Immunisation has and continues to save millions of lives and to prevent much suffering and disability. (Photo: Shutterstock)News & Features
13th October 2025 | Elri Voigt
Childhood immunisation programmes have saved many millions of lives and prevented much suffering. Yet, immunisation programmes have lost momentum over the last decade or so. In this #InTheSpotlight special briefing, Spotlight unpacks the available data and considers how immunisation efforts might be revitalised.
Polio, a viral infection that targets the nervous system, used to be one of the most feared diseases in the world. But the development of an effective vaccine in the 1950s changed everything.
Today, most countries are considered polio-free, with the exception of two regions in Afghanistan and Pakistan, says leading vaccine expert Professor Shabir Madhi, the Dean of the Faculty of Health Sciences at Wits University.
This victory along with the global eradication of smallpox, another highly contagious and often deadly viral infection, is testament to the effectiveness of immunising children against illnesses. In fact, Madhi says immunisation is “considered to be one of the most cost-effective health interventions”, second only to access to potable water.
For every $1 invested in immunisation, the return on investment is around $20, says Madhi, citing this 2021 study.
The reason for that, he says, is that when you’re vaccinating children and increasingly adolescents and adults, you are not only protecting against disease, but also improving longevity, cognitive function, and the likelihood of people moving forward as being productive members of society. “It’s all about a healthier being leading to a healthier future,” he says.
The World Health Organization (WHO) estimates that globally between 3.5 to 5 million lives are saved because of vaccines every year.
How it works
In a nutshell, explains Madhi, vaccines work by training the immune system to recognise specific pathogens, either a virus or bacteria. This allows the immune system to mount a quicker, more effective attack against the pathogen than it would when exposed to it for the first time through natural infection.
Immunity against disease does occur naturally, he says, as our immune systems learn to fight against pathogens when we are exposed to them throughout our lifetimes. The first time the body is exposed to a virus or bacteria, the immune system will identify it as a “foreign invader”. The body then produces antibodies and special cells called cytotoxic T-cells, which attack the foreign cells to eventually get rid of them completely.
Babies are born with an “immature immune system”, meaning their immune system has never encountered the bacteria and viruses that cause disease and so it doesn’t know how to fight those yet. Some protection is provided in the first few weeks of life from antibodies babies get from their mothers. But when these fade, the baby is susceptible to illnesses.
Madhi says relying on a baby or young child to get infected with a virus or bacteria naturally is a gamble that “comes at a cost”. While many children may get mildly ill or not get sick at all, there will be those that get severely ill and possibly die.
“You can’t guess which individuals are going to develop severe disease and which individuals might have a mild infection,” he says. “So, it doesn’t make too much sense, unless you are prepared for a good number of children to die, to wait for children to become immune to infection [naturally].”
There are many types of vaccines. Innactivated vaccines, for example, use a dead version of the pathogen (virus or bacteria), live-attenuated vaccines use a much weakened form of a pathogen, other types of vaccines contain only small parts of the relevant pathogen – the common aim is to show the immune system what a specific germ looks like and teach it how to fight it, without the risk of illness.
The immune system, once exposed to components of a pathogen through a vaccine, is then able to form antibodies against it and develop special memory cells that reminds it of what to do when it encounters that virus or bacteria again. “In doing so, [the immune system is] trained in a safe manner, and it’s trained in such a way that it can mount a rapid response to its foreign invading pathogens and consequently prevent infection with those pathogens progressing to severe disease,” explains Madhi.
Many vaccines are given as a combination dose, meaning one shot will protect against several diseases at once. For some vaccines, multiple doses are needed to allow the immune system to develop the adequate number of antibody and memory cells. These memory cells and antibodies work together to help the body fight the pathogen in question.
When someone is exposed to a pathogen they have been vaccinated against, the memory cells help speed up the immune system’s antibody production. Madhi says this can happen within one or two days, as opposed to the three to four weeks it would take if that person hadn’t been vaccinated or never exposed to the pathogen before.
What vaccines do children get in SA?
In South Africa’s public health sector, Madhi says we are immunising children against 12 different diseases – including both viral and bacterial ones. These are polio, Hepatitis B, rotavirus, tetanus and diphtheria, pertussis, haemophilus influenza B, pneumococcus, measles, mumps, and rubella. Children are also vaccinated against tuberculosis, but the protection provided by this vaccine eventually fades.
For most of the diseases we vaccinate against, Madhi says, the highest burden is in the first one to two years of life.
If the national guidelines are followed, by the time a child is 18-months-old, they are considered fully vaccinated against those 12 diseases, with the option of receiving some boosters. These translate to 14 vaccine doses between birth and 18 months. In the private sector, children are often given additional vaccines like those for chicken pox and hepatitis A.
Most school aged girls are offered vaccination against several strains of Human papillomavirus, a virus that can cause cervical cancer.
Then there are also several vaccines recommended for pregnant women – to protect them from illness and providing antibodies that can be passed to their babies to protect them in the first few weeks of life. As Spotlight recently reported, government is considering whether or not to start providing a vaccine given to pregnant women that protects their babies from RSV. RSV is the single most important cause of hospitalisation as well as the dominant cause of lower respiratory tract infections in young children, Madhi points out.
How are immunisation programmes measured?
Measuring the performance of childhood immunisation programmes is not a simple matter of whether individuals are immunised or not. This is because children receive several vaccines, and multiple doses of some vaccines, all over a period of around 18 months. A few key markers of programme performance have however crystalised.
Madhi says the general benchmark internationally is the percentage of children who have received all three doses of the DTP vaccine – a combination jab that protects against Diphtheria, Tetanus and Pertussis (sometimes referred to as DTP3). The first and second doses of the measles vaccine are also commonly used to measure how well immunisation programmes are doing – these are referred to as MCV1 and MCV2.
In South Africa, children are given four doses of the Hexavalent vaccine, which is a six in one combination against diphtheria, tetanus, pertussis, polio, Haemophilus influenzae type b and hepatitis b in the first two years of life. This is our benchmark instead of DTP3, and is referred to as HEXA4. In South Africa, by the time a child is 18-months-old, they should among others have received four doses of the Hexavalent vaccine, and two doses of the measles vaccine.
The WHO’s target coverage for DTP3, or HEXA4 in the case of South Africa, is 90% or higher. For MCV2 it is 95% or higher. The National Department of Health says the target coverage rate for all childhood vaccines by 12 months is 90%.
Global trends
A study published in The Lancet medical journal in July looked at immunisation data between 1980 and 2023. Broadly, it noted two trends that have played out on a global scale. The first was that between 1980 and 2023 global coverage of the key vaccines against many childhood diseases nearly doubled.
But, secondly, these long-term trends don’t give the full picture, because coverage gains slowed between 2010 and 2019 in several countries, including some high-income countries. The COVID-19 pandemic made the problem worse, with sharp declines in coverage, which has still not returned to pre-COVID-19 levels.
Another leading immunisation report, the WHO/UNICEF joint estimates of national immunization coverage (WUENIC) for 2024, found that globally some progress has been made in several countries compared to the year before, but coverage is still far from where it should be.
“Compared to 2023, around 171 000 more children received at least one vaccine, and one million more completed the full three-dose DTP series. While the gains are modest, they signal continued progress by countries working to protect children, even amid growing challenges,” the WHO said in a press release.
However, around 20 million infants missed at least one dose of a DTP-containing vaccine in 2024, and around 14.3 million children never received a single dose of any vaccine. (Spotlight previously reported in detail on the WUENIC immunisation coverage estimates for 2023.)
From improvement to stagnation in SA
South Africa’s public immunisation programme, known as the Expanded Programme on Immunisation (EPI), was only introduced in 1994, says Madhi. Since then, there have been “massive improvements in vaccine coverage”. In fact, South Africa largely led the introduction of new, life-saving vaccines on the African continent.
The bad news is that over the last 10 to 15 years, these gains have stagnated, and current vaccine coverage is far from satisfactory, Madhi says. We hover at just under 75% for DTP3 and about 82% for the measles second dose, according to the latest WUENIC data – far below the WHO targets of 90% and 95% for these two indicators.
Government mostly uses administrative data to measure immunisation coverage. Essentially, the National Department of Health looks at the number of vaccines that have been distributed to healthcare facilities across the country and then uses Census SA data to get an estimate of how many children have been born. Using those two parameters, the department then estimates vaccine coverage.
However, Madhi warns, this kind of data has some limitations. To do this properly, you need an accurate denominator and confirmation of whether all vaccines issued to facilities are actually being used. At best, Madhi says the administrative data currently is providing a “crude measure” of vaccine coverage.
He suggests a better way of measuring immunisation coverage would be to have an electronic register that links a unique patient identifier (a kind of health ID number) to vaccinations received. This will help “adequately map” immunisation coverage and help identify areas where there might be under immunisation.
In the absence of such a register, the next best thing is a vaccine coverage survey, although such surveys can be very expensive to run. South Africa’s last such survey was conducted in 2018-2019. That survey found that only 76.8% of children received all age-appropriate vaccines from birth to 18 months – well below the National Department of Health and WHO’s targets.
Zero-dose children
Concerningly, the survey also noted that 4.3% of children were completely unvaccinated – a group referred to as zero-dose children. According to the 2024 WUENIC report, South Africa had an estimated 278 000 zero-dose children in 2023.
Outside of an immunisation coverage survey, Madhi says it is difficult to measure how many zero-dose children South Africa really has. This is because zero-dose children are for instance much more likely than other children to have little or no contact with the health system and are thus less likely to be reflected in official health records.
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Immunisation coverage, and zero-dose children in particular, is sometimes described as a “canary in a mine” for the healthcare system. As Madhi explains, if there are zero-dose children, it “means your basic primary healthcare is failing”. A big part of primary health is preventative healthcare, and so “if you can’t get something right as basic as making sure that children are vaccinated, it means that we’ve got massive problems”.
Global decline in vaccine confidence
Since the beginning of the COVID-19 pandemic, there has been an overall decline worldwide in the percentage of people who perceive vaccines as important for children. This is according to an analysis by UNICEF based on a 2022 study by the Vaccine Confidence Project.
East and Southern Africa, which saw a drop in vaccine confidence during the peak of the COVID-19 pandemic, mostly rebounded by 2022. By comparison, South Africa’s rebound was much less “dramatic”, according to Francine Elvia Ganter Restrepo, a Regional Social and Behavior Change Specialist for UNICEF Eastern and Southern Africa.
This decline in vaccine confidence, she says, is likely tied to “the political discourse around vaccines at the time of the [COVID-19] vaccine rollout and the proliferation of misinformation”.
But mistrust in vaccines has clearly outlived the COVID-19 pandemic in some places. Maybe most notably, the United States Secretary of Health and Human Services Robert F. Kennedy Jr. has in recent months made controversial changes in a critical United States vaccine oversight body and to the direction of clinical research. Many of these changes seem motivated by a distrust in the established science on vaccines.
Reasons children in South Africa are not getting vaccinated
While vaccine scepticism is a factor, Madhi and other experts we’ve spoken to are clear that it is not the key driver of South Africa’s low immunisation rates.
“Some of the major challenges is not necessarily, reluctance or lack of education, [or] lack of knowledge on the part of parents on the importance of vaccines – but rather the challenges that parents face in getting their children vaccinated,” says Madhi.
These include structural issues at primary healthcare facilities, like vaccines being out of stock, long queues, and clinics often not being open over weekends, causing parents to become disillusioned with the system. Travel to and from clinics to get all the various jabs is also unaffordable for some.
Madhi says that children are more likely to not be vaccinated when they have a teenage mother, or a mother who has not received more than a primary school level education and is living in a rural setting.
So what do we do?
For Madhi, the first place to start to address South Africa’s stagnating immunisation rates is to have “robust systems in place” to track vaccine coverage. “You can’t fix the problem until you’re able to measure the problem. And right now, we’re not in a position to adequately measure the problem in real time to then develop strategic interventions,” he says.
He suggests setting up an electronic vaccine registry, much like the one that was in place during the COVID-19 vaccination campaigns. This registry should have every healthcare facility that offers vaccinations connected to it, and data on the actual vaccines administered can be upload by nurses – hopefully replacing the paper-based systems still widely in use. For all this to work, there needs to be robust data systems in place with unique patient identifiers.
Having access to this kind of data in real time would let us keep an eye on districts and sub districts that are underperforming, says Madhi, and help us to identify why immunisation targets aren’t being reached – for example by linking lower vaccination rates to vaccine stockouts. Once you know why children aren’t getting vaccines, he says, targeted interventions can be developed.
Changes should also be made to the country’s immunisation strategy, suggests Restrepo. This could include making sure that any updates come with money set aside for demand creation and dealing with service delivery challenges.
The coming years
If South Africa remains on its current trajectory, Madhi reckons the likely scenario is that we’ll keep seeing more of the type of outbreaks we’ve seen over the last decade or so. These include outbreaks of measles, diphtheria, and whooping cough. Apart from the financial cost of treating these illnesses, they can also result in disability, and in some cases deaths.
This is a sobering prospect, especially in a country where we already have an underfunded and overburdened public healthcare system.
The Lancet study projects three future scenarios for immunisation coverage. As you can see in the graph above of projected DTP3 coverage, the potential trajectories diverge substantially.
As we’ve reported at Spotlight over the last few years, the COVID-19 pandemic and associated disruptions caused an abrupt decline in the number of children in South Africa getting the vaccines they need. The push by the National Department of Health to catch-up on those missed doses deserves some credit.
But zoom out a bit and the picture is bleak. The massive progress of the first decade or so after the end of apartheid has given way to stagnation well below the levels that both the WHO and our own health department says we need to reach.
It is tempting to blame vaccine scepticism for this stagnation, but as Madhi and several other experts have explained, other factors are playing a bigger role in South Africa. As with HIV and other health issues, how far people live from clinics, how long they have to queue once there, and how they are treated by healthcare workers all impact how likely they are to come back. To get a child fully vaccinated typically requires at least seven clinic visits if you look at the Road to Health booklet mothers are given in the public sector.
If low vaccination rates are a symptom of the dysfunction in much of our public healthcare system, then the difficult work of addressing that general dysfunction will have to be part of the solution. That is work that can and must continue.
But as with TB and HIV, our immunisation programme also needs more time in the spotlight and for our health leaders to pay more attention to it. Should the political will be there to take immunisation more seriously, better tracking of immunisation data and intervening in underperforming areas seems sensible first priorities. Hopefully it is an issue Health Minister Dr Aaron Motsoaledi and our provincial MECs for health will take up.
Ultimately, as we’ve shown in the special Spotlight briefing, immunisation has and continues to save millions of lives and to prevent much suffering and disability. Madhi is right that it is one of the most effective types of health interventions we have. It is a moral imperative that we make full use of its massive potential to improve people’s lives.
*Reviewed by Professor Shabir Madhi. Spotlight takes full responsibility for any errors.
