Over the past year, South Africa has been ravaged by Covid-19. To date, more than 1.5 million cases have been confirmed and more than 50,000 deaths. The true number of cases is likely to be more than 10 million, and we know that the 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 five years and older (21.6 per 100,000 person years) 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 to five million cases of severe illness and 290,000 to 650,000 deaths. 

There is no indication that flu and Covid-19 vaccines interfere with each other, but because both might cause mild reactions, it’s probably best to separate them by two weeks. 

Like SARS-CoV-2, influenza 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 by 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 South Africa and abroad, we registered very few confirmed cases of influenza for three 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 from the radar, so the hard lockdown seems to have played a role in cutting off transmission routes for the illness. Lockdown also meant prolonged school closures, and because children are an important base for intense flu transmission, this reduced transmission. 

However, when lockdown was lifted we didn’t see an influenza resurgence. This is not just due to 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 influenza vaccination uptake was made in 2020. The World Health Organisation recommends that nationally determined high-risk populations should be vaccinated against flu and South Africa publishes yearly updates on which groups should be prioritised. Prioritisation 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 South Africa 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 mean 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 influenza and Covid-19 as soon as you can. 

There is no indication that flu and Covid-19 vaccines interfere with each other, but because both might cause mild reactions, it’s probably best to separate them by two weeks. 

The flu vaccine is inactivated, which means it instructs your immune system to recognise the virus in future, protecting you from serious disease. Due to changes in the structure of the virus over time, current vaccines need to be given every year. Adverse events from the jab are rare and predominantly entail some tenderness at the injection site and, in some people, cold-like symptoms in the following 48 hours. This is not due to influenza infection as the vaccine cannot cause infection. The symptoms relate to the immune system doing its job and supercharging itself for action. Because flu vaccines are produced in eggs, people with egg allergy should not have the inactivated shot and discuss an alternative (live-attenuated). 

Third-wave preparedness demands an awareness of the potential harm to the population and health system from a seasonal flu epidemic. Now is the time to strengthen prevention measures, avoid mass gatherings and for the high-risk groups to receive the flu vaccine, which will be rolled out in South Africa from March. DM/MC

Marc Mendelson is a Professor of Infectious Diseases at Groote Schuur Hospital and the University of Cape Town.