, “but it is not used as much as it should be, because it is seen as too expensive. We are trying to bring this technology within the reach of anyone and everyone who needs it.”

Issued by: Lacea Loader
Director: Strategic Communication

Telephone: +27 (0) 51 401 2584
Cell: +27 (0) 83 645 2454
E-mail: news@ufs.ac.za
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