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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

During 2011: Achievements at the UFS

2011-12-01

Sarah Shannon

Dr Alex Amtaika, Department of Political Science

During a conference at Khon Kaen University in Thailand, Dr Alexius Amtaika from our Department of Political Science was elected as Executive Director and Convener of the International Committee of Scholars of Local Government. This honour was bestowed upon Dr Alexius during the first International Conference on Local Government at Khon Kaen University.

Sarah Shannon

We all have heard stories about inspirational people, who defy the odds, fight circumstance every day and never give up. Sarah Shannon has cerebral palsy but has never stopped dreaming and achieving them.

Sarah is also a competitive swimmer, and is currently ranked seventh in the world in her class of disabilities.

She is currently completing her postgraduate certificate in Education, Foundation Phrase, through Unisa. She is also studying Sociology at our university.

DW Bester and Sannah Mokone, Rhodes Scholars

Of the four open Rhodes Scholarships available to students from all universities in Southern Africa, two of our students won these prestigious scholarships. DW Bester, B.Sc. Hons. Actuarial Science student, and Sannah Mokone, BPub-cum laude student, joined Oxford University in the United Kingdom in September 2011 to further their studies.

The Rhodes Scholarships, arguably one of the most prestigious scholarships in the world, were founded in 1903 in the will of Cecil John Rhodes and cover the full costs of study at Oxford University.

While academic excellence is a pre-condition for consideration for the Rhodes Scholarship, these scholarships are unique in that Rhodes Scholars are outstanding young students who excel academically, but very importantly, demonstrate leadership, are committed to making a difference in the world, and have the energy to fulfill their ambitions.

Dr Derik Coetzee, Department of Sport and Exercise Sciences

When you suddenly receive a call during a World Cup year and requested to come and assist in leading the Springboks, then you have to know, you have something to offer. This is what happened to Dr Derik Coetzee from our Department of Exercise and Sports Sciences. This year he once again became involved in the Springbok rugby team, after he had been die Bokke’s conditioning trainer from 2004 to 2007.

His primary task as conditioning head was to help in seeing to it that the Springboks reached their best level of play – psychologically, physically an emotionally. Amongst others, his duties included the optimisation of the players’ muscle and explosive power, speed, anaerobic ability and technical skills.

Jefferson J Dirks-Korkee en Mart Kotzé

Jefferson J Dirks-Korkee, from Willowmore in the Eastern Cape, and Mart Kotzé from Bloemfontein, recently made history by being the first students from our Department of Drama and Theatre Arts featuring in an Afrikaans South African film Skoonheid, the first ever to be shown at the Cannes Film Festival.

The movie won the Queer Palm Award at the 2011 Cannes International Film Festival, where Robert de Niro was the chairperson of the panel of judges.

Prof. Muriel Meiring, Department of Haematology and Cell Biology

Prof. Muriel Meiring, Specialist Scientist in our Department of Haematology and Cell Biology, is responsible for establishing the Specialised Haemostasis Laboratory at our university and the Universitas Hospital’s National Health Laboratory Service. She established this centre as a reference centre for Von Willebrand disease, a genetic bleeding disorder, in South Africa. This laboratory is internationally recognised for their research and as a reference laboratory.

Prof. Meiring develops and tests antithrombotic (anti-clotting) agents and her long list of publications, research awards and congress presentations has earned her a nomination for the Department of Science and Technology’s Distinguished Woman Scientist Award. She was one of two scientists of the National Health Laboratory Services (NHLS) to receive the award – Prof. Meiring being the only woman from our university.

Medical facilities from all over the country make use of her and her team’s expertise when testing for blood disorders and she hopes to expand the centre even further.

Melinda Jonker

Melinda Jonker, one of our third-year financial economic students, won the overall national competition of the prestigious Traders Trophy competition at the Johannesburg Stock Exchange (JSE).

The competition, sponsored by Nedbank Capital and Oxyor in Amsterdam, requires participants to trade actual JSE-listed shares against one another on a simulated platform. The winner is determined not only by the highest profit, but also by the technique used throughout the trading session.

Christopher Diab, also a student from our Department of Economics, won the regional UFS competition.

ASSAf members

Seven of our academic colleagues have been elected as members of the Academy for Science of South Africa (ASSAf). They are Proff. Hendrik Swart, Physics; André Roodt, Chemistry; Zakkie Pretorius, Plant Sciences; Max Finkelstein, Mathematics; James du Preez, Microbial, Biochemical and Food Biotechnology; Maryke Labuschagne, Plant Breeding; and Neil Roos from our Postgraduate School.

Due main objective of the Academy is to promote and apply scientific thought in the service of the society, in order to determine the quality and scope of the role that the Academy can plays in the country’s life and progress, and eventually apply it

Other colleagues who are currently members of ASSAf include Proff. Jonathan Jansen, Vice-Chancellor and Rector; Johan Henning, Dean: Faculty of Law; and Frans Swanepoel, Senior Director: Research Development.

Samantha Renda-Dollman

Samantha Renda-Dollman, a BSc (Zoology) student on our Qwaqwa Campus, has obtained 19 distinctions out of the 22 modules she has written since 2009.

Her hard work earned Samantha the prestigious Dux Student award of our 2011 Annual Student Affairs Excellence Awards, held at our Qwaqwa Campus. This makes her the best overall academic performer of the entire student body on this campus.

Jaco Griessel

Jaco Griessel, an Honours student at our Odeion School for Music, received a prestigious Mandela Rhodes bursary for 2012 to study towards his Master’s degree next year.

Jaco, who is currently busy with his BMus Honours degree, is a performer par excellence, with many achievements to his name. In 2010, he received the Fanie Beetge Prize for the best undergraduate student in Systematic Music Studies. A year before, he received the same prize as best undergraduate student in Historic Music Studies. He shall continue his Master’s degree with Music Composition as field of specialisation at our university in 2012.

Prof. Helena van Zyl, UFS School of Management

Prof. Helena van Zyl, Director of the UFS Business School, was elected as President of the South African Association of Business Schools (SABSA). Since the beginning of 2010 she has been acting as president. Prof. Van Zyl is the first woman to occupy this position and also the first woman who is currently heading a business school in South Africa. She will serve SABSA as the president for the next two years.

Prof. Zakkie Pretorius, Department of Plant Sciences

Research by Prof. Zakkie Pretorius from our Department of Plant Sciences, has become part of Phase II of a mayor global project to combat deadly strains of a wheat pathogen that poses a threat to global food security.

Prof. Pretorius focuses on the identification of resistance in wheat to the stem rust disease and will assist breeders and geneticists in the accurate phenotyping of international breeding lines and mapping populations. In addition, Prof. Pretorius will support scientists from Africa with critical skills development through training programmes.

The Ug99 strain was discovered in Kenya in 1998, but are now also threatening major wheat-growing areas of Southern and Eastern Africa, the Central Asian Republics, the Caucasus, the Indian subcontinent, South America, Australia and North America.

Prof. Danie Strauss, research fellow in the Faculty of Humanities

Prof. Danie Strauss, a research fellow in our Faculty of the Humanities, won the Dooyeweerd Prize from the Board of the Association for Reformational Philosophies in Amsterdam. Prof. Strauss, former Dean of our Faculty of the Humanities and head of our Department of Philosophy, won the prize for his book Philosophy: Discipline of the Disciplines. The prize is awarded for work in the field of systematic philosophy.

Nida Jooste and Ryan Lamb, Abe Bailey Travel Bursary holders

Nida Jooste and Ryan Lamb are two of the proud recipients of Abe Bailey Travel Bursaries. Both students are academic achievers, but also excel in other fields. This is what set them apart from the rest of the applicants for the bursaries.

Ryan (23), a Medical Physics Honours student at our Faculty of Health Sciences, received the Senate’s Medal for the best Bachelor’s Degree student at the UFS. He was one of 100 students at the Brightest Young Minds Summit this year and was one of the 2008 delegates to the World Youth Forum, hosted by the International Association for Poetry and Solidarity in Italy.

Nida (21) is a very familiar face on our Bloemfontein Campus, as she served as the Deputy Chairperson of our Interim Student Council in 2011.

Loerie Award for Tarran Jacobs, Elizabeth Forson and Mafohlela Mahlatsi

The creativity of a group of students from our university was rewarded with a bronze Loerie Award after they won an internal competition. Tarran Jacobs, Elizabeth Forson and Mafohlela Mahlatsi, all third-year Marketing Communication students, won the award for an advertisement they designed for Cansa.

Each year, the third-year Marketing Communication students of our Department of Communication Science have the opportunity to flex their creative muscles in the Copy-writing class. The challenge is to design two advertisements for any charity organisation by applying the knowledge they gained from the subject in a practical way. The top three groups are then entered for the Loerie and Pendoring awards – two of the most prestigious awards in the South African advertising industry.

The top three groups designed advertisements for Cansa, the South African Blood Service and Crime Line.

Hendrik Kruger and Anke Malan walk away with awards at Pfizer UKZN Young Health Scientists Research Symposium

Two students in our Faculty of Health Sciences won awards at a Pfizer UKZN Young Health Scientists Research Symposium.

Hendrik Kruger, a medical student, represented his group, which won the clinical category with the paper “Injury patterns of occupants surviving motor vehicle accidents in the Free State”. This presentation was based on a study which is the first of its kind in South Africa.

The group with Anke Malan from our Department of Nutrition and Dietetics as presenter received the prize in the community-based category with the presentation ’Knowledge, practices and perceptions of undergraduate students at the UFS regarding the risk factors of osteoporoses’. Anke’s team was also nominated as the overall winner of the symposium. Presentations were delivered in three categories, namely clinical, community-based and laboratory research.

Prof. Louis Scott, Department of Plant Sciences

Prof. Louis Scott from our Department of Plant Sciences was formally rewarded the Fellowship of Royal Society of South Africa (RSSA).

Prof. Scott is an internationally recognised Palinologist at our university and a B-rated scientist.

Fellows of the RSSA are considered to be part of a very elite group of South African scientists who have achieved international acknowledgment.

Prof. Aldo Stroebel, International Academic Programmes in the Office of the Vice-Chancellor

Prof. Aldo Stroebel has been elected as a Founding Member of the South African Young Academy of Science (SAYAS).

He is Associate Professor in our Centre for Sustainable Agriculture, Rural Development and Extension, as well as the Director of International Academic Programmes in the Office of the Vice-Chancellor.

The Young Academy has as its objectives to represent young scientists in advising the government on science and technology policy and human resource development. In addition, they will prepare the SAYAS to join the Global Young Academy (GYA) to engage with high-level international bodies, including the World Economic Forum.

Prof. Lodewyk Kock, Department of Microbial, Biochemical and Food Biotechnology

Prof. Lodewyk Kock was a sought-after keynote speaker at various conferences and seminars around the globe on our nanotechnology breakthrough research.

He delivered keynote lectures at international conferences of repute in the USA, China and Greece. In the USA he delivered a the keynote address at the Conference & Exhibition on Pharmaceutical Regulatory Affairs (Pharma-2011), held in Baltimore, and was a keynote speaker at the 2nd World Congress on Biotechnology in Philadelphia. He was also invited to present various lectures abroad.

He posted two video lectures in e-conference format on his research on the web page of the journal Translational Biomedicine. He was also invited by the International Society of Translational Medicine (ISTM) to head their “Molecular Imaging” Division.

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