Whither Covid-19? An interview with SA’s chief virus hunter

Whither Covid-19? An interview with SA’s chief virus hunter
Nurses in Tygerberg Hospital's Covid-19 isolation unit during a media tour. (Photo by Misha Jordaan / Gallo Images via Getty Images)

Professor Lynn Morris has a lifetime of experience fighting viruses. In her last 27 years at the National Institute for Communicable Diseases, she has encountered HIV, Ebola, TB, Listeria, Klebsiella and a multitude of ‘lesser’ pathogens. She thinks that Covid-19 presents one of the greatest challenges yet to both South Africa and the world.

On Wednesday, 11 March, Maverick Citizen Editor Mark Heywood met Professor Lynn Morris at her offices at the National Institute for Communicable Diseases (NICD) in Johannesburg to take stock of where we are with regards to Covid-19, what the NICD is doing and what should be the key messages to the country.

South Africa is fortunate to have an NICD and its staff of experts in communicable disease, virology and epidemiology. Strange though it may seem to say, we are also fortunate that we have learnt lessons from the prevention of HIV, Tuberculosis (TB) and most recently, listeriosis. As a result, when in early January 2020, the outbreak of a novel coronavirus in Wuhan, China, caught the attention of health authorities around the world, South Africa had a world-class institution, systems and skilled people ready to kick into overdrive.

Professor Lynn Morris-Interim Executive Director at the NICD. (Photo supplied)

According to Morris, in the wake of the fear of Ebola spreading to SA in 2014, the National Department of Health set up an Emergency Operations Centre (EOC) at the NICD to coordinate and direct the multiple areas required for an effective outbreak response. The EOC acts as a “nerve centre”, with banks of screens, computers and a “real-time” tracking and mapping capacity.

Morris points out that in SA, surveillance – and prevention – will also be aided by the fact that Covid-19 is a notifiable medical condition (fortunately it falls under the category of a “severe pneumonia of unknown aetiology”), meaning that any positive test must by law be reported to the NICD. Case identification will also benefit from the existence of a functioning sentinel surveillance system for influenza that operates every year during the flu season.

“Do you know that 11,000 people died last year of flu and that we have a flu surveillance bulletin?”, she asks me.

I admit not.

Well, we live and learn in a time of Covid-19.

However, although it is in a permanent state of readiness, the EOC can only be activated by the minister of health. It has only been scrambled twice before; once to respond to the Listeria outbreak in 2018 and another time to play a role in contact tracing of patients and their relatives unlawfully removed from the Life Esidimeni hospital.

Faced with the possible arrival of Covid-19 in South Africa, Minister of Health Dr Zweli Mkhize, activated the EOC on 29 January 2020. On 5 March, just over a month later, South Africa’s first case was diagnosed.

We knew it was coming, but according to Morris, this meant that “South Africa has had a relatively good lead time to prepare for Covid-19”. Since 29 January, the staff of the NICD have not been in wait-and-see mode, but preparing furiously and working tirelessly to prepare for the inevitable.

Since then, Morris estimates that almost 3,000 health workers have been trained, including in the private health sector; there has been constant communication with the World Health Organisation (WHO), and the preparation of protocols, case definitions, surveillance systems and guidelines.

This week, for example, the NICD is about to issue three separate Guidelines on Mass Gatherings, Schools, and HIV and TB.

The prevention intervention so far

So, what has happened since March 5th, I ask?

Morris responds that the NICD’s role is primarily around training, laboratory diagnosis, contact tracing, surveillance, treatment and public information. She is careful to point out that she cannot comment on steps that are being taken to ready the health system as a whole.

That said, up to this point, an intensive focus has been containment of Covid-19 to the first group of people diagnosed and, critically, in trying to prevent the onset of “community transmission”.

What this means in practice is that every person who is diagnosed is interviewed as soon as possible in order to begin the process of “contact identification and tracing”. A contact of a confirmed case is automatically considered a Person Under Investigation (PUI), and is phoned, swabbed (that is, a specimen from a person’s throat is taken for testing), and asked to self-isolate for 14 days. On average, each of the 13 cases we had by yesterday (11 March) had up to 20 contacts.

Today that number is up to 17. Tomorrow it will be many more.

But is that going to be enough to prevent secondary transmission? Shouldn’t the focus for testing be wider?

As of 11 March, the government has only reported testing approximately 700 people. Yet, in some countries like South Korea, it appears as if it has been the introduction of mass testing that has been most effective in case identification and thereafter in preventing secondary transmission.

Testing is the key, many people argue.

Morris agrees. She says that there is an aggressive plan to ramp up testing and this includes possibly even establishing mobile testing sites through the National Health Laboratory Service of which NICD is a division. She confirms “there is a link between how much testing you do and your epidemic curve”.

“We have ordered a lot of test kits, but at the moment, we have to focus testing on the people most at risk. If everyone starts wanting a test, even if they are not at risk and show no symptoms, it will clog the system.”

But her answer does contain several prongs.

First, she points out that South Africa has a good system for routine surveillance and that this is happening actively. What that means is that at this moment at health facilities all over the country, as well as at what are called sentinel surveillance sites, doctors and nurses are on the look-out for “influenza like illnesses, severe and acute respiratory illnesses and a change to patterns of illnesses”.

Any person who fits the current NICD/WHO case definition is tested and visited.

Initially, the case definition used by the NICD was anyone who has travelled to Europe or Asia and is displaying symptoms. However, the case definition has now been extended to anyone with a severe respiratory illness.

This week, this routine surveillance has also begun to include testing specimens from these sites for Covid-19.  

At this point, Morris volunteers a bit more information on the test and the virus itself. She says that apart from in China, there is no serological test (a test for the antibodies created in response to a virus), like the standard test for HIV.

Such a test would permit wider screening of the population and will almost certainly be developed in time.

As a result, testing is by what is known as PCR, a molecular test that looks for the genetic material of the virus itself. This can be done at any molecular laboratory and in South Africa we are “fortunate” that, because of the massive scale up of testing for HIV, the PCR test is widely used and available through both the NHLS, and through private laboratories like Lancet and Ampath.

As a veteran Aids activist, I remind Morris that the price of these tests in the private sector (about R1,200), is a barrier to access for poor people. I then ask about their actual cost and how well the NICD is cooperating with the pathology laboratories?

She says that when a person meets the case definition, the test is now being provided free in the NHLS, but is expensive in the private sector. As for the actual cost, that is not something the NICD has calculated yet. I infer that’s because the NICD responds to need, not profit. As for private, she refers me to Lancet for answers on that.   

Know the virus

Public knowledge of the virus itself, Morris stresses, is vital to both prevention and treatment. There is a great deal of misinformation circulating through social media and people should be advised to only use trustworthy sources for information, in this case the NICD and the WHO which has a special, constantly updated, section on the coronavirus outbreak.

So what do we need to know?

“Firstly, we are almost certain that the virus is spread through droplets and not aerosol.” What this means is that if we practice social distancing, keeping up to one-and-a-half metres from a person who may have cough symptoms of Covid-19, we will not be infected.

“Droplets, after being coughed or sneezed, fall to the ground. They do not remain in the air.”

This is also why following other recommendations for infection control is so important. “We can’t shake hands anymore. Use the elbow bump instead. It’s why we should wash our hands regularly and avoid touching our faces. People should cough or sneeze into tissues or their sleeves.”

Believe it or not – until we have a vaccine or treatment – these simple instructions, if followed by millions of people, could prevent millions of infections and save thousands of lives.

It is also important, she emphasizes, that people adhere to public health messages.

“Those with symptoms need to come forward for testing. Those who have been in contact with confirmed cases need to do all they can to isolate themselves and self-quarantine. If that’s impossible because of the overcrowded conditions in which you live, practice infection control and make sure all your family members do the same.” 

Prospects for treatment and a vaccine

Finally, I ask about what we know about the virus itself, the prospects of a vaccine and treatment. I point out that one of the things HIV and the Treatment Action Campaign (TAC) taught us is that people will observe public health messages far better if they have a basic scientific understanding of the science of a disease, how it is transmitted and approaches to its treatment.

Expecting people to follow orders like sheep doesn’t work for health or anything else. TAC called this “treatment literacy”.

Morris confirms that, as we would expect, there is intense scientific investigation going on into Covid-19 and an unprecedented international collaboration. She says that the virus appears to target a particular receptor (ACE2, it’s called), in cells in the lung’s epithelial tissue and – the good news – there does not appear to be much mutation of the virus (which makes it very different from HIV).

She says, it’s important to keep in mind that although nobody in the world has any immunity, and that a portion of infected people get very ill and require life-saving intensive care, about 98% of people recover. “For most people, there’s a very good immune response to it.”

Scientific work on a vaccine is underway; we have the advantage of existing vaccine trials for HIV that can be repurposed for Covid-19; and it’s reasonable to believe a vaccine will be developed. But that will take time – and at this moment, we don’t have time. It’s what we do now that will decide the impact of the first wave of the virus.

As for treatment: “There is a lot of activity. The WHO has held two high-level meetings that South Africa has participated in and has worked furiously to come up with a treatment protocol on hospitalised patients that can be used all over the world.”

“There is also an international trial going on at multiple sites with four arms that are testing various drugs, including an antiretroviral drug, Kaletra, against a placebo. Already, a mechanism has been agreed with the South African Health Products Regulatory Authority (SAHPRA) to fast-track registration of any treatment that emerges.” 

After an hour, our time was up. Morris had to leave for an international conference call on her greatest passion and area of expertise, the search for an HIV vaccine. I owned up to my own moments of panic and asked her how worried she is?

She said that she is an optimist, while admitting that “we are most worried because we don’t know where this is going. We are doing all we can to contain Covid-19 to a few people, but most epidemiologists believe that we will get community transmission and that’s a different ball game.”

“Winter is close, so one of our messages is get a flu vaccine this year. It won’t protect you against the Covid-19, but we don’t want to be dealing with a flu epidemic when our systems may be overrun by this. In the event that there is community transmission, we are going to have to change the way we live.”

That, it would seem to me, is inevitable.

There was life Before Covid-19 (BC) and there will be life After Covid-19 (AC), but the world will be fundamentally changed. But what we do now will determine by how much and at what cost. DM


Lynn Morris is the Interim Executive Director of the National Institute for Communicable Diseases (NICD) and Principal Medical Scientist in the HIV Virology Section, Centre for HIV and STIs at the NICD. She holds a joint appointment as Research Professor at the University of the Witwatersrand and is an Honorary Senior Scientist at CAPRISA and Director of the South African Medical Research Council’s Antibody Immunity Research Unit. She completed her undergraduate studies at Wits University and obtained a DPhil from the University of Oxford in 1988. Morris is an NRF A-rated researcher who has made significant contributions to our understanding of how the antibody response to HIV develops and is responsible for conducting validated end-point assays for HIV vaccine clinical trials. She has been recognised through several awards and has supervised 30 PhD and MSc students, published over 270 papers holding a current author H-Index of 59 and features on the Web of Science list of highest cited researchers in the world.

Valuable Resources:

NICD, Frequently Asked Questions

WHO, Coronavirus outbreak


"Information pertaining to Covid-19, vaccines, how to control the spread of the virus and potential treatments is ever-changing. Under the South African Disaster Management Act Regulation 11(5)(c) it is prohibited to publish information through any medium with the intention to deceive people on government measures to address COVID-19. We are therefore disabling the comment section on this article in order to protect both the commenting member and ourselves from potential liability. Should you have additional information that you think we should know, please email [email protected]"

Please peer review 3 community comments before your comment can be posted


This article is free to read.

Sign up for free or sign in to continue reading.

Unlike our competitors, we don’t force you to pay to read the news but we do need your email address to make your experience better.

Nearly there! Create a password to finish signing up with us:

Please enter your password or get a sign in link if you’ve forgotten

Open Sesame! Thanks for signing up.

MavericKids vol 3

How can a child learn to read if they don't have a book?

81% of South African children aged 10 can't read for meaning. You can help by pre-ordering a copy of MavericKids.

For every copy sold we will donate a copy to Gift of The Givers for children in need of reading support.

A South African Hero: You

There’s a 99.8% chance that this isn’t for you. Only 0.2% of our readers have responded to this call for action.

Those 0.2% of our readers are our hidden heroes, who are fuelling our work and impacting the lives of every South African in doing so. They’re the people who contribute to keep Daily Maverick free for all, including you.

The equation is quite simple: the more members we have, the more reporting and investigations we can do, and the greater the impact on the country.

Be part of that 0.2%. Be a Maverick. Be a Maverick Insider.

Support Daily Maverick→
Payment options