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Estimated 85% of Gautengers had COVID-19 at least once before Omicron wave

An estimated 85% of people living in Gauteng had already had COVID-19 at least once before the outbreak of the Omicron wave in late 2021, according to a study in the New England Journal of Medicine.

The immunity from such infection, coupled with the rollout of vaccines to at least one-third of the population, contributed to major decoupling of infections relative to severe COVID-19 during the fourth wave, compared with the three earlier waves, said the researchers.

The study’s lead author, Professor Shabir Madhi, dean of the Faculty of Health Sciences and professor of vaccinology at Wits University, and executive director of Wits VIDA, said that the survey, the second since March 2020, was important to establish the force of infections in South Africa, since the first survey showed that the recorded cases presented a severe underestimation of the true state of the outbreak. This was because there had not been enough testing, he told Daily Maverick.

“These findings indicate that we have reached a turning point in the pandemic, even in countries with a modest uptake of vaccines but where there has been a high force of natural infection, which has resulted in a massive loss of lives,” he said.

This also means that despite breakthrough infections or reinfections having probably been common during the Omicron wave, immunity induced by vaccine or past infection generally protected well against severe COVID-19 disease, hospitalisation, and death.

The aim was to determine sero-positivity against SARS-CoV-2 before the fourth wave of COVID-19, in which the Omicron variant was dominant, said Madhi. Sero-positivity measures for the presence of antibodies against the virus as a metric of past infection – in this case, the SARS-CoV-2 virus.

The study analysed data provided by collaborators at the National Institute for Communicable Diseases (NICD) on trends in recorded COVID-19 cases, hospital admissions and deaths since the start of the pandemic, complemented by COVID-19 attributable death rates evaluated using excess mortality data from the South African Medical Research Council (SAMRC).

Dry blood spots from 7,010 randomly selected individuals in Gauteng were tested to determine sero-positivity.

Notable findings were:

• Sero-positivity ranged from 56.2% in children younger than 12 to 79.9% in individuals older than 50
• At a sub-district level, sero-positivity was as high as 85% in the inner city, densely populated areas
• Sero-positivity was 68% in unvaccinated individuals and 93% in vaccinated individuals.

These data indicate that although less than 1m cases of COVID-19 had been recorded when the sero-survey was completed in Gauteng, this represented less than 10% of the 10.4m people imputed to having been infected by the virus at least once since the start of the pandemic and before the Omicron wave.

‘Hybrid immunity’

The study found that although only one-third of the population in Gauteng had received at least a single dose of COVID-19 vaccine before the Omicron wave, the data suggested that most of the vaccinated individuals also had natural infection-induced immunity (ie, hybrid immunity). Extensive protection against severe COVID-19 was also prevalent in unvaccinated individuals, based on using sero-positivity as a proxy for presence of protection against severe COVID-19.


The analysis of trends in COVID-19 cases, hospitalisation and death rates over the course of the pandemic reported major decoupling of incidence of infections relative to COVID-19 hospitalisation and death during the Omicron dominant wave, compared with earlier waves.

Notably, compared with the Delta-dominant third wave in SA – which contributed to 44% of COVID-19 hospitalisations and 50% of deaths since the start of the pandemic in Gauteng – the Omicron wave only contributed to 10% hospitalisations and 3% of deaths.

The decoupling was also evident in people older than 50, among whom 61% had received at least a single dose of the vaccine before the Omicron wave, who had contributed to more than 80% of COVID-19 deaths in SA.

In the older than 50 years age group, only 2% of deaths since the start of the pandemic in Gauteng occurred during the Omicron wave, whereas 53% occurred in the Delta variant dominant wave, which transpired when vaccine roll-out had only belatedly started in SA.

A turning point

Madhi says that in South Africa, 490 people per 100,000 have died of COVID-19. This puts South Africa in the top 10 countries globally of COVID-19 fatality rates.

“When excess deaths are factored in, three times the official figure of 97,000 people in South Africa have died of COVID-19. The actual number of deaths from COVID-19 in South Africa is closer to 300,000 people,” he says.

Vaccinate to maximise immunity

The findings have significant implications for Africa, a continent where vaccines and resources to support vaccine rollout are limited and where hospitalisation for COVID-19 severely constrains public health facilities and resources.

“Our study's findings necessitate a recalibration of not only how we deal with the pandemic, which appears to be at its tail end, but also how we make the most efficient use of vaccines across Africa where only approximately one-tenth of the population have received at least a single dose of the vaccine,” says Madhi.

“The focus of COVID-19 vaccine rollout in countries with low coverage has to be primarily targeted at achieving more than 90% in high risk groups, rather than some percentage of the population – considering that the majority have inadvertently developed protection against severe infections in countries such as SA, after natural infection.”

Vaccines, however, still have an important role to play in people who have past infection, as other studies have recently shown that such hybrid immunity (i.e., induced by a combination of vaccine and past infection) induces a more robust and broader repertoire of immune responses that would heighten protection even against mild COVID-19, and reduce the infectiousness compared with immunity induced by natural infection or vaccines alone.

“Also, high risk individuals need the full series of vaccines to optimise their individual protection against severe COVID-19, even if previously infected by SARS-CoV-2,” says Madhi.

He told Daily Maverick: “If we know how many people were infected it helps us to understand the future risk of resurgences and the trajectory of the pandemic. I wasnʼt surprised at all by these results.”

Study details
Population Immunity and Covid-19 Severity with Omicron Variant in South Africa

Shabir Madhi, Gaurav Kwatra, Jonathan Myers, Waasila Jassat, Nisha Dhar, Christian Mukendi, Amit Nana, Lucille Blumberg, Richard Welch, Nicoletta Ngorima-Mabhena, and Portia Mutevedzi.

Published in New England Journal of Medicine on 23 February 2022

The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified on November 25, 2021, in Gauteng, South Africa. Data regarding the seroprevalence of SARS-CoV-2 IgG in Gauteng before the fourth wave of coronavirus disease 2019 (Covid-19), in which the Omicron variant was dominant, are needed.

We conducted a seroepidemiologic survey from October 22 to December 9, 2021, in Gauteng to determine the seroprevalence of SARS-CoV-2 IgG. Households included in a previous seroepidemiologic survey (conducted from November 2020 to January 2021) were contacted; to account for changes in the survey population, there was a 10% increase in the households contacted, with the use of the same sampling framework. Dried-blood-spot samples were tested for IgG against SARS-CoV-2 spike protein and nucleocapsid protein with the use of quantitative assays. We also evaluated COVID-19 epidemiologic trends in Gauteng, including cases, hospitalisations, recorded deaths, and excess deaths from the start of the pandemic through January 12, 2022.

Samples were obtained from 7010 participants, of whom 1319 (18.8%) had received a Covid-19 vaccine. The seroprevalence of SARS-CoV-2 IgG ranged from 56.2% (95% confidence interval [CI], 52.6 to 59.7) among children younger than 12 years of age to 79.7% (95% CI, 77.6 to 81.5) among adults older than 50 years of age. Vaccinated participants were more likely to be seropositive for SARS-CoV-2 than unvaccinated participants (93.1% vs. 68.4%). Epidemiologic data showed that the incidence of SARS-CoV-2 infection increased and subsequently declined more rapidly during the fourth wave than it had during the three previous waves. The incidence of infection was decoupled from the incidences of hospitalisation, recorded death, and excess death during the fourth wave, as compared with the proportions seen during previous waves.

Widespread underlying SARS-CoV-2 seropositivity was observed in Gauteng before the omicron-dominant wave of COVID-19. Epidemiologic data showed a decoupling of hospitalisations and deaths from infections while Omicron was circulating.


NEJM study – Population Immunity and Covid-19 Severity with Omicron Variant in South Africa (Open access)


Daily Maverick article – ‘Measures to prevent infection failed’ – study finds 85% of Gauteng residents were likely infected in first three Covid-19 waves (Open access)


See more from MedicalBrief archives:


SA cohort study shows reduced chance of death or severe illness with Omicron


Discovery Health’s large real-world analysis of Omicron


Natural immunity offers ‘robust protection’ in severe Omicron – Qatar study


Infection + vaccination delivers better protection than immunisation only — Large US study



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