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COVID-19 virus SARS-COV-2, ARN enclosed in protein shell COVID-19 B.1.1.529 South Africa strain 3d renderingCredit: CIPhotos/ iStock/Getty Images Plus

South African scientists have found early signs of an increased risk of reinfection associated with the Omicron variant of SARS-CoV-2, providing epidemiological evidence for the new variant’s ability to evade immunity from prior infection.

An analysis of routine surveillance data from South Africa from 4 March 2020 to 27 November 2021 show that the reinfection risk profile of Omicron is substantially higher than that associated with the Beta and Delta variants during the second and third waves. These findings were released on the pre-publication platform,, on 2 December 2021.

Anne von Gottberg, a clinical microbiologist at the Centre for Respiratory Diseases and Meningitis at South Africa’s National Institute for Communicable Diseases, said it was still difficult to determine the reinfection rate, but that early modelling indicated a higher rate.

At a press briefing hosted by the World Health Organization (WHO) late last week, Gottberg said that insights from cases recorded so far in the country implied that vaccination could still be effective in protecting people against severe illness caused by Omicron infection.

Omicron, first detected in Botswana and South Africa, is the latest source of fear and uncertainty in the global fight against the COVID-19 pandemic. It has resulted in the introduction by several countries in the Global North of travel restrictions on people travelling from Africa.

Peter van Heusden, a bioinformatician at the South African National Bioinformatics Institute (SANBI), told Nature Africa that the variant “seems to be quite widespread already which means the travel bans really make little sense.”

Oyewale Tomori, a professor of virology and chairman of Nigeria’s Ministerial Expert Advisory Committee on COVID-19, told Nature Africa that the next few days would “provide more time for scientists to fill the gaps needed for better understanding of the disease and appropriate control.”

Tracking Omicron

According to the WHO Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE), in recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. Omicron has been described as having more than 50 mutations out of which the virus’ spike protein alone, responsible for the entry of the virus into host cells, contains more than 30 mutations. Similarly multiple mutations across the virus genome have been reported for the variant.

Many of the new mutations in Omicron are not yet well characterized and have not been identified in other circulating variants. More studies are needed to determine the mutations’ effect on the capacity of the virus to transmit, on vaccine effectiveness and immune response, and disease outcome.

The development also has a potential effect on testing. The WHO noted that while current SARS-CoV-2 PCR diagnostics continue to detect this variant, several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure). This test could therefore be used as a marker for this variant, pending sequencing confirmation.

Progressive efforts in South Africa

In May 2020 South Africa established Network for Genomic Surveillance South Africa (NGS-SA), a vast network of academic institutions, private labs and the National Health Laboratory Services (NHLS), to respond to the pandemic It performs research on genomics, virology, clinical aspects of the disease, diagnostics, vaccines and prior infection.

Willem Hanekom, director of the Africa Health Research Institute (AHRI) in KwaZulu-Natal, South Africa, and a NGS-SA leader said the clinical profile of the variant was still unknown. “Some people say the disease is less severe, but we have to be very careful, we will only know in about two weeks,” he said.

Gottberg explained 249 genome sequences were done so far in South Africa after the discovery and 183 is positive for the Omicron variant, at the time of interview with Nature Africa. “Cases will increase exponentially, and there is a system in place to check for reinfections,”.

Marietjie Venter, Head of the Zoonotic Arbo and Respiratory Virus Programme at the Centre for Viral Zoonoses, Department Medical Virology, University of Pretoria, South Africa observed that Omicron cases in some countries had no link to South Africa, suggesting it had already been circulating wider and went undetected elsewhere.

Venter said: “Each of the previous waves were caused by a different variant in South Africa which outcompeted the previous variant. The high level of natural population immunity after each wave suggests that natural immunity does not last long, or does not provide good protection against the next variant.”

Abdou Salam Gueye, WHO Regional Emergency Director for Africa, said only 102 million people in Africa (7.5% of the population) has been fully vaccinated. “More than 80% of people have not had a single dose.”