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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: Appointments

2011-12-01

Dr Lis Lange: Senior Director: DIRAP

Dr Lis Lange, an Argentinean by birth, immigrated to South Africa twenty years ago – a few weeks after Nelson Mandela had walked through the gates of Victor Verster. For the past ten years, she has been involved in quality assurance for higher education institutions at the Council on Higher Education at national level.

She is assisting our university in the areas of quality assurance and academic planning, contributing to the development of deep intellectual debate and multi-disciplinary research.

Prof. Charles Dumas, Department of Drama and Theatre Arts

Prof. Charles Dumas, Extraordinary Professor in our Department of Drama and Theatre Arts, will be spending three months per year for the next three years at our university to help develop filmmaking, specifically focusing on the development of the Video Unit Planned for the Department.

Prof. Dumas started the year off with the production, Our Father’s Daughters, which was produced during the Mini-festival as well as at the Reitz Four reconciliation meeting. The production was also turned into a short film. Prof. Dumas gave film-acting classes to the third-year drama students. He directed multiple productions, such as the third-year module production Ipi Zombi, the Grahamstown Festival production, Seven Guitars and the Dance/drama production, Race, Reconciliation and the Reitz Four.

Prof. Daniel Plaatjies, UFS Business School

Prof. Daniel Plaatjies is the former Director and Head of the Graduate School of Public and Development Management at the University of the Witwatersrand. He was mainly responsible for the leading, directing and managing of strategic academic programmes, teaching, research, governance, service management and monitoring. Prof. Plaatjies, who was appointed as Visiting Professor at our Business School this year, will as part of his new duties at our Faculty of Economic and Management Sciences, be lecturing part-time and supervise our PhD students.

Prof. Johann Neethling, Department of Private Law

Prof. Johann Neethling’s career is now completing its full circle with his appointment as Senior Professor in our Department of Private Law. In 1965 he was a first-year at this university. With his nine law text books and nearly 200 articles, together with 40 years’ experience in academic training he is of inestimable value to this Department. His publications contribute to the establishment of our university as a research institute.

Prof. Hussein Solomon, Department of Political Science

Description: 2011 Appointments_Hussein Solomon Tags: 2011 Appointments_Hussein Solomon

Prof. Hussein Solomon joined our university this year as Senior Professor in the Department of Political Science. Formerly he worked in peace NGOs, advised diplomats and acts as a serving officer in the South African Air Force.

His area of research expertise includes conflict and conflict resolution in Africa; South African Foreign Policy; international relations theory; religious fundamentalism and population movements within the developing world. He is also the author of a number of books, including one on global jihad and one on India's secret relationship with apartheid South Africa.

He is also member of the internationally renowned Our Humanity in the Balance (OHIB) organisation, where his role is to bring these disparate communities together and to focus energies on a common project.

Prof. André Keet, International Institute for Studies in Race, Reconciliation and Social Justice

Prof. André Keet, our Director of the International Institute for Studies in Race, Reconciliation and Social Justice, joined the University of Pretoria on a part-time basis in 2008, whilst being a Commissioner on the Commission for Gender Equality. Later he left the Commission and joined the University of Fort Hare. “I was happy to join academia and now also serve on the Stellenbosch University Council; therefore I am very aware of the challenges facing higher education,” he said.

His vision for the Institute is to support higher-education transformation, promote non-discrimination, reconciliation and human rights, build national, regional and international networks, and developing ‘new’ languages, knowledge and discourses for reconciliation and social justice, all to the benefit of our university and South Africa.”

Prof. Helene Strauss, Department of English

Prof. Helene Strauss completed her PhD at the University of Western Ontario, London, Canada, where she taught courses on Film Studies, Children’s Literature and South African Literature and Culture. “I was subsequently appointed as an Assistant Professor in the Department of English and Cultural Studies at McMaster University, Hamilton, Canada.” She joined our Department of English this year.

Prof. Strauss has an on-going preoccupation with questions concerning social justice, race, gender and ethical interpersonal interaction in South Africa and beyond.

Prof. EC Ejiogu, Centre for Africa Studies

After 22 years in the United States of America, Prof. EC Ejiogu decided to return to Africa – to his roots – to join our university’s Centre for Africa Studies at the beginning of 2011.

Before joining the Centre, he was Assistant Research Professor in the Centre for Innovation at the University of Maryland, College Park. As Senior Researcher at the Centre, he has already helped with the streamlining of the academic programme, restructuring it to enable students to gain skills necessary to deliver a research proposal towards a dissertation after their three years of study. He has also taken up PhD and Master’s supervision.

His latest publications include a book published in March 2011 with the title, Roots of Political Instability in Nigeria, and a book co-edited with Prof. Kwandiwe Kondlo, Director of the Centre for Africa Studies, Africa in focus: Governance in the 21st century, published in April 2011.

Pura Mgolombane, Vice-Dean: Student Affairs

Bringing with him a decade of experience in Student Affairs our new Assistant-Dean for Student Life and Leadership, Pura Mgolombane, has big plans for student development. He says his office wants to help Kovsies increase its throughput rate and produce socially well-adjusted and employable graduates in South Africa, the continent and anywhere in the world.

Before joining Kovsies, he was employed as Director: Student Life, Governance and Culture at Walter Sisulu University. Pura, who has a background in Human Resources, Business Management and Corporate Law, says his academic training has empowered him with skills to ensure that the Student Life and Leadership is properly led, governed and managed.

Prof. Hasina Ebrahim, School for Social Sciences and Language Education

This former academic from the University of Kwa-Zulu Natal was appointed as Associate Professor at our School for Social Sciences and Language Education in the Faculty of Education. Amongst others, she is the project coordinator for the Faculty’s Early Childhood and Foundation Phase Teacher Education Programme and the MEd and PhD supervisor in the programme.

Prof. Ebrahim is also the Deputy-President of the first South African Research Association for Early Childhood Education (birth to nine). “This is certainly a milestone to profile the university in terms of its thrust towards excellence in research,” she says. One of the main aims of the association is to shape the research agenda for a marginalised field in South Africa.

Prof. Corli Witthuhn, Faculty of Natural and Agricultural Sciences

Description: 2011 Appointments_Corli Witthuhn Tags: 2011 Appointments_Corli Witthuhn

Prof. Corli Witthuhn, a former Bloemfonteiner, attained her PhD in Microbiology at our university. Therafter, in 1999, she was appointed as a lecturer at Stellenbosch University and later as Vice-Dean.

Currently she is our Vice-Dean in the Faculty of Natural and Agricultural Sciences. She hopes to sustain her research here at our University.

Her life motto? “Opportunities are presented in the form of obstacles,” she says.

Prof. Melanie Walker

Prof. Melanie Walker is a prominent South African scholar who has been working as Professor of Higher Education Studies at the world-leading University of Nottingham in the UK, where she been Director of Postgraduate Students and a Director of Research in the Faculty of Social Sciences. She will join the University of the Free State in February 2012 as Senior University Professor in the Postgraduate School.

She is a graduate of the University of KwaZulu-Natal and the University of Cape Town, where she completed her PhD, after teaching in disadvantaged secondary schools for a number of years. Prior to working at Nottingham she worked at the Universities of Sheffield, West of England and Glasgow, as well as the Universities of Cape Town and the Western Cape. She is also a Fellow of the Human Development and Capability Association. She is currently Director of Research Training and a senior researcher in the EU-funded Marie Curie EDUWEL project, which includes senior researchers from eight European countries and 15 early-stage researchers.

With a long-standing commitment to social-justice research and equality practices, she is currently widely recognised internationally as leading in the application of the capability approach and human development to higher education policy and practice. Among others, she has led or participated in research projects funded by the NRF (South Africa), the Higher Education Academy (UK), HEFCE (UK), EU, and ESRC/DfID, which funded the Public-Good Professionals’ Capability Index research project.

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