Work on COVID-19

microbiology, virology, epidemiology, surveillance and public health research and training to support government’s response to communicable disease threats.

Professor Cheryl Cohen, who is head of the Centre for Respiratory Diseases and Meningitis at the NICD, explains that the institute does important work in relation to diseases such as pneumonia.

The centre monitors infectious respiratory diseases and meningitis in South Africa.

Prof Cohen manages a team of technologists, scientists, epidemiologists and data specialists.

“We focus on some of the important causes of pneumonia, such as influenza, respiratory syncytial virus and pneumococcus. Many of these diseases are vaccine preventable or have vaccines in the pipeline,” she says.

Much of the work done by the the Centre for

Respiratory Diseases and Meningitis involves building evidence to support vaccine introduction and then monitoring the impact of vaccines on reducing disease if they are implemented, she adds.

The centre also monitors several pathogens that can cause outbreaks, like meningococcus and influenza.

“For this, we need to have ongoing surveillance to be able to detect these early and respond,” says Prof Cohen.

The NICD has played a crucial role in monitoring COVID-19 trends and addressing important questions like how fast the virus spreads, how many people are affected and who is most affected.

“The centre drives surveillance and response for COVID-19 and influenza. We also have an active applied research programme that provides information that informs decision making,” says Prof Cohen.

Research is also conducted to establish how severe the illness caused by different variants is and how effective the interventions used to control illness are.

Omicron variant

In November 2021, the NICD confirmed that the Omicron variant was detected in South Africa following genomic sequencing collaborations between the NICD and private laboratories.

Prof Cohen says this was possible due to the close relationship the NICD has established with many private lab groups in South Africa.

“A lab noticed an unusual signal in the polymerase chain reaction tests and contacted us. We realised we needed to urgently sequence the isolates, which we did,” she explains.

“Once we had analysed the data, we realised it was a new strain with several mutations and so this data was >

rapidly shared with the Network for Genomic Surveillance in South Africa and loaded onto public databases,” she adds.

Prof Cohen says the identification of the new variant confirms that the capabilities of South African scientists are world class.

The institute works with partners within South Africa and globally to ensure ongoing communication and collaboration and sharing of any new techniques to further upskill the NICD scientists so they can make breakthrough findings.

Challenges facing the NICD

If you’re wondering how fatigued Prof Cohen and her team after COVID-19 has kept them occupied for almost two years, her response is: “Seriously, I am exhausted”.

“Fatigue and diminishing resources are our biggest challenges. We need to move to more sustainable systems to monitor COVID-19 as we accept that the disease is here to stay. We need to learn to live with it while limiting the negative impacts,” she says.

Prof Cohen says more than half the work they currently do is COVID19-related.

“We have to continue monitoring other diseases. Cases of other respiratory diseases dropped during the pandemic as a result of non-pharmaceutical intervention.

“But as restrictions relax, there is a real risk of outbreaks because of a gap in immunity as these pathogens have not circulated for two years,” she says.

For these reasons, monitoring other causes of pneumonia and meningitis is particularly important right now.

Regardless of the challenges, Prof Cohen would not trade her job for anything in the world because she finds it endlessly interesting with always something new to do.

“COVID-19 has been difficult, but in some ways this is what every infectious diseases epidemiologist is preparing for – a completely new disease that enables us to use all our established and new surveillance systems, training and experience to understand the patterns of illness. It’s exciting,” she says.

Prof Cohen qualified as a medical doctor from the University of the Witwatersrand and is a Fellow of the College of Pathologists of South Africa in the discipline of microbiology.

She is also an associate professor in epidemiology at the University of the Witwatersrand and obtained an MSc in Epidemiology from the London School of Hygiene and Tropical Medicine in the United Kingdom and a PhD from the University of the Witwatersrand.

In her role at the NICD, she works closely with the South African Department of Health to generate evidence to guide policy for the control and management of respiratory diseases.

Prof Cohen led the establishment of a national surveillance programme for severe acute respiratory infections in South Africa in 2009.

She is also a member of several national advisory committees and several international World Health Organisation working groups, mainly related to influenza and other respiratory viruses.