Health experts expect this year’s flu season in South Africa to be far less severe than flu seasons prior to the Covid-19 pandemic, but more severe than last year.

The National Institute of Communicable Diseases (NICD) says that reduced transmission of the influenza virus over the past two years has led to waning immunity against flu, and with the relaxation of Covi-19 restrictions it is likely there will be more flu cases this year compared to 2021.

But more cases don’t necessarily mean an immediate return to pre-Covid-19 levels.

Shabir Madhi, Professor of Vaccinology at the University of the Witwatersrand, explains that although it is difficult to accurately predict what will happen during this flu season, “we can take some lead from what is happening in the northern hemisphere”.

He says the flu season in the United States, which is now tailing off, has been substantially less severe than in pre-pandemic seasons. The United States Centers for Disease Control and Prevention reports that for the 2021 to 2022 flu season 2,000 to 5,800 deaths occurred and between 3.5 million and 5.8 million people had flu illnesses. 

This is a massive drop from the 2019 to 2020 flu season which caused between 39 million and 56 million flu illnesses, and 24,000 to 62,000 deaths.

Madhi says the exact reason for the massive drop in cases and deaths in the United States still remains unknown. 

“It might still be related to limited mobility of people, particularly intercontinental travel. This is an important feature in terms of recirculation,” he says.

Added to this, Madhi says physical distancing, masking and other interventions would have assisted in interrupting flu transmission. 

“It’s difficult to predict but we probably will see a worse flu season compared to 2020 to 2021 when we virtually had no flu. But I still feel optimistic that we will have a relatively modest flu season compared to pre-Covid flu seasons,” he says.

Responding to written questions Professor Cheryl Cohen, head of the NICD Centre for Respiratory Diseases and Meningitis and Dr Sibongile Walaza, an epidemiologist at the centre say, “most flu cases are never tested and diagnosed so we do not know the full numbers in South Africa. We do surveillance at specific sites in South Africa and flu circulation in 2020 and 2021 has been lower compared to previous years.”

The influenza virus is usually imported from the northern hemisphere and then starts circulating in South Africa around May/June. But it can also subside and then come back around August. 

“There is less chance of the flu virus being imported into South Africa with less travel. As human mobility increases, there is likely to be an uptick in flu cases,” Mahdi says.

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Importance of vaccination

The NICD recommends that people at high risk of getting severe influenza illness or complications take the flu vaccine. It says the flu jab remains the primary means to prevent influenza infection and to reduce risk of severe illness. The NICD website also advises that to prevent being infected with flu you need to wash your hands frequently with soap and water or an alcohol-based hand rub and avoid contact with sick people.

Groups targeted in the Department of Health’s 2022 influenza vaccination campaign are healthcare workers, individuals aged 65 or older, individuals with cardiovascular disease (including chronic heart disease, hypertension, stroke and diabetes), chronic lung disease (including asthma and chronic obstructive pulmonary disease) and individuals living with HIV, as well as pregnant women.

With less flu transmission during the Covid-19 pandemic, immunity to the flu virus will have waned which is why it is essential immunocompromised individuals get the flu vaccine, says Madhi. 

There are an estimated 17 million people in South Africa who are considered to be priority groups for vaccination. 

“But less than 10% of these people actually get vaccinated because not enough vaccine is procured and there is not a culture of people taking up flu vaccines,” says Madhi.

Matching vaccines to flu strains

“But in addition to the immunity gap, it’s also extremely difficult to predict the characteristics of the next strain that circulates,” Madhi explains. “That’s one of the reasons the flu vaccine used in the northern hemisphere has had almost no effectiveness against the current flu virus because it’s a mismatch between what is circulating and what is included in the vaccines.”

In the northern hemisphere, where the flu season is coming to an end, the current flu vaccines performed “poorly”, according to Madhi.

Influenza mutates frequently and the efficacy of flu vaccines are dependent on how well they protect against the circulating virus strains. New flu vaccines have to be made every year in order to reflect the mutations and different strains of the virus around the world.

This year’s strains and vaccines

Of the flu strains detected in South Africa, influenza A, particularly, and B are the most transmissible. Through the NICD influenza monitoring system, the influenza virus strains identified to date have been the usual seasonal influenza B strain with the Victoria and Yamagata lineages and influenza A with subtypes H3N2 and H1N1.

According to Cohen and Walaza the trivalent vaccine covers all three important types of influenza A/H1N1, A/H3N2 and B/Victoria. In addition to the strains covered in the trivalent vaccine, the quadrivalent vaccine also covers the B/Yamagata strain. 

In 2022, the trivalent vaccine is available in the public sector and the quadrivalent vaccine is available in both the private and public sectors. The vaccines are free in the public sector to high-risk individuals.

They say the updated guidelines are that Covid-19 vaccines can be administered at the same visit as a flu jab. Opposite arms should be used for the two vaccines. 

How well do the flu vaccines work?

Cohen and Walaza agree with Mahdi that flu vaccine performance varies each year depending on how well the strain in the vaccine is matched to the strain which circulates. 

“We do not know what strains will circulate this year. Vaccine performance is usually evaluated after the season,” they say.

Most countries in the northern hemisphere are now using the quadrivalent vaccine with the H3N2 strain dominating their flu season. Genetic drift within the strain itself determines how well the vaccines work. 

Mahdi says, “the reality is that the quadrivalent vaccine has very little value and more so now since the pandemic where the Yamagata lineage of the B strain has largely disappeared.”

He adds that the inclusion of the Yamagata and Victoria lineages in the vaccine has “limited public health value”, had more to do with “marketing than anything else” and “doubled the price of the vaccine”. 

Mahdi is “pessimistic”, given the experience in the northern hemisphere, that the vaccines will do much better in South Africa this year. 

“Fortunately, it’s going to be offset by us having a relatively attenuated flu season again this year,” he says.

The efficacy of the vaccines changes depending on the season and on how closely the vaccines match with the strains that end up circulating. “It can be anything between 10% and 80%. Unfortunately, it is currently sitting closer to 10% than 80%,” he says. 

Respiratory syncytial virus

Meanwhile, South Africa is experiencing its worst outbreak in 10 years of respiratory syncytial virus (RSV) which is the most common cause of bronchiolitis and lower respiratory tract illness among young children. It is highly contagious and infection with RSV does not result in permanent or long-term immunity and re-infections can occur.

“This year has been a particularly severe season. At the moment the positivity rate for RSV in children being admitted to Chris Hani Baragwanath Hospital is 60%,” says Madhi. 

According to the NICD, in 2022 so far RSV has been detected in 19% (105/529) of children aged <5 years, hospitalised with lower respiratory tract illness at sentinel pneumonia surveillance sites. The details of which are summarised in the weekly respiratory pathogens surveillance report.

The number testing positive for RSV among children aged <5 years started to increase in week 5 (week ending 13 February) and continues to increase, with 35% (28/81) and 32% (24/74) of children hospitalised with LRTI at sentinel sites in week 9 (week ending 6 March) and 10 (week ending 13 March) testing RSV positive, respectively. DM/MC

This article was published by Spotlight — health journalism in the public interest.