Researchers immediately weighed in at several levels and became involved in or initiated research projects on various aspects of the pandemic.
Prof Nico Gey van Pittius, FMHS Vice-Dean: Research, pays tribute to SU researchers’ commitment and hard work despite the disruptive effects of the pandemic on daily lives and emotional states.
“We are finding ourselves in extraordinary circumstances – a situation that none of us have been in before. This has brought about unique pressures and we find ourselves in situations of increasing abnormality, and sometimes even chaos. Despite the effects that the pandemic has had on our ability to function normally, we’ve seen great enthusiasm from our staff for research to tackle the pandemic head on.”
He quotes Frodo in Lord of the Rings, when he tells Gandalf: “I wish this need not have happened in my time.” Gandalf replies: “So do I, and so do all of the people that live to see such times. But it is not for them to decide, all we have to decide is what to do with the time given to us.”
“We cannot do much about what is happening to us, but what we can do is to do decide what to do with the time that is given to us,” says Gey van Pittius. “In the time of Covid-19, we have shown the world how our research is contributing to the Faculty’s goals of advancing health and equality in South Africa and beyond. It reflects the impact that we have on society and the positive difference that we make in the world.”
Among others, FMHS projects range from involvement in the testing of a promising Covid-19 vaccine, to research measuring the impact of the pandemic on physical and mental health worldwide, specifically also on children; the influence of non-communicable diseases; the impact of Covid-19 on people living with disabilities; the development of a cough screening app; the effect of changes in surgical practices in hospitals; safer mass sports events; the Covid experiences of people living with disabilities; as well as outcomes for Covid-19 survivors. Below follows short summaries of some of these projects.
Testing of a vaccine
The FMHS is part of a large international research trial testing one of the most promising Covid-19 vaccine candidates.
This vaccine (ChAdOx1 nCoV-19) was developed by Oxford University in the United Kingdom (UK) and was tested at seven sites in South Africa, along with the UK and Brazil. The study is funded by the Bill & Melinda Gates Foundation and in South Africa is led by Prof Shabir Madhi of the University of the Witwatersrand.
Dr Shaun Barnabas of the FMHS is leading the Tygerberg trial site. In South Africa some 2000 volunteers took part. The study involves two doses of the test vaccine given a month apart.
The study was closely monitored by the South African Health Products Regulatory Authority, the Data Safety and Monitoring Board and other regulatory authorities, as well as institutional ethics committees.
The researchers expect some results in the first quarter of 2021.
Cough screening app
Many countries struggled to keep up with coronavirus laboratory testing. In an effort to reduce the number of tests needed, South Africa adopted non-ideal testing strategies at times, testing only symptomatic patients and not accounting for contacts of cases or asymptomatic cases.
A team of researchers from the FMHS’ Division of Molecular Biology and Human Genetics, the SU Department of Electrical and Electronic Engineering, the University of the Witwatersrand and freelance programmers partnered to develop a screening app that makes use of a trained algorithm to discern whether or not someone might be Covid-19
Their aim was to improve screening to ensure that those most in need of a laboratory test can be prioritised. Their solution was to develop a smartphone app that can identify a coronavirus cough, along with a symptom checklist to screen patients. Several studies have shown the feasibility of using sound analysis to differentiate between coughs caused by different illnesses.
The app will be made available free-of-charge and will guide users in the privacy of their own homes if they should have themselves tested. It will help to improve allocation of resources and reduce transmission of the virus by limiting the need to visit a testing facility.
A similar ongoing project for TB has already produced some very promising preliminary results.
Global physical and mental health (COH-FIT)
The Collaborative Outcomes Study on Health and Functioning during Infection Times (COH-FIT) is the largest study of its kind measuring the impact of the Covid-19 pandemic on physical and mental health worldwide.
The project was launched by a network of more than 200 international investigators, led by Prof Christoph Correll (Germany) and Dr Marco Solmi (Italy). It aims to collect information from more than 100 000 participants from 142 countries and on 6 continents, including 25 000 South Africans. It has been endorsed by major international scientific societies and in South Africa is led by Prof Soraya Seedat and Dr Georgina Spies, both from the FMHS. The project is collecting information now, as well as at six and twelve months after the Covid-19 pandemic will have been declared over by the World Health Organisation (WHO), targeting acute and longer-term effects. The project aims to make a difference by identifying risk and protective factors for physical and mental health problems during a pandemic/lockdown/physical contact restriction period.
Collecting this information from the general public will help identify potential therapeutic targets to prevent poor health outcomes and increase chances of improved outcomes in particularly vulnerable individuals. The generated information will provide guidance on where resources should be allocated to make the biggest difference. The survey is available at www.coh-fit.com
Supporting families (CO-SPACE)
Researchers from the FMHS, in partnership with the University of Oxford, are involved in the project Supporting Parents, Adolescents and Children during Epidemics (CO-SPACE).
Covid-19 has led to an elevated awareness of threat in the environment and has caused major disruptions to families’ lives, through social distancing, school closures and lockdown. While research has provided valuable information about how parents and caregivers can support their children’s mental health in general, what would be most effective in the current context is unknown. This is also a rapidly changing situation, where different pressures will arise for children, young people and their families over time.
This longitudinal survey has the following aims: To track children and young people’s mental health throughout the Covid-19 crisis; and to identify what parental responses and actions protect children and young people from deteriorating mental health (over time, and at particular stress points), and how that varies according to child and family characteristics.
The SU study is running alongside the study by the University of Oxford during the lockdown period in the UK, and aims to provide information about the South African setting, as this will allow the researchers to combine data and draw comparisons across settings. The findings will be used to inform the development and distribution of resources and to support families. Some 175 South Africans are participating in the study.
International survey on mental health (COMET)
The Covid-19 pandemic is a large-scale crisis that asks people to change their social behaviour, and is likely to impact on the fabric of societies that are affected. Cultural factors have been shown to play a role in the development of mental disorders. COMET, in which FMHS researchers are participating, is a cross-country longitudinal
investigation of predictors associated with mental health symptoms following the Covid-19 crisis.
The study examines relevant predictors (such as age and gender) in relation to mental outcomes (such as symptoms of depression and anxiety). The first Covid-19 wave occurred in each participating country (the Netherlands, Italy, France, Spain, Germany, Sweden, Switzerland, the UK, Turkey, South Africa, Indonesia, China, Australia and the USA), while it was expected that wave two, three and four would take place within a few months after the first wave.
The study has assessed mental health in over 7 700 people, including 525 South Africans. Early findings suggest South Africa faces stiff challenges; notably, comparatively severe income reduction. The assessment also showed significantly higher levels of depression, anxiety and post-traumatic stress disorder compared to other countries.
Covid-19 and SA children (COVID-Kids)
This study, a collaboration between the Department of Paediatrics and Child Health and the Desmond Tutu TB Centre, includes two research parts: a description of routine care data of all children presenting with SARS-CoV-2 disease and the enrolment of children with suspected Covid-19 illness into a cohort study.
The cohort study rigorously investigates the clinical impact, immunology, respiratory morbidity, psychological impact and transmission dynamics of SARS-CoV-2 in South African children. Children younger than 13 years, HIV-/+, were recruited from Tygerberg Hospital. They included children with acute respiratory illness and high risk for Covid-19; acute respiratory illness of unknown aetiology; household SARS-CoV-2 exposure, or any symptoms
and a positive SARS-CoV-2 test.
Clinical assessment and data collection are done at enrolment and during follow-up to three months. In addition, all cases of Kawasaki disease or paediatric inflammatory multisystem syndrome (PIMS) potentially associated with Covid-19 are captured.
At enrolment, respiratory samples were sent for testing for SARS-CoV-2 and an additional respiratory panel of 16 common respiratory viruses. A saliva sample was also collected and stored for future mucosal immunology and SARS-CoV-2 testing to compare cycle thresholds between saliva and respiratory samples as an indication of infectiousness. Respiratory morbidity is determined at enrolment and three months later. In total, 80 children and caregivers are enrolled in the cohort study.
The routine care data collection has resulted in the first accepted publication in the Clinical Infectious Disease Journal: “Clinical experience with SARS CoV-2 related illness in children – hospital experience in Cape Town, South Africa”.
Global Psychotrauma Screen Project
FMHS researchers are part of a global initiative, led by the University of Amsterdam, which aims to improve understanding of the unique reactions to Covid-19 related traumatic events when compared to reactions to other traumatic events. They further aim to understand how these reactions differ across different cultures and during the different phases of the Covid-19 pandemic.
Persons older than 16 who have experienced any frightening (traumatic) event, whether related to Covid-19 or other events such as a serious accident or fire, physical or sexual assault or abuse, earthquakes or floods, wars, seeing someone be killed or seriously injured, or having a loved one die through homicide or suicide, were invited to participate in this study called the Global Psychotrauma Screen – cross-cultural responses to Covid-19 versus other traumatic events. This short survey, available in 23 languages, screens for a wide range of potential outcomes of trauma, as well as for risk and protective factors.
This questionnaire was designed to be simple, cross-culturally valid, and easy to administer in a variety of circumstances, such as shortly after mass trauma, but would also tap potential consequences up to decades after trauma. Results from this study will help to better inform preventative and curative interventions. The researchers received 6 162 responses from 83 countries.
Mental health of SA expats
Researchers from the FMHS and the Autonomous University of Madrid collaborated in a project which aims to investigate anxiety, depression and psychotrauma in South African expatriates during and in the aftermath of the Covid-19 outbreak.
The aim is to better understand the expatriate populations’ responses to and concerns over a pandemic such as Covid-19, to inform clinical management in the aftermath of the outbreak, and also to develop systems and strategies to improve management of psychological responses and mental wellbeing during future health pandemics.
An online questionnaire was used to gather demographic and medical information, and assessed for anxiety, depression, resilience, current and childhood trauma, quality of life and Covid-related stressors. Data has been collected from consenting expatriates from 27 countries who lived under social isolation restrictions. A follow-up questionnaire was distributed in September to evaluate whether identified symptoms have improved, on a population and an individual level.
Primary healthcare and Covid-19
During the Covid-19 pandemic primary care (PC) nurses have been the first point of contact and they are in close contact with communities. In a collaborative project between researchers of the FMHS’ Department of Nursing and Midwifery and the Department of Global Health, the preparedness of PC nurses for Covid-19 and the influence of the pandemic on primary healthcare services in the Western Cape was investigated.
Preliminary findings from an online survey that was sent to postgraduate PC students and alumni working in the Western Cape, indicated that 44,4% of participants were confident about the infection, prevention and control training they received and 58% felt prepared to provide direct care to suspected Covid-19 cases. PC nurses demonstrated resilience to adapt and manage Covid-19 whilst continuing essential services.
However, Covid-19 had a negative influence on other primary healthcare services. Challenges included adequate training, infrastructure, the availability of personal protective equipment and Covid-19 testing of healthcare workers. PC nurses need comprehensive support to manage stress and anxiety.
Lessons learned and gaps identified may inform strategies to ensure better support forprimary care nurses. Continued innovative ways of delivering preventative and other services during a pandemic are needed to ensure future pandemic preparedness.
Convalescent plasma: evidence review of clinical benefit and harm
In response to a request by the National Essential Medicine List Committee (NEMLC) of the Department of Health for rapid evidence about the use of convalescent plasma (the antibody-containing liquid fraction of blood from recovered Covid-19 patients) to treat patients with severe Covid-19, a team from the FMHS’ Centre for Evidence-based Healthcare (CEBHC) assisted in conducting a rapid review to answer this urgent question.
Based on ten observational studies and one trial, it is not known whether including convalescent plasma in the treatment of Covid-19 has any effect on adverse reactions or outcomes critical for decision-making. The NEMLC used this evidence to suggest not using convalescent plasma for severe Covid-19 outside of a clinical trial setting at the present time.
Colchicine: evidence review of clinical benefit and harm
In response to the NEMLC’s request for rapid evidence for the use of colchicine (medication for pain and inflammation, often used for gout) in the treatment of Covid-19 patients who require hospitalisation, a team from the CEBHC assisted in conducting a rapid review to answer this urgent question.
Based on the evidence from one trial, it is not known whether including colchicine in the treatment of such patients has any effect on critical decision-making outcomes. Adverse events were more frequent for colchicine, but none were deemed serious. The NEMLC used this evidence to recommend strongly against the use of colchicine, outside of a clinical trial.
Obesity and Covid-19 severity and mortality
Apart from studies to find treatments, researchers are working to better understand the risk factors predicting Covid-19 disease severity and mortality. This knowledge could help health professionals with treatment decisions for these patients, and the general public to reduce their risks and stay safe.
Obesity, defined as having a body mass index (BMI) of 30 kg/m² or higher, is characterised by a state of chronic low-grade inflammation. Obesity has been associated with impaired immunity and is a known risk factor for many health conditions, including lung and heart diseases.
In collaboration with researchers from McMaster University in Canada and the University of Jakarta in Indonesia, Dr Celeste Naude en Ms Anel Schoonees from the CEBHC are conducting a systematic review to assess if obesity is an independent risk factor for disease severity and mortality in Covid-19 patients.
Covid-19 and non-communicable diseases (NCDs)
The CEBHC and the Department of Global Health of the FMHS, in collaboration with the Universities of Cape Town and of the Western Cape, conducted a rapid review of international research on and experiences of risk, screening, management and support of people with Covid-19 and NCDs such as diabetes, hypertension, asthma, occupational lung diseases, coronary heart disease, heart failure and stroke.
It was developed to inform the South African response in the context of a country with multiple disease burdens, in particular chronic infectious diseases and NCDs, and an already overstretched health system.
Following a comprehensive search strategy of multiple databases covering 1 October 2019 to 20 June 2020, 44 systematic reviews, 13 primary studies not included in the reviews and 26 ongoing studies were included.
Hypertension, heart failure, diabetes, arrhythmia, and ischaemic heart disease were associated with the risk of hospitalisation. Hypertension was the most prevalent underlying disease in confirmed hospitalised Covid-19 cases. Pre-existing cardiovascular disease, hypertension, diabetes and cerebrovascular system diseases were associated with increased odds of severe Covid‑19, ICU admission and death.
Preventing Covid-19 infection in those with NCDs and optimising control of NCDs is key in this regard.
Interventions for improving access to food
The number of people globally who don’t have enough food to eat has been increasing since 2015. Food insecurity – a lack of physical, social and economic access to sufficient, safe and nutritious foods – has been further exacerbated by lockdown measures to prevent the spread of Covid-19. These measures restrict people’s movement and ability to work, limiting physical and economic access to food, and disrupt food supply; disproportionately affecting the poor and vulnerable.
A Cochrane review, conducted by researchers from the SA Medical Research Council, SU and international partners, was published in August 2020 and provides a comprehensive evidence base evaluating community-level interventions to improve access to food in low- and middle-income countries (LMICs) by looking at their effect on food security, dietary diversity and nutritional status. The researchers identified 59 studies, mainly in Africa and Latin America, assessing various intervention categories. The body of evidence shows that unconditional cash transfers, such as welfare programmes where money is provided to households, can improve food security, but the team is less certain about the effects of other interventions.
Viral transmission on public ground transport
In response to the Covid-19 pandemic, numerous countries implemented interventionsto minimise the risk of transmission among the public. Evidence was needed to inform public health strategies for limiting transmission on public transport.
The CEBHC, in collaboration with the McMaster University in Canada, conducted a rapid review on interventions that reduce viral transmission on public ground transport. After screening 74 records, including the WHO’s database of “global research on coronavirus disease”, four eligible studies were identified. These studies suggest an increased risk of viral transmission with public transportation use that may be reduced with improved ventilation.
International and national guidelines suggest the following strategies: keep the public informed, stay at home when sick, and minimise public transport use. Where use is unavoidable, environmental control, respiratory etiquette and hand hygiene are recommended, while a risk-based approach needs to guide the use of non-medical masks.
Changes in surgical practices
During the national hard lockdown, hospital surgical practices changed significantly to prepare for Covid-19. Many hospitals implemented measures to prepare for a potential Covid-19 surge. Researchers from the FMHS; Centre for Global Surgery and the Division of Surgery partook in a nationwide study on these changes.
Surgeons were recruited through their professional associations via an online survey. The study focussed on changes in hospital practices around, among others, surgical decision-making, operating theatres, surgical services and the potential long-term effect of these changes. A total of 133 surgeons from 85 hospitals representing public and private hospitals nationwide responded, and the following changes were reported:
84 hospitals (99%) cancelled or reduced non-cancer elective operations; 61 (71,8%) continued all cancer operations; 21 (24,7%) continued only symptomatic cancer operations; and 3 (3,5%) cancelled all cancer operations.
39 hospitals (45,9%) continued the same access; 44 (51,8%) reduced access; and 2 (2,3%) stopped all emergency operations.
Routine postoperative visits were cancelled in 33 hospitals (36,5%) and conducted by telephone or video in 15 (16,6%); 74 hospitals (87,1%) cancelled or reduced new outpatient visits; and 64 (75,3%) reallocated some surgical beds to Covid-19 cases.
In addition, non-emergency operations and clinic visits were drastically reduced or cancelled, surgical wards and operating theatres were reconfigured, and some surgical staff were deployed to other hospital services such as Covid-19 testing, medical/Covid-19 wards, the emergency department and the ICU, or were told to stay at home in order to free up hospital beds and resources for Covid-19 patients.
In conclusion, hospital surgical de-escalation in response to Covid-19 has greatly reduced access to surgical care, which could result in a backlog of surgical needs and an excess of morbidity and mortality. A large backlog of surgical conditions needing care was expected after the peak.
Safer mass sports events
The Covid-19 pandemic brought about an abrupt halt to many forms of physical activity and the sports industry. The FMHS participated in an international project to develop a free online tool to help event organisers to assess and mitigate the Covid-19 risk during mass endurance sports events.
The Infectious Diseases Outbreak Management tool was developed in record time by a group of experts from a number of the world’s leading sports organisations, including World Athletics, the International Cycling Union and the International Institute for Race Medicine. Prof Wayne Derman, Director of the Institute of Sport and Exercise Medicine, was a member of this task force.
The tool is intended to help organisers assess the risk of staging an event, establish the preparedness of the community and the event organisation for the risks of Covid-19, and clarify any necessary steps to further mitigate and reduce the risk.
To use the tool, sports event organisers enter detail about a planned event online, after which a customised report is produced that can assist organisers to make decisions to protect the local community, the participants, the volunteers, the workforce and the staff. The tool recognises the status of the pandemic where the event is taking place, for example whether it is active, receding or subject to additional waves. It is available at idom.worldathletics.org
Working in the time of Covid-19
Since April 2020, occupational therapy, physiotherapy, podiatry, as well as speech-, language- and hearing practitioners in Gauteng public healthcare facilities, have been keeping reflective journals of their Covid-19 experiences and insights as part of a study by the FMHS’ Division of Occupational Therapy.
In addition to the policy-making benefits such evidence holds, a more immediate effect ofthe project has come to light. Participants report regular reflections help them cope with their stress. One describes it as “cathartic”. Reflections show the strain that clinical staff are experiencing. This is illustrated by the following reflection by a departmental head after a confirmed Covid-19 case among their patients:
“Anxiety and fear were the reigning emotions. Staff were convinced they had all had some contact with patient. The irrational thoughts and messages between staff caused such mayhem. Made us aware how fully unprepared we were to deal with the inevitable. It took calm and at some points an authoritarian response to have people actually listen through their fears and understand protocols and procedures. I myself had a sense of hopelessness come over me at some point and needed to take some time just to re-centre and face the onslaught of the fear mongering.”
The Together Project
SU is leading a Covid-19 treatment trial in South Africa called TOGETHER 3, supported by the Bill and Melinda Gates Foundation. The consortium is a tri-alliance with Brazil and the United States, who are conducting TOGETHER 1 and TOGETHER 2 respectively.
The primary research question is to assess the efficacy of experimental interventions to prevent lower respiratory tract infection among non-hospitalised persons with Covid-19 who are at high risk of Covid-19 progression and hospitalisation.
The consortium is prioritising existing therapies that can be repurposed for Covid-19 since they offer more affordable and scalable therapeutic options for LMICs. They are studying the antiretroviral lopinavir-ritonavir and will include additional treatment arms.
The study is being conducted by the FMHS’ Family Centre for Research with Ubuntu and theMolecular Biology Clinical Research Unit.
Promoting adherence to public health interventions in communities
A group of academics and researchers from the FMHS’ Division of Health Systems and Public Health, in collaboration with other medicine and health sciences faculties and departments, have embarked on a project to establish Public Health Research and Innovation Hubs.
Building on a number of social impact activities currently funded by SU, it is envisaged that these hubs will be a locus for co-creating knowledge and for the development of tailored solutions to empower community leaders, members and organisations to promote non-pharmacological public health interventions during the time of Covid-19 and beyond.
The group is building on existing relationships with community members who are leading community-based initiatives in Bishop Lavis and Mitchells Plain.
Using a combination of traditional and contemporary research methodologies, information regarding community needs, approaches and perceptions regarding public health, the social determinants of disease and the Covid-19 response are explored.
Ultimately, it is envisaged that a partnership between SU, the community, the public and other related government sectors and the private sector will be established and that within each community these partners will work with SU to co-create, design and tailor public health innovations and solutions for each community.
Outcome of Covid-19 survivors
During this pandemic it is essential to learn as much as possible through observational studies across a breadth of patient populations and care settings. To this end a multidisciplinary consortium of researchers from SU, the University of Witwatersrand and the University of Namibia have undertaken a study that endeavours to describe the clinical course and outcome of Covid-19 survivors from private and state funded hospitals in Cape Town, Johannesburg and Windhoek.
The study provides data on the functional outcome and health related quality of life of survivors up to six months after discharge. The unique data set will add to the understanding of the disease within our unique context, as well as to the global understanding of the disease.
Understandably, the initial focus of healthcare practitioners and researchers was on the management of the acute disease, and the development of a vaccine. However, as the disease ravaged through communities, researchers needed to start thinking beyond the initial acute pandemic and determine the potential long-term impact of the disease on the outcome of survivors.
Understanding the health consequences and the recovery trajectory of Covid-19 is the first step in the planning of rehabilitation services to ensure optimal functioning and health related quality of life of Covid-19 survivors.
Understanding the need for ongoing rehabilitation of survivors of moderate and severe Covid-19 after hospital discharge, could facilitate the planning and implementation of rehabilitation service provision to patients in South Africa and Namibia.
Experiences of people with disabilities and their organisations
People with disabilities are among the most vulnerable to Covid-19 infection. The rapidly increasing pressure on the health system may leave them even more vulnerable andexcluded. This increases their risk for morbidity and mortality following infection.
Many disabled adults and children have compromised respiration or risk factors for Covid-related mortality, such as cardiac disease, hypertension or diabetes. These and many other concerns necessitate research to understand the effects of Covid-19 on their lives.
Researchers from the FMHS’ Centre for Disability and Rehabilitation Studies and theDepartment of Global Health undertook this study to explore the experiences of organisations for people with disabilities during the pandemic in South Africa, as well as to gather experiences directly from disabled people.
The study was conducted virtually through surveys and interviews. The researchers envisage that it will raise awareness about the needs of disabled people in the context of Covid-19, and assist in ensuring that Covid-19 responses are disability-inclusive and are used to improve planning, practice and policy.
‘We are finding ourselves in extraordinary circumstances – a situation that none of us have been in before. This has brought about unique pressures and we find ourselves in situations of increasing abnormality, and sometimes even chaos. Despite the effects that the pandemic has had on our ability to function normally, we’ve seen great enthusiasm from our staff for research to tackle the pandemic head on.’ – Prof Nico Gey van Pittius