Introduction
The COVID-19 pandemic (2019–2022) represented a profound global crisis, disrupting health systems, economies, governance structures, and everyday life on an unprecedented scale.1 Globally, health systems had to operate under uncertainty, making high-stakes decisions with incomplete or rapidly evolving information.2 The pandemic revealed the importance of adaptive governance, continuous data collection, and multi-sectoral coordination to mitigate both direct health impacts and broader societal consequences. The critical role of research and academic expertise was evident in the establishment of scientific advisory systems to support government decision-making. Countries such as the United Kingdom, New Zealand, Malaysia, Canada, and the Philippines implemented these systems early,3 while South Africa established Ministerial Advisory Committees (MACs) to provide urgent evidence-based scientific advice to the Minister of Health. The implementation and public release of MAC recommendations remained at the Minister’s discretion although the committees played an important role in informing government responses during the pandemic.
In South Africa, the pandemic occurred within a context of deep socio-economic inequality, constrained public health infrastructure, and long-standing governance challenges.4 The rapid spread of SARS-CoV-2 placed extraordinary pressure on hospitals, health workers, and policymakers, exposing systemic weaknesses such as uneven resource distribution, limited intensive care unit capacity, and workforce shortages.4,5 Government-imposed lockdowns and movement restrictions produced widespread socio-economic effects, including job losses, disruption of education, and heightened social vulnerability.6 These intersecting pressures underscored the fragility of health systems and the importance of evidence-informed decision-making and coordinated crisis response.
Higher education institutions (HEIs) and research organisations emerged as pivotal actors. Researchers across the biomedical sciences (broadly defined in this study to include epidemiology, virology and clinical medicine), together with public health specialists, social scientists, economists and others, rapidly mobilised to generate evidence on viral transmission, clinical management, health system capacity, socio-economic impacts, and behavioural responses.7 Research outputs informed critical policy decisions, including the calibration of lockdown measures, hospital preparedness planning, vaccination strategies, and public risk communication, while contributing to global scientific understanding.8,9
Beyond biomedical sciences, social and behavioural research played a crucial yet often under-recognised role in understanding community experiences during the pandemic.10 Such studies illuminated compliance with public health regulations, vaccine hesitancy, trust in institutions, and differential socio-economic impacts of COVID-19.11,12 A recurring tension emerged in evidence-informed policymaking. While South Africa’s advisory structures included expertise from both biomedical and social science disciplines, the findings of this study suggest that pandemic decision-making often prioritised biomedical evidence. Although social scientists were included in both main MAC structures and subcommittees, biomedical expertise was central to urgent clinical and epidemiological responses, while social science insights remained essential for ensuring that interventions were contextually appropriate, equitable, and effective.13,14 This underscores the need for interdisciplinary approaches integrating clinical, social, and economic perspectives to strengthen public health responses.
This study examines the role of higher education and research in addressing COVID-19 in South Africa, focusing on contributions to adaptive, learning-oriented health systems and preparedness for future epidemics. It analyses how research was mobilised, how evidence informed policy and practice, and where gaps emerged between knowledge production and policy uptake. It identifies lessons for health system reform, interdisciplinary collaboration, digital health, and institutional capacity for learning, innovation, and adaptive response. The study contributes to the literature on pandemic governance and higher education by showing how South Africa’s research and higher education systems responded to COVID-19, highlighting both their adaptive capacity and the structural and epistemic inequalities that shaped knowledge production and policy uptake.
Situated within the concept of learning health systems, where knowledge is continuously generated, integrated, and applied to strengthen health system responsiveness,15 the study identifies institutional arrangements that can strengthen evidence–practice linkages and build more inclusive, adaptive, and equitable health systems to advance universal health coverage. The objectives are to: (1) analyse stakeholder perceptions of the contribution of COVID-19 research within South African HEIs during the pandemic’s early stages; (2) examine the relationship between research and policymaking, including successes and limitations in translating evidence into action; and (3) identify lessons for future crises, particularly regarding the integration of social and biomedical sciences, digital innovation, leadership, and institutional mechanisms to strengthen health system resilience. Together, these findings demonstrate how higher education and research can support both crisis response and long-term health system strengthening.
Method
This study draws on a broader country report commissioned by the Department of Planning, Monitoring and Evaluation in collaboration with the National Research Foundation and the Government Technical Advisory Centre, for which the authors developed a dedicated chapter. Building on this work, the paper adopts a qualitative, exploratory design using methodological triangulation to examine perceptions of the role of higher education and research in South Africa’s COVID-19 response, and the institutional and research–policy dynamics shaping these responses. A qualitative approach was appropriate given the study’s focus on capturing in-depth experiences, perceptions, and institutional processes related to knowledge production and research–policy engagement during a period of crisis. The study was informed by an interpretivist perspective, which emphasises understanding participants’ experiences and interpretations within their specific contexts.16
Data were collected from three sources: 20 key informant interviews; a review of literature on COVID-19 research and policy, and research reports and working papers produced during the pandemic. Key informant interviews were conducted with senior stakeholders involved in South Africa’s COVID-19 research and policy response, including: deputy vice-chancellors, heads of academic departments, directors of research units (including: occupational health, pre-clinical and animal health sciences, and social work and psychology), senior government officials responsible for health research, representatives of national research and funding bodies, and members of COVID-19 MACs. Participants included individuals engaged in science policy advisory roles, clinical trials and biomedical research coordination, and national research funding and science engagement portfolios.
Participants were purposively selected based on documented involvement in pandemic-related research and policy engagement, identified initially through organisational and institutional reports. Snowball sampling was subsequently used to broaden participation across institutions and disciplinary fields. While snowball sampling may introduce network homogeneity, this risk was mitigated through purposive selection and efforts to include participants from diverse institutional, disciplinary, research, policy, and advisory contexts. Disciplinary diversity enabled the study to capture multiple perspectives on how research was mobilised, communicated, and utilised during the pandemic. Nevertheless, some perspectives may not have been represented.
Twenty of the 42 individuals approached agreed to participate. The sample provided perspectives from: public universities (including historically disadvantaged and historically advantaged institutions), national research organisations, funding bodies, government departments, and MACs. Data collection continued until sufficient thematic depth and recurrence were observed. Given participants’ seniority and specialised roles, institutional affiliations and specific positions are not reported to maintain confidentiality.
Interviews explored experiences of conducting research under emergency conditions, engagement with policymakers and advisory structures, perceptions of research uptake, and institutional enablers and constraints shaping knowledge production. These domains were designed to elicit reflections on both direct involvement in research–policy engagement and perceptions of how research evidence was used within policy processes. Interviews were conducted remotely in English, lasted 45–60 minutes, were audio-recorded with consent, and transcribed verbatim.
The document review examined approximately 600 peer-reviewed publications, policy briefs, grey literature, research reports, and working papers published between 2020 and 2022. Sources were identified through targeted searches of Scopus, Google Scholar, and institutional repositories using combinations of keywords including: ‘COVID-19’, ‘higher education’, ‘research’, ‘science-policy interface’, ‘research funding’, ‘South Africa’, and ‘pandemic response’. Documents addressing higher education, research activity, or science–policy interactions during COVID-19 were included; those unrelated to higher education or policy processes were excluded.
Data were analysed inductively using thematic analysis following Braun and Clarke.17,18 Interview transcripts and documentary sources were systematically coded to identify recurring patterns relating to research mobilisation, policy engagement, interdisciplinarity, institutional capacity, and digitalisation. Codes were iteratively reviewed and grouped into broader themes emerging from the data rather than predetermined theoretical categories. Coding was conducted by a single researcher using NVivo software to support the systematic organisation, retrieval, and refinement of themes. Analytical credibility was enhanced through triangulation across interviews, documentary sources, and institutional research outputs. Convergences and divergences across these data sources were examined to strengthen the depth and robustness of the analysis.
Ethics approval was obtained from the Human Sciences Research Council Research Ethics Committee (REC 1/23/09/20) as well as by the North-West University Health Research Ethics Committee (NWU-0000-22-A1) and the University of Johannesburg Faculty of Humanities Research Ethics Committee (REC-01-285-2022) prior to data collection. All participants provided informed consent, and confidentiality was maintained through the use of pseudonyms and role-based identifiers rather than institutional affiliations. Participants were provided with information about the study and informed of their right to withdraw at any stage.
The authors acknowledge their positionality as researchers embedded within the South African higher education sector and involved in a commissioned study. While this positioning provided valuable contextual insight, it also required ongoing reflexive engagement through systematic coding, triangulation, and critical reflection throughout the research process.
Findings
This section elucidates the multifaceted role of research in crisis response and lessons for future epidemic preparedness by examining the perceptions of participants on the contributions of HEIs, the nature of knowledge production, and challenges encountered during the pandemic.
Research informing policy and practice
Participants consistently emphasised the rapid mobilisation of research capacity during the early stages of the pandemic. Universities redirected existing expertise and infrastructure towards COVID-19-related research, producing epidemiological models, clinical guidelines, and behavioural studies that in some instances directly informed government decision-making. As one participant noted: “We were approached to undertake the first national COVID-19 set-up prevalence survey looking at antibodies. The challenge was actually to determine what proportion of South Africans were infected by COVID-19 but did not know” (ILS). This urgency required higher education and research institutions to operate in real-time while balancing academic rigour with immediate societal needs. Research outputs informed the work of MACs, provincial health departments, and hospital management teams, whose advisories addressed issues including testing and surveillance strategies, clinical treatment guidelines, vaccination policies, public health regulations, and health system preparedness. For example, the Network for Genomic Surveillance in South Africa (NGS-SA), which included UKZN, UCT, UFS, UP, and Wits, played a pivotal role in identifying emerging variants of SARS-CoV-2.19 Their work provided early warnings of variant proliferation and informed vaccination strategies and lockdown policies.
Findings suggest that modelling studies undertaken by HEIs also informed government decisions on hospital preparedness and ICU capacity.19,20 Research demonstrated how therapeutics such as remdesivir could enhance ICU efficiency during periods of increased admissions.21 Beyond clinical interventions, social science research was perceived to have informed public compliance with regulations, vaccine hesitancy, and the social impact of lockdown measures. As one participant reflected:
I think the real strength of what we did was to give the public that voice … on very critical questions, like vaccines. Allowing the public to express themselves did work and told us something very important … reading through those open responses showed that people in South Africa are not anti-science. In fact, it’s the opposite … the hesitancy was about wanting to understand better. It was not, ‘I reject this because of whatever thing’, and I think that was truly interesting, particularly at a time when you can feel bombarded with that kind of fake news and conspiracy theories. (ICR)
The contributions of higher education were not limited to policy advice. Participants’ perceptions suggest that HEIs also played a vital role in innovation, producing PPE, ventilators, sanitisers, and developing new technologies to manage COVID-19 patients, as noted by one participant:
That is one of the focuses where we put our strengths to participate in the production of PPEs. We have entered into two consortia, one with the CSIR where the research finding is in producing the respirator … the other consortium is with the four universities, that is, North-West University, Vaal University of Technology, TUT and CUT, and it’s been supported by Merseta. (IND)
This aligns with existing literature. The University of Cape Town22 documents its engagement in ventilator design and distribution, while Stellenbosch University developed robots to monitor patients. Similarly, the University of Johannesburg developed a ‘happiness index’ to track emotional well-being during the pandemic, enabling government departments to tailor psychosocial interventions.23 These examples illustrate how research functioned as a core component of emergency response and crisis governance, linking scientific knowledge, technological innovation, and community engagement.
Uneven uptake and epistemic hierarchies
Despite successes in some instances, interviewees highlighted a persistent gap between research production and policy uptake. They were of the view that while biomedical and epidemiological evidence was rapidly incorporated into government decision-making, social and behavioural sciences were often marginalised. As one leader observed: “The government’s decision was to go with information from public health experts. And to show that they had faith in the public health experts’ political lobbies, which came from the alcohol industry. The point I’m making here is that in a number of instances, the science prevailed, [and] the science was what was followed” (ICS).
Participants’ accounts suggest that certain forms of knowledge were valued more highly than others, reflecting perceived epistemic hierarchies within health governance. The composition of MACs illustrates this dynamic, with COVID-19 MACs overwhelmingly populated by epidemiologists, virologists, and microbiologists, while the Social and Behavioural Change MAC relied largely on representatives from faith-based organisations and civil society.24 For example, the primary MAC created in March 2020 with 51 members was dominated by four biomedical streams: clinical care, public health, laboratory investigation, and research, with expertise in infectious diseases, intensive care, paediatrics, diagnostics, vaccines, therapeutics, regulation, modelling, implementation science, and only some social science expertise.14,25 Although intended to address gaps in the original COVID-19 MAC, the Social and Behavioural Change MAC remained epistemically limited. The committee institutionalised stakeholder representation, particularly faith-based and community organisations, rather than establishing broad disciplinary representation from the social sciences and humanities.24 While biomedical expertise was essential for immediate crisis management, including hospital capacity, testing, and treatment protocols, research26 suggests that the limited integration of social science insights may have constrained responses to vaccine hesitancy, misinformation, and the socio-economic consequences of lockdowns.
Research by academics at UKZN revealed that rumours linking vaccines to infertility were widespread, underscoring the importance of social science interventions in dispelling misinformation and encouraging uptake.27 Similarly, UCT documented public mistrust in government vaccination programmes as a key factor contributing to hesitancy.28 These findings reinforce the need for learning health systems that integrate epidemiological, clinical, and social knowledge.
Institutional inequalities and research capacity
The findings further suggest disparities in research capacity across South African HEIs. Historically white universities (HWUs) were better positioned to sustain research during the pandemic, supported by established laboratories, digital infrastructure, and access to emergency funding.29 In contrast, other universities experienced severe disruption, including halted projects, limited laboratory access, and shortages of consumables. One participant reflected: “Well, I suppose doing so much online means that you are vulnerable to network connectivity. And we do have problems … and [I] couldn’t present because of connection you know … there is variability in internet access, and in network quality” (IRH). Another participant stated: “And, obviously, [there] were questions, or of race and class … that my privileged middle-class white existence, also enabled me to do things … and to in part have the access to resources … my race and class possession has enabled me to create that research record” (ICR).
These inequalities shaped whose knowledge was produced and whose voices informed national preparedness, highlighting the need for policy and funding mechanisms that strengthen research capacity across all HEIs.
Digitalisation and new modes of knowledge production
Digital technologies played a crucial role in enabling research continuity and collaboration. Video conferencing platforms, online survey tools, and data-sharing applications allowed researchers to maintain project momentum despite restrictions on in-person engagement. As one participant noted: “I think our experience with digitalisation [due to] COVID-19 has opened up a whole group of new research questions for us …” (ICW).
Digitalisation facilitated collaboration across institutions and disciplines. For example, the University of Johannesburg collaborated with the Human Sciences Research Council and civil society organisations to track vaccine sentiment and assess public mental health.30,31 However, the shift to digital platforms also exposed infrastructural constraints that affected the continuity of research activities as noted above. These challenges intersected with race and class, as was noted in ICR’s narrative. Digitalisation also intensified workloads and blurred boundaries between personal and professional life. Academics involved in COVID-19 research experienced burnout linked to extended work hours and psychological demands and strain: “It’s been a hard time for the family because both parents are doctors … you can encounter this issue of burnout in many spaces” (ILCM).
Despite these challenges, digital technologies supported flexibility, collaboration, and rapid dissemination of evidence, underscoring their potential contribution to learning health systems when equity and well-being are prioritised.
Discussion
The findings underscore the central role of higher education and research in addressing the challenges posed by the COVID-19 pandemic and offer lessons for health system reform in South Africa. The pandemic highlighted the value of learning-oriented health systems in which evidence is generated, disseminated, and applied in real-time to inform decision-making.
The findings further suggest that South Africa’s higher education and research sector was an important, although uneven, component of the country’s learning health system during COVID-19, contributing evidence, innovation, surveillance, and policy support. However, learning was not fully integrated, as biomedical evidence was perceived to be more readily translated into decision-making than social, behavioural, and community knowledge. Participants described effective learning as requiring sustained interaction between researchers, policymakers, health services, and communities, with diverse forms of evidence informing adaptation and responsive action. Strengthening these relationships beyond periods of crisis is essential for building a more inclusive, equitable, and resilient health system.
The findings further propose that research–policy integration was often strongest where policy decisions relied on biomedical and epidemiological evidence, particularly in areas such as infection control, hospital preparedness, vaccination strategies, and genomic surveillance. Modelling studies produced by higher education institutions informed decisions regarding lockdown levels and the allocation of critical resources,21 demonstrating the value of timely, high-quality research for adaptive governance.
The findings suggest that participants perceived persistent epistemic hierarchies that influenced the uptake of social science and behavioural research. Participants and earlier research frequently perceived advisory structures as favouring biomedical expertise, limiting the incorporation of evidence related to compliance, vaccine hesitancy, and the socio-economic consequences of the pandemic.10 This finding is important given that effective epidemic management requires the integration of biomedical, social, and economic perspectives.27,28 The perceived marginalisation of social science highlights continuing challenges in institutionalising inter- and transdisciplinary approaches.
The data also suggest that structural inequalities across HEIs influenced the extent and nature of research contributions during the pandemic. Historically advantaged universities were better positioned to redirect resources towards COVID-19 research, while resource constraints limited participation by historically disadvantaged institutions.28 These disparities have implications for the inclusivity and effectiveness of academic health systems.
Digitalisation supported and enabled research continuity and collaboration across contexts, but simultaneously exposed inequalities related to access, workload, and well-being.32–34 Institutional strategies are therefore required to promote equitable and sustainable digital research ecosystems.
Leadership and governance challenges were evident throughout the pandemic. Across interviews, participants described advisory committees as being strongly oriented towards biomedical expertise, reflecting broader power dynamics and preferences for particular forms of knowledge. Strengthening epidemic preparedness requires governance that supports reflexivity, learning, and integration and mobilisation of diverse expertise within adaptive governance structures.35
Public engagement and co-production of knowledge emerged as important dimensions of an effective response. Participants highlighted the role that HEIs played in facilitating participatory research and public communication that enhanced trust and compliance.27,28,36 These practices align with academic health system principles that emphasise iterative learning and responsiveness to community needs.
Situated within the global knowledge system,37 South Africa demonstrated scientific leadership through genomic surveillance and by leveraging HIV and TB research infrastructure for vaccine trials. However, travel restrictions following transparent variant reporting exposed persistent inequities in global science governance.38 Both interviews and documentary evidence pointed to gaps in the integration of social science evidence, community engagement, African language knowledge translation, mental health research, and equitable research capacity. Expedited ethics processes and reliance on short-term emergency funding raised concerns about the sustainability of research systems.39 These lessons point to the need for sustained investment in research infrastructure, interdisciplinary expertise, and long-term community partnerships to ensure effective pandemic preparedness.
Finally, HEIs contributed to innovation through new technologies, protocols, and community-level interventions. Inter- and transdisciplinary collaboration across medicine, public health, engineering, social sciences, and digital technologies and related fields proved essential for scalable and context-sensitive solutions.40
Limitations
This study has several limitations. Its qualitative design and focus on selected higher education institutions may not capture the full range of pandemic-related research activities across South Africa. As the findings are based on participants’ perceptions, future research could employ quantitative or mixed-methods approaches to examine patterns of evidence use, disciplinary representation, and research–policy engagement, and explore their relationships with outcomes such as vaccine hesitancy and mental health. While the study considers research outputs and policy impacts, it does not directly assess patient-level health outcomes. Nevertheless, the triangulation of interviews, policy documents, research outputs, and sectoral analyses provides valuable insights into the production, dissemination, and uptake of knowledge during a public health crisis.
Recommendations
Based on the findings, this study highlights the need for a strategic approach to strengthening the role of higher education and research in health system preparedness and response. Central to this is institutionalising inter- and transdisciplinary advisory mechanisms that integrate biomedical, social and behavioural sciences into health emergency governance, supporting more holistic, contextually informed decision-making.
Strengthening learning health systems requires sustained mechanisms for knowledge generation, translation, and use, including rapid evidence liaison units, interdisciplinary advisory platforms, and regular after-action reviews involving researchers, policymakers, health workers, and communities. Effective public communication is also needed to counter misinformation, build trust, and support informed decision-making during health emergencies.
Equitable investment in research capacity, particularly within historically disadvantaged institutions, remains essential to address inequalities in knowledge production, broaden participation in policy processes, and strengthen preparedness. Investment in digital infrastructure, connectivity, digital literacy, and multilingual knowledge translation is equally important to support research collaboration, data sharing, and responsive health systems while reducing existing inequalities.
Embedding the principles of resilient academic health systems within broader health system reform provides a further pathway to strengthening preparedness. Transdisciplinary collaboration, effective knowledge translation, and continuous feedback between research, policy, practice, and communities can foster more adaptive and responsive systems.
Future research could examine the composition and expertise profiles of MACs and systematically analyse committee advisories to assess the balance between biomedical and social science inputs. Such work would complement the present study, which draws on participant accounts and existing literature rather than a direct empirical analysis of committee membership or outputs.
Together, these measures provide an integrated strategy for strengthening epidemic preparedness, supporting more inclusive and adaptive health systems, and advancing universal health coverage. This approach is consistent with growing post-pandemic evidence on adaptive governance, integrated knowledge systems, equitable research ecosystems, and resilient health systems.7,27,29
Conclusion
The COVID-19 pandemic exposed both strengths and vulnerabilities within South Africa’s health and research systems. Higher education institutions and research organisations played a critical role in the response by mobilising expertise, adapting existing infrastructures, and fostering inter- and transdisciplinary approaches that generated evidence, informed policy, supported health service delivery, and shaped public understanding. Their contributions guided decisions on infection control, hospital preparedness, vaccination, and risk communication. At the same time, the findings suggest that the pandemic exposed persistent structural inequalities, perceived epistemic hierarchies, and uneven research–policy translation, highlighting disparities in access to knowledge, resources, and institutional influence. Participants perceived that social and behavioural research was underutilised within government and advisory structures despite its importance for understanding public behaviour, trust, and compliance, demonstrating that effective epidemic preparedness requires more than biomedical expertise alone.
These findings underscore the importance of embedding learning, interdisciplinarity, and equity within health system reform. Future preparedness depends on sustained investment in research capacity, particularly within historically disadvantaged institutions, alongside mechanisms that support rapid knowledge translation, inclusive governance, and the integration of diverse forms of expertise. While digitalisation and technological innovation offer opportunities to strengthen collaboration, data collection, and public engagement, they must be implemented in ways that do not reproduce existing inequalities. Equally important is leadership that promotes reflexivity, inclusivity, and evidence-informed decision-making within adaptive governance structures.
By strengthening the role of higher education and research within learning health systems, South Africa can enhance epidemic preparedness, support more equitable knowledge production and use, and build a more resilient health system. The pandemic demonstrated that research is not merely an academic activity but a foundational component of effective public health policy, societal resilience, and health system transformation. Embedding these lessons into policy and practice will be critical for advancing universal health coverage and ensuring that future responses draw on more inclusive, integrated, and equitable research systems.
Abbreviations
Acknowledgements
The authors would like to thank the Centre for Social Change, University of Johannesburg, and Prof. Kate Alexander for providing the funds to support this project’s data collection and transcription. They also acknowledge the use of ChatGPT (version 5.0) to assist with reducing word count, with explicit instructions to preserve all substantive content and conceptual integrity.