Flu Season is Here, with Experts Keeping a Close Eye on New Flu Strain

By Elri Voigt
Many regions in the Northern Hemisphere experienced a slightly earlier start to their flu season, driven in some part by a novel variant of influenza A(H3N2). As our flu season also kicks off slightly earlier than usual, Spotlight reports on the detection of this variant in South Africa and what we might expect from this year’s flu season.
As the mercury slowly starts dropping across the country, so does the risk of picking up flu. For many, this might only mean a few days of illness and discomfort, but for some, especially the elderly, it can be life-threatening.
Despite temperatures throughout most of the country remaining moderate so far, this year’s flu season has started, somewhat ahead of schedule. This is according to the National Institute for Communicable Diseases (NICD) in a press release issued on Wednesday.
What we refer to as flu, is commonly caused by one of two types of influenza viruses, influenza A and influenza B. These two are further typed into different lineages, the most common for influenza A is A(H1N1) and A(H3N2) and for influenza B, the B-Victoria and B-Yamagata.
The Yamagata lineage has not been detected since 2020 and is thought to have gone extinct, said Dr Sibongile Walaza. She is a medical epidemiologist and head of epidemiology at the Centre for Respiratory Disease and Meningitis at the NICD.
A key reason why influenza viruses continue to circulate year after year is how fast they mutate and learn to dodge our immune defenses. These mutations eventually result in different subtypes of lineages that are called clades, within which there can be further sub-clades.
It was a sub-clade of the A(H3N2) virus, known as sub-clade K, that led to the flu season starting earlier than usual in some parts of the Northern Hemisphere. The World Health Organization (WHO) reported that the variant was identified in 2025 and spread fast.
“This [sub-clade] contributed to an earlier start to the influenza season in many countries, with several reporting higher‑than‑usual levels of activity. ‘Subclade K’ accounted for the majority of influenza viruses reported across regions,” the WHO stated in a press release.
Sub-clade K was also responsible for an unusual spike in flu cases in South Africa in October and November 2025. Walaza told Spotlight there weren’t enough flu cases detected to cross the seasonal threshold for an additional flu wave, but the increase so late in the year, outside of the typical flu season, was unusual.
Early start
Usually, South Africa’s flu season starts sometime in April or May and spans the winter months, said Walaza, but it is difficult to predict exactly what will happen in any particular year.
This year’s flu season officially started in the second week of March, according to the NICD’s latest report, albeit at a low transmission level for now. 134 samples were tested between 16 and 22 March. Of those, 12 (9%) tested positive for influenza, 12 (9%) were cases of RSV and 3 (2.2%) tested positive for SARS-CoV-2.
In a rather unusual occurrence, the NICD reported that the start of this year’s RSV season coincided with that of the flu season. RSV refers to respiratory illness caused by the Respiratory syncytial virus. The RSV season usually starts before the flu season, but infections can occur all year round.
“The fact that both the flu and RSV seasons are starting at the same time means clinicians could potentially see a high burden of patients with respiratory illness in medical facilities in the coming weeks,” the NICD said in the press release.
Two potential scenarios
Professor Tulio de Oliveira, the director of the Center for Epidemic Response Innovation at Stellenbosch University, said the reality is that we do not know what to expect for this year’s flu season.
“[At]t the moment, we are working with potentially two different scenarios,” he told Spotlight.
The one scenario is that we may be in for a more extreme flu season, he explained, since last year was an unusually mild season and population immunity against the viruses that cause flu may currently be lower. The other scenario, depending on which flu virus circulates, is that South Africa may have some herd immunity because of the unusual spike in flu cases near the end of last year.
In other words, it all comes down to which flu viruses, and their subtypes end up circulating.
“I think this year we’ll have the three influenza lineages [A(H3N2), A(H1N1)pdm09 and influenza B-Victoria] circulating, but in terms of which one is going to be dominant in the season, it’s difficult to tell in advance,” Walaza said.
What we know about sub-clade K
Based on what we’ve seen so far, it does seem that sub-clade K is more transmissible, but it doesn’t appear to cause more severe disease, according to Walaza. De Oliveira added that sub-clade K has between seven and 10 mutations on the surface protein that allow it to bind to a cell’s receptor and enter the body, making it more infectious.
Whether or not it will be the driver of our flu season this year remains to be seen, but Walaza said that within the sporadic cases of flu detected and sequenced so far this year, most of the cases have been sub-clade K. In an NICD report from March, of the 24 influenza samples that were sequenced between 29 December 2025 and 22 March 2026, 11 were confirmed as being sub-clade K.

Experts will be keeping a close eye on circulating flu viruses with real-time genomic surveillance.
“South Africa is considered to be one of the top virus genomic surveillance places in the world,” De Oliveira said. “[A]t the moment, we don’t see a big reason for concern [about the flu season],” he said. “We do genomic surveillance every week, both with public and private laboratories – and if we see anything unusual, that’s going to be highlighted very promptly.”
Trends seen in previous flu seasons
Overall, in the last ten years, influenza A seems to be the driver of the majority of flu cases in South Africa, said De Oliveira, usually causing a big wave of flu cases at the start of the season. This is usually followed by a smaller wave of influenza B cases. In this time period, the influenza A subtype that dominates during the flu season appears to alternate between A(H1N1) one year and A(H3N2) the following year, but it also doesn’t always follow this pattern.
Zooming in more closely, Walaza said that over the last six years, 2020 and 2021 were outliers, with reduced transmission during 2020 due to the measures taken to curb the spread of the SARS-CoV-2 virus and out of season influenza transmission in 2021. Since 2022, the number of people getting flu every year has returned to roughly similar levels as before 2020.
Last year’s flu season was slightly unusual since it had started in late March, according to Walaza, but wasn’t as intense as some of the previous years as transmission remained at a low threshold level. Flu cases peaked in mid-May and then rose again slightly in October and November.
Data on influenza comes from three sentinel monitoring programmes managed by the NICD, which cover both the public and private healthcare sectors, said Walaza. A sample of healthcare facilities in the public sector and doctors in the private sector are asked to supply swabs taken from people with influenza-like illnesses or respiratory illnesses. Some general practitioners in the private sector are also enrolled in a programme called Viral Watch.
She said that the swabs are sent to the NICD laboratory and tested for the presence of different viruses, including SARS-CoV-2, influenza, RSV, parainfluenza, human metapneumovirus and rhinoviruses. If the samples test positive for flu, the sample is further tested to identify the lineage. This data is included in the weekly reports published on their website.
Members of the public can contribute to flu surveillance through an online web platform called CoughWatch. People are invited to enroll and provide weekly information on whether they have symptoms of flu or other respiratory illnesses. This is aimed at picking up trends among people who aren’t necessarily getting sick enough to go to the doctor or clinic, said Walaza and can hopefully serve as an early warning system for increases in respiratory illnesses, including flu.
CoughWatch has already opened for enrollment this year. (More information can be found here).
Flu vaccination uptake in South Africa remains low
Each year, the WHO releases recommendations on what should be in upcoming flu vaccines for the Northern Hemisphere and then later the Southern Hemisphere, usually announced around six months before the start of the respective flu seasons.
This year’s flu shot’s formulation is a trivalent one, said Walaza meaning it contains inactivated strains of all three influenza strains, including coverage for the A(H3N2) sub-clade K. Because it contains an inactivated virus, the vaccine itself cannot give someone the flu.
The level of protection offered by flu shots vary, but generally it ranges in effectiveness against preventing infection from about 30% to 60%. This means the shot will offer most people protection from severe disease and death, but it won’t necessarily prevent them from getting sick with the flu altogether.
One of the things that makes it difficult to predict effectiveness ahead of time is the possibility that a strain might circulate that is not well covered by the flu shot. De Oliveira said this “mismatch” is what we saw play out in some of the regions in the Northern Hemisphere in their last flu season.
Despite the partial mismatch between the vaccine used in the northern hemisphere and sub-clade K, several surveillance reports from the Northern hemisphere show that the vaccine nevertheless provides some protection against severe flu caused by sub-clade K.
The WHO also recently touched on this, saying that: “While current influenza vaccines help reduce the burden of disease, their effectiveness can vary by season, product, and population group. Protection is limited to one season”. The majority of flu vaccines purchased each year are by upper-middle and high-income countries, the WHO noted.
Usually, South Africa’s National Department of Health procures about 1 million flu shots for the public health sector, said Walaza and sometimes not all these doses are used.
While flu shots are made available each year, the uptake of these shots in the private sector appears to be low. Based on data collected through the NICD’s Viral Watch initiative – last year the uptake of the influenza vaccine in the private sector, among those enrolled in the programme, was only around 3.4%. This is based on data collected from 768 people enrolled, of those, 26 had gotten a flu shot. As far as Spotlight could establish, there currently isn’t any routine publicly available data on uptake in the public sector. One study of around a thousand people aged 65 and older, found that just over 32% of them had gotten the flu jab in 2018.
Spotlight asked the National Department of Health how many flu vaccines were procured for this year’s flu season. A response had not been received by the time of publication.
Low flu vaccine uptake can in part be attributed to South Africa having much milder winters and less severe flu seasons than the Northern Hemisphere, said De Oliveira.
Lack of awareness of the flu vaccine can also play a role, according to Walaza. She encourages more education and efforts by healthcare workers to inform at risk groups of the flu shot and when it will be available.
The flu shot is recommended for people who are at risk of severe disease, including older persons, pregnant women, people who are immunocompromised or with chronic medical conditions, as well as healthcare workers. But anyone aged six months and older can get the shot.
“The influenza vaccine will be available in pharmacies from the first week of April. The early start to the season means that this year, the vaccine is only becoming available as the season is getting started, so members of the public who fall into groups at high risk for severe influenza are urged to get their vaccines as soon as possible,” the NICD press release stated.
The potential of next generation flu vaccines
Earlier this year, the WHO released results from an assessment report on the value of having improved flu vaccines. “If improved, next-generation, or universal influenza vaccines are available and widely used between 2025 and 2050, they could prevent up to [an estimated]18 billion cases of influenza and save up to 6.2 million lives globally,” the report stated.
“This assessment makes clear the potential benefits that improved influenza vaccines could offer across different settings,” said Dr Philipp Lambach, WHO technical lead of the project. “It provides all those working on future influenza vaccine investments, policy development and research priorities a common set of evidence to catalyse vaccine development.”
According to the WHO, as of February 2026, there are 46 next-generation influenza vaccines in clinical development.
Republished from Spotlight under a Creative Commons licence.
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