recently published South African study set out to determine sero-positivity against SARS-CoV-2 before the fourth wave of COVID-19, in which the omicron variant was dominant. Sero-positivity measures the presence of antibodies against the virus; it indicates past infection. The study focused on Gauteng, the country’s economic hub. Ozayr Patel asked Shabir Madhi to unpack the results and explain why the findings suggest that South Africa has reached a turning point in the pandemic.

What we found

The results show the levels of sero-positivity – in other words what percentage of people have antibodies to the virus – among just over 7,000 people from whom samples were taken. From these results the following rates were calculated:

  • In those under 12 years of age, none of who received a COVID-19 vaccine, 56% showed presence of antibodies to SARS-CoV-2

  • In those over 50 it was 80%, including 70% if unvaccinated and 93% if vaccinated

  • In high density inner city areas the sero-positivity prevalence was 85%

Using the seroprevalence data, together with COVID-19 attributable deaths using excess mortality data from the South African Medical Research Council, the study was also able to impute the risk of dying following infection by SARS-CoV-2 prior to the Omicron wave in South Africa. This infection fatality risk for COVID-19 was 0.57% pre-omicron in Gauteng. This is substantially higher than 0.019% imputed for seasonal flu, which infected one-third of the population each year pre-COVID, calculated using similar methods.

Vaccination coverage: We discovered high levels of hybrid immunity: that is immunity gained from a combination of previous infections plus vaccinations.

At the time of the onset of the omicron wave, 36% of people in Gauteng had at least one dose of the vaccine. This was higher – 61% – in those over the age of 50. (This cohort was responsible for more than 80% of deaths pre-omicron.)

Based on sero-survey, 70% of vaccinated people were also infected pre-omicron. Hence they would have had substantial hybrid immunity, which has been shown to induce a broader repertoire of immune responses against the virus. Such hybrid immunity in South Africa has, however, come at the cost of loss of 300,000 lives based on South African Medical Research Council excess mortality estimates. These are three-fold higher than the official recorded number of deaths.

Based on another study, the hybrid immunity is expected to confer greater protection against infection and mild COVID-19 compared with immunity only from vaccine or natural infection.

Hospitalisations and death rates: Our study also analysed the temporal trends in COVID-19 cases, hospitalisations and deaths (recorded and COVID attributable from excess mortality) from the start of the pandemic up until the tail end of the Omicron wave. The study found a massive decoupling between the number of people becoming infected with the virus relative to COVID hospitalisation and death rates during the course of omicron compared with earlier waves. This was true across all adult age groups.

The omicron wave was associated with 10% of all hospitalisations since the start of the pandemic, whereas 44% of hospitalisations had transpired during the course of the Delta variant wave. More impressively, only 3% of COVID deaths since the start of the pandemic occurred during the omicron wave, compared with 50% during the delta dominant wave.

The findings of decoupling of infections and severe or fatal COVID-19 were similar in the 50-59 year age group. In this group the omicron wave contributed to 15% of recorded COVID hospitalisations and 2% of deaths since the start of pandemic. This compares with 46% of hospitalisations and 53% of deaths occurring in the third wave, dominated by delta. The data for people over 60 years old was similar.

The survey also found that 58% of children under 12 years of age (all unvaccinated) were sero-positive. They were not more heavily affected during the Omicron wave.

The delta dominant wave which was the most severe in South Africa, coincided with South Africa’s belated COVID vaccine rollout. The high death rate during that wave is an indictment of the missed opportunities that could have prevented a large percentage of the deaths which transpired. In particular, the delayed procurement and roll out of COVID-19 vaccines in South Africa, as well as the ill-informed decision to against the WHO recommendation on the continued use of the AstraZeneca vaccine which was available to in South Africa when the Beta variant was circulating in South Africa.

In summary, the omicron wave contributed to less than 5% of all COVID-19 deaths in Gauteng. Since the start of the pandemic, the delta variant wave contributed to 50% of all of the deaths. The balance is split roughly equally between the first and second waves caused by ancestry and the beta variant.

Our findings also show that natural infection has been high and is playing a major role in how the pandemic has unfolded especially in countries with low to moderate COVID-19 rollout. These high levels of infections have, however, resulted in a massive loss of lives; which to date is likely under-estimated in low and middle income countries as shown from the South African data.

What the findings tell us

The findings indicate that South Africa is moving into the convalescent phase of the COVID pandemic – the recovery phase. This is likely to be the same in other countries with low or modest vaccine uptake, but high force of past infections. As such, South Africa needs to recaliberate its approach to the pandemic and to start managing it as we would do for other respiratory infections which too cause large number of hospitalisations and deaths.

There are still a few unknowns. Another resurgence is likely, and there might well be another variant. But it would be very surprising if further variants are able to evade the T-cell arm of the immune system which is stimulated by vaccines and natural infection. The T-cell (cell mediated immunity) arm of the immune system, appears to be the main mediator of protecting against severe COVID-19, even when there are breakthrough infections in vaccinated people or reinfections.

So why do I believe that we are at the tail end of this pandemic? It depends what metric you use. If it’s about infections, we’re not at the tail end. If it’s about the number of deaths that will transpire from COVID-19 during 2022, relative to the number of deaths that will transpire from other preventable causes of death in countries such as South Africa, then I believe the country has pretty much arrived towards the end of this pandemic.

In South Africa about 10,000 to 11,000 people die of seasonal influenza every year. In 2019 tuberculosis killed 58 000 in 2019. But we are not declaring an emergency in South Africa to deal with flu or tuberculosis. Deaths from HIV, and complications from HIV, are about 70,000. But South Africa isn’t shutting down the country to prevent deaths and infections from these diseases.

Now what?

Only 12% of people across the continent have received one dose of vaccination. The implications of our findings are that:

  • Vaccine coverage must be enhanced by ensuring that adequate booster doses are given to those who require it. We might need to continue boosting. This might need to be on an annual basis for the next two to three years, especially for high risk individuals. The time line for this is until we have more experience on the durability of protection of vaccines, particularly in settings with a high prevalence of hybrid immunity (where protection may be even longer lasting. )

Campaigns should be focused primarily on high risk groups, including getting over 90% of people over 50 years of age vaccinated before the next resurgence anticipated. This should be the focus rather than the current arbitrary target of vaccinating 40%-70% of the population.

  • It’s still beneficial to expand vaccinations in settings with high sero-positivity. Studies on hybrid immunity show this delivers more robust and broader repertoire immune responses that could heighten protection against infection, and reduce the magnitude of future resurgences.

  • It’s also important that key non-pharmacuetical interventions are kept in place. This includes wearing masks in crowded poorly ventilated indoor places, and particularly high risk individuals when there is an increase in virus transmission activity.

Our findings support the optimism expressed at the beginning of 2022 in South Africa that a turning point had been reached in the pandemic. Many in high income countries dismissed this view as not applicable to their settings despite high vaccine coverage. But their experience has since generally aligned with South Africa’s.

Read more: South Africa has changed tack on tackling COVID: why it makes sense

Lastly, better COVID vaccines are required. But the world is no longer at “code red”. And it’s time to rebuild livelihoods, economies and all other facets of life that were affected over the past two years. This is particularly true in fragile low and middle income countries.

Source : The Conversation


When South Africa's hardy yet overworked health system shifted to address the COVID pandemic, the work of diagnosing people with HIV - and maintaining contact with those who already have the virus - was neglected.

As the Omicron variant continues to sweep the world, registering a record number of infections in Japan, Russia and Romania amongst others, the country where the strain was first documented is now preparing to bid it goodbye.

Omicron was first picked up by technicians in a laboratory in South Africa. A few weeks later, a handful of doctors at the main hospital in the country's capital, Pretoria, provided the first analysis of its behaviour after admitting dozens of new COVID patients.

It was at that point that Steve Biko Academic Hospital's Dr Fareed Abdullah told the world that Omicron was not like the variants which fuelled previous waves.

Live COVID updates from UK and around the world

From John Sparks South Africa copy


The strain was highly infectious but it was significantly less likely to put people in hospital - or cost them their lives. Major studies in the UK and US on the severity of the disease have confirmed these initial observations made in South Africa.

"Are we closer to the end of this wave than the beginning?" I asked.

"The data is showing that we're right at the end of the wave, our case rates are almost where they were pre-wave level, we really have a view now of the whole wave and can describe it properly," said Dr Abdullah, as he stripped off his protective garments outside the hospital's ICU ward.

Yet there is another issue now concerning this clinician and the rest of the medical community in South Africa.

Seroprevalence surveys indicate that more than three-quarters of the population have already generated immunity from previous COVID-19 infections - one reason why Dr Abdullah and others think the fall-out from Omicron was relatively mild.

However, there is one group who are thought to be at particular risk - any of the millions of people in South Africa who suffer from weakened immune systems, like those with HIV.

HIV is a key public health concern in South Africa with an estimated eight million people (13% of the population) living with the disease. There is tried and tested medicine for this, called antiretrovirals. It keeps HIV at bay, thereby allowing the body's immune system to function normally. But patients need to take the medication consistently.

When South Africa's hardy yet overworked health system shifted to address the COVID pandemic, the work of diagnosing people with HIV - and maintaining contact with those who already have the virus - was neglected.

Steve Biko Academic Hospital's Dr Fareed Abdullah
Image:Steve Biko Academic Hospital's Dr Fareed Abdullah

Public health organisations like Right to Care estimate that some 3.6 million have either gone undiagnosed or are not currently on a consistent antiretroviral regime.

"In South Africa, we want to make sure that more and more people with HIV get into treatment so they don't fall into that category, but in my humble opinion, that is where the epidemic is shifting now," says Dr Abdullah.

Finding and reintegrating those carrying the HIV virus into the system is just one part of the challenge however.

New strains could evolve

Early on in the pandemic, scientists discovered that the immunocompromised tend to suffer from particularly long and severe COVID infections with prolonged periods of infectiousness.

In addition, work done by scientists in Durban has shown how COVID can mutate inside the bodies of those with untreated HIV. In one case, they traced a coronavirus sample to a 36-year-old HIV patient who was struggling to adhere to her antiretroviral treatment regime. Over the course of her seven-month COVID infection, the virus acquired 32 mutations.

The risk is clear. New variants of concern could evolve - and be transmitted - by those with weakened immune systems.

"It means a major reorganisation of the health service because these people are difficult to find. How do you make the diagnosis in these people? But that is where modern medicine has to take us, rapidly," says Dr Fareed Abdullah.

In a town called Klerksdorp in South Africa's North West Province, health workers are trying to re-establish contact with dozens of HIV patients who have fallen off the local health authority's radar.

From John Sparks South Africa copy
Image:New variants of concern could evolve - and be transmitted - by those with weakened immune systems

'I was so sick'

A 40-year-old woman called Sylvia van Wyk stopped taking antiretroviral tablets two years ago - and when she picked up COVID, she couldn't get rid of it.

"I was so sick, I couldn't do nothing, nothing at all, my mum was there for me, she was washing me, feeding me, I couldn't do nothing for myself, nothing," she said.

Sylvia had COVID for three agonising months but when she re-started her HIV treatment, her body fought the virus off.

"Why did you stop taking (your antiretrovirals)?" I asked.

"Truly speaking, I was entertaining too much, I was entertaining, I wasn't taking care of my health," she said.

South African scientists warn that it is crucial that people like Sylvia continue to take their HIV treatments for fear of the development of some, "really nasty variants," in the words of one leading figure.

It will require a determined pivot from an already-exhausted health service but our collective health may depend on it.

Source : Sky News

ABUJA, Dec 13 (Reuters) - Nigeria will destroy around one million expired COVID-19 vaccines, Faisal Shuaib, head of the National Primary Health Care Development Agency (NPHCDA), said on Monday, adding his agency was working with drug regulator NAFDAC to set a date for their destruction.

Nigeria's health minister Osagie Ehanire said last week some COVID-19 doses donated by rich Western countries had a remaining shelf life of only weeks, adding to the country's challenges in vaccinating its people. read more Fewer than 4% of adults in Africa's most populous nation of over 200 million have been fully vaccinated.

Shuaib said the country had been accepting vaccines with short shelf lives from international donor nations in an attempt to use them quickly and provide some level of protection for Nigerian due to vaccine scarcity in the past.

Shuaib said Nigeria will no longer accept vaccines with a short shelf life, citing a presidential committee decision.

Last week, Reuters reported that around one million COVID-19 vaccines were estimated to have expired in Nigeria last month without being used. read more

Still, the World Health Organization's vaccine director Kate O'Brien said in a briefing on Thursday the proportion of wasted doses is smaller in countries receiving doses through COVAX than in many high-income countries. read more

DAKAR, Dec 13 (Reuters) - At least 200,000 COVID-19 vaccines have expired in Senegal without being used in the past two months and another 200,000 are set to expire at the end of December because demand is too slow, the head of its immunisation programme said on Monday.

African governments have been calling for more COVID-19 vaccines to help catch up with richer regions, where vaccine rollouts have been humming along for more than a year.

Yet, as the pace of supply has picked up in recent weeks some countries have struggled to keep pace. Logistical problems, the short shelf life of vaccines that arrive from donors, and vaccine hesitancy have all kept doses from reaching arms.

Up to 1 million COVID-19 vaccines expired in Nigeria last month, Reuters revealed.

"The main problem is vaccine hesitation," said Ousseynou Badiane, who is in charge of Senegal's vaccine rollout. "The number of cases is decreasing. They ask: 'why is it important to get vaccinated if the illness is not there now'?"

The majority of the expired doses were made by AstraZeneca (AZN.L) and supplied via COVAX, the dose-sharing facility led by the GAVI vaccine alliance and the WHO, he said.

Low vaccination rates in Africa will help prolong the pandemic and raise the risk of new variants emerging, such as the Omicron variant that was first identified in southern Africa and Hong Kong and is now spreading in many countries.


Senegal has recorded more than 74,000 COVID-19 infections and 1,886 deaths, far below the numbers seen in many nations hit harder by the virus. The pace of infection has dropped off since a third wave in July spurred a spike in vaccine demand. The country occasionally records no new daily cases.

But apathy hurts the vaccination drive. Senegal has administered nearly 2 million doses of vaccines so far, Reuters data shows, enough to fully vaccinate only about 5.9% of the population.

It is currently vaccinating between 1,000 and 2,000 people per day, Badiane told Reuters, down from 15,000 during the summer. At this pace, it cannot use all the vaccines it has.

"We are not optimistic" about using the other 200,000 doses before they expire at the end of the month, he said. "We don't expect any demand increase before then."

Part of the problem is the short shelf life of vaccines that arrive from donors that include the United States and China. Senegal refuses to take vaccines with a shelf life shorter than three months, but even that creates difficulties.

Badiane hopes the government can introduce some kind of restrictions on the unvaccinated to drive up inoculation rates, including the use of a health pass as many other countries have done.

"Without the restriction, the population will not get vaccinated," he said.