COVID-19: Considerations, controversies and challenges in South Africa

06 May 2020 | Story Carla Bernardo. Photo Michael Hammond. Read time 7 min.
Leading tuberculosis researcher Professor Keertan Dheda was invited to contribute to a special COVID-19 issue of the “Wits Journal of Clinical Medicine”.
Leading tuberculosis researcher Professor Keertan Dheda was invited to contribute to a special COVID-19 issue of the “Wits Journal of Clinical Medicine”.

Celebrated University of Cape Town (UCT) researcher Professor Keertan Dheda recently co-authored an article on the approaches, techniques and controversies associated with the diagnosis of the Coronavirus Disease 2019 (COVID-19).

The article, “Diagnosis of COVID-19: considerations, controversies and challenges in South Africa”, forms part of a special COVID-19 issue of the Wits Journal of Clinical Medicine, published in late April, and was co-published with editorial permission in the African Journal of Thoracic and Critical Care Medicine.

Dheda’s co-authors are his colleagues from the Centre for Lung Infection and Immunity (CLII), based at the UCT Lung Institute, doctors Shameem Jaumdally, Malika Davids, Phindile Gina, Anil Pooran, Edson Makambwa, Ju-Wei Chang and Ali Esmail; Lancet Laboratories’ Professor Eftyxia Vardas; and Stellenbosch University’s Professor Wolfgang Preiser.

 

“This information will likely translate into better patient outcomes and improved control of the epidemic.”

In the article, Dheda and his co-authors outline an approach to considering the diagnosis in those who present with respiratory symptoms, address challenges such as those posed by disease stage and costs, the complex laboratory infrastructure required for different types of tests, and the challenges in obtaining specific types of biological samples. They also provide an overview of the different types of tests and technologies that can be used for detecting COVID‑19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Dheda, head of the CLII, explained that because diagnostics of COVID‑19 is part of a “rapidly changing landscape”, this kind of collaboration by researchers and institutions is important for the development of better and more streamlined methods for the diagnosis of the disease.

He added that more sensitive and reliable frontline tests, which are less costly and less complicated, are needed. The utility of different testing approaches, such as genomic versus antibody-based tests, also needs to be unravelled, and completely new approaches to diagnosis need to be developed.

“This information will likely translate into better patient outcomes and improved control of the epidemic,” said Dheda.

Specific considerations

He explained that there are many infectious and non-infectious causes of shortness of breath when patients present to healthcare facilities. In some of these cases, this may be due to non-infectious causes. In others, this may be due to pneumonia, which has several causes such as influenza, other viral pathogens, bacterial pneumonia and tuberculosis (TB).

“In our setting, TB remains an important cause of acute lower respiratory tract infection, otherwise called pneumonia,” he said.

“Given the limited testing capacity, a clinical approach is required to select patients for COVID-19 diagnostic testing.”

But specific considerations concerning COVID‑19 pose some challenges.

An example of this is that close contacts of those with COVID-19 might contract the disease but might not have any symptoms. Alternatively, Dheda explained, symptoms may develop, but patients do not require hospitalisation or respiratory support; this is known as early-stage disease.

 

“The diagnosis can be missed, and repeat testing may be required.”

In this early phase, genomic tests, which detect the genetic material of the virus, have a false negative rate of between 30 and 40%.

“The diagnosis can be missed, and repeat testing may be required,” said Dheda.

He added that the genomic test, also known as reverse transcription polymerase chain reaction (RT-PCR), remains the frontline diagnostic test for symptomatic persons, but it requires complex laboratory infrastructure and a turnaround time of a few hours. The genomic test is therefore not generally a rapid point-of-care (POC) test which can produce a result within a short space of time at the site where treatment or care-related decisions are made.

Approaches and platforms

Newer POC genomic platforms have also been developed, including tests developed by companies like Abbott and Cepheid. The latter’s GeneXpert testing platform is especially relevant to South Africa because there is already widespread and established infrastructure to use these types of test cartridges.

A test cartridge is a ‘lab in a matchbox’, which enables a biological sample to be inserted into a small cartridge containing all the ingredients for a PCR reaction.

“There is a fully automated platform that can determine whether a patient has TB, COVID‑19, or influenza – depending on which test cartridge is used,” Dheda explained.

He added that the cartridge can be used in portable battery-operated systems that they have been using in scalable mobile clinics.

“We will be using this approach for community-based testing in the Klipfontein and Mitchells Plain districts of Cape Town,” he added.

Further challenges

A further challenge is obtaining biological samples; it is a trade-off between convenience and sensitivity, Dheda said.

Using sputum samples is associated with much higher test sensitivity, but these samples are more complicated to obtain and are associated with higher infection control risks. In contrast, obtaining nasopharyngeal samples – from the back of the upper part of the nose – is associated with less infection control risks, but sensitivity is lower.

Dheda said that a completely different type of technology detects antibody responses to the SARS-CoV-2 virus. In response, various testing platforms and devices have emerged; many are rapid POC tests and are cheap and convenient to use.

However, these platforms and devices have their problems. He explained that many of these tests may be falsely negative in those who are symptomatic in the early phase, the first week, of the disease.

“Exactly how to combine the POC antibody-based tests and the genomic tests are currently the subject of intensive research,” he said.

 

“We are also unsure whether everyone develops an antibody response robust enough to protect them when exposed to infection again.”

The antibody-based tests are useful for surveillance studies and generating ‘immunity passports’, which may be useful for determining who receives the vaccine, or whether essential or frontline workers can return to their jobs.

But, said Dheda, the concept of immunity passports has not yet been validated, and whether having COVID‑19 once renders somebody immune and at very low risk of a second infection remains unclear.

“We are also unsure whether everyone develops an antibody response robust enough to protect them when exposed to infection again,” he said.

It remains to be seen whether SARS-CoV-2 disappears within a year or two like the SARS outbreak in 2003, or whether it will evolve, resulting in recurrent waves of infection like what happens with influenza.

“Only time will tell.”


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UCT’s response to COVID-19

COVID-19 is a global pandemic that caused President Cyril Ramaphosa to declare a national disaster in South Africa on 15 March 2020 and to implement a national lockdown from 26 March 2020. UCT is taking the threat of infection in our university community extremely seriously, and this page will be updated with the latest COVID-19 information. Please note that the information on this page is subject to change depending on current lockdown regulations.

Minister of Health, Dr Joe Phaahla, has in June 2022 repealed some of South Africa’s remaining COVID-19 regulations: namely, sections 16A, 16B and 16C of the Regulations Relating to the Surveillance and the Control of Notifiable Medical Conditions under the National Health Act. We are now no longer required to wear masks or limit gatherings. Venue restrictions and checks for travellers coming into South Africa have now also been removed.

In July 2022, the University of Cape Town (UCT) revised its approach to managing the COVID-19 pandemic on UCT campuses in 2022.
Read the latest document available on the UCT policies web page.

 

Campus communications

 
2022

Adjusting to our new environment 16:50, 23 June 2022
VC Open Lecture and other updates 17:04, 13 April 2022
Feedback from UCT Council meeting of 12 March 2022 09:45, 18 March 2022
UCT Council
March 2022 graduation celebration 16:45, 8 March 2022
Report on the meeting of UCT Council of 21 February 2022 19:30, 21 February 2022
UCT Council
COVID-19 management 2022 11:55, 14 February 2022
Return to campus arrangements 2022 11:15, 4 February 2022

UCT Community of Hope Vaccination Centre

On Wednesday, 20 July, staff from the University of Cape Town’s (UCT) Faculty of Health Sciences came together with representatives from the Western Cape Government at the UCT Community of Hope Vaccination Centre at Forest Hill Residence to acknowledge the centre’s significance in the fight against COVID-19 and to thank its staff for their contributions. The centre opened on 1 September 2021 with the aim of providing quality vaccination services to UCT staff, students and the nearby communities, as well as to create an opportunity for medical students from the Faculty of Health Sciences to gain practical public health skills. The vaccination centre ceased operations on Friday, 29 July 2022.

With the closure of the UCT Community of Hope Vaccination Centre, if you still require access to a COVID-19 vaccination site please visit the CovidComms SA website to find an alternative.

 

“After almost a year of operation, the University of Cape Town’s (UCT) Community of Hope Vaccination Centre, located at the Forest Hill residence complex in Mowbray, will close on Friday, 29 July 2022. I am extremely grateful and proud of all staff, students and everyone involved in this important project.”
– Vice-Chancellor Prof Mamokgethi Phakeng

With the closure of the UCT Community of Hope Vaccination Centre, if you still require access to a COVID-19 vaccination site please visit the CovidComms SA website to find an alternative.


Thank You UCT Community

Frequently asked questions

 

Global Citizen Asks: Are COVID-19 Vaccines Safe & Effective?

UCT’s Institute of Infectious Disease and Molecular Medicine (IDM) collaborated with Global Citizen, speaking to trusted experts to dispel vaccine misinformation.



If you have further questions about the COVID-19 vaccine check out the FAQ produced by the Desmond Tutu Health Foundation (DTHF). The DTHF has developed a dedicated chat function where you can ask your vaccine-related questions on the bottom right hand corner of the website.

IDM YouTube channel | IDM website
 

 

“As a contact university, we look forward to readjusting our undergraduate and postgraduate programmes in 2023 as the COVID-19 regulations have been repealed.”
– Prof Harsha Kathard, Acting Deputy Vice-Chancellor: Teaching and Learning

We are continuing to monitor the situation and we will be updating the UCT community regularly – as and when there are further updates. If you are concerned or need more information, students can contact the Student Wellness Service on 021 650 5620 or 021 650 1271 (after hours), while staff can contact 021 650 5685.

 

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