What South Africa must do to prepare for the third wave double whammy of Covid-19 and flu this winter

What South Africa must do to prepare for the third wave double whammy of Covid-19 and flu this winter
(Photo: EPA-EFE / Johan Nilsson)

Pandemic preparedness for the third wave of Covid-19 must include a strong influenza prevention strategy, including vaccination.

First published in the Daily Maverick 168 weekly newspaper.

Over the past year, SA has been ravaged by Covid-19. To date, more than 1.5 million cases and more than 50,000 deaths have been confirmed. The true number of cases is likely to be more than 10 million, and we know that unexplained deaths, most of which are due to Covid-19, sit well above 100,000. With ongoing community transmission and subsequent error-prone viral replication, new variants of SARS-CoV-2 will probably emerge and may favour further transmission.

None of us knows when the third wave will hit, but most of us in public health and science believe our Covid-19 vaccination roll-out will not be quick enough to prevent this, nor subsequent waves. If the next wave coincides with the winter respiratory virus season, particularly a seasonal flu epidemic, a double whammy will hit South Africa and its health system.

Influenza kills about 10,000 people of five years and older each year in South Africa, a relatively small number compared with the past year’s Covid-19 deaths but still a heavy toll. Furthermore, worldwide, it causes between three and five million cases of severe illness and 290,000 to 650,000 deaths.

Like SARS-CoV-2, flu is transmitted by hitching a lift on droplets from our upper respiratory tract, and by people transferring virus-carrying droplets by hand from surfaces to their nose, mouth and eyes. Therefore, like Covid-19, it is prevented through masking, physical distancing, avoiding poorly ventilated indoor areas, good hand hygiene and isolating when symptoms occur, coupled with testing. The latter is especially important since the clinical illness is very similar to Covid-19.

Perhaps not surprisingly in 2020, in SA and abroad, we registered very few confirmed cases of influenza, for several main reasons. First, the ultimate form of physical distancing – a hard lockdown – started just as the flu season began. The winter season usually starts in the Western Cape, as do other winter respiratory viral outbreaks. Indeed, a National Institute for Communicable Diseases memo from 9 April 2020 reported an increase in influenza cases in the province from late February to the end of March 2020. This mirrored what we were seeing in our hospitals, with severe cases admitted to intensive care in the first months of the year. However, during and following lockdown, flu cases disappeared, so the hard lockdown seems to have helped in cutting off transmission routes for the illness. Lockdown also meant prolonged school closures, and as children are an important base for intense flu transmission, this reduced transmission.

However, when lockdown was lifted we didn’t see a flu resurgence. This has more to do with just the effect of a lockdown. As already highlighted, like SARS-CoV-2, the flu virus is spread by respiratory droplets, so masks, physical distancing, hand hygiene, among other measures, in all likelihood helped avoid a winter flu epidemic in 2020.

Last, because of the fear of a double whammy, a strong push for flu vaccination uptake was made in 2020. The World Health Organisation recommends that nationally determined high-risk populations should be vaccinated against flu, and SA publishes yearly updates on which groups should be prioritised. A prioritisation process is necessary since fewer than one million doses are procured annually. High-risk groups include pregnant women (at particular risk of severe influenza pneumonia), people with HIV and other causes of immune suppression, people with chronic lung, neurological or cardiac disease, metabolic diseases such as diabetes and morbid obesity, the elderly (65 and older) and healthcare workers. The number of people in SA who should be vaccinated against influenza is in the tens of millions, but we can only work with the supply we have. Furthermore, as we are seeing with Covid-19, vaccine hesitancy or a perceived lack of risk means some vaccine doses are unused.

The absence of a hard lockdown in 2021, the recent move to Level 1, the return to school and our poor compliance with public health protection measures before the second Covid-19 wave mean SARS-CoV-2 might be joined by flu as winter approaches.

What can you do to prevent the double whammy of Covid-19 and flu? First, continue to comply with public health interventions that have become part of our everyday lives. Second, avoid poorly ventilated indoor areas where people are gathered, which are fertile ground for superspreader events. Third, if you are in one of the risk groups for serious complications of influenza, get vaccinated against flu and Covid-19 as soon as you can.

There is no indication that flu and Covid-19 vaccines interfere with each other. For pragmatic reasons and seeing that mild reactions to the vaccines may occur for both, it’s probably best to space Covid-19 and influenza vaccines by two weeks.

Influenza vaccine is an inactivated vaccine that instructs your immune system to recognise influenza virus in future, protecting you from serious disease. Owing to changes in the structure of the influenza virus over time, current influenza vaccines need to be given every year. Adverse events from influenza vaccine are rare and predominantly entail some tenderness at the injection site and, in some persons, symptoms like a cold in the first 48 hours following vaccination. This is not due to you being infected with influenza, as the vaccine is not able to cause infection. Rather, the symptoms that some people experience relate to their immune system doing its job and supercharging itself for action. As influenza vaccines are produced in eggs, persons with egg allergy should not have the inactivated influenza vaccine but should rather discuss the option of an alternative influenza vaccine that is not produced in eggs.

Pandemic preparedness for the third wave of Covid-19 demands that cognisance be taken of the potential harm that the added stress of a seasonal flu epidemic could do to our health system and the population living in SA. Now is the time to strengthen prevention measures and avoid mass gatherings, and for high-risk groups to get vaccinated with the imminent arrival of the flu vaccine in SA and its roll-out. DM168

Marc Mendelson is a professor of infectious diseases at Groote Schuur Hospital and the University of Cape Town.

This story first appeared in our weekly Daily Maverick 168 newspaper which is available for free to Pick n Pay Smart Shoppers at these Pick n Pay stores.


"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]"

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