Omicron variant likely born of HIV patient, says South African scientist who discovered it

The variant probably incubated in a person with an immune-compromising condition, according to Centre for Epidemic Response and Innovation’s Tulio de Oliveira

Researchers have already seen coronaviruses with frightening mutations arise in Covid-19 patients whose natural defences have been suppressed

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A lot remains a mystery about Omicron, which has more than twice the number of mutations as the Delta variant. Photo: NIAID via ZUMA Wire/TNS

Published: 5:30pm, 6 Dec 2021

The Omicron variant, now present in at least 23 countries around the world, was probably incubated in the body of a person with an immune system battered by HIV or another immune-compromising condition that can cause a prolonged coronavirus infection, according to the South African scientist who detected the fast-spreading genetic mutant.

Tulio de Oliveira, director of South Africa’s Centre for Epidemic Response and Innovation at Stellenbosch University, said the emergence of Omicron in a patient unable to clear the virus quickly was “the most plausible” origin story for the world’s newest variant of concern.

Researchers in the United States and Europe have seen coronaviruses with frightening mutations arise in Covid-19 patients whose natural defences have been suppressed by drugs to fight cancer, manage autoimmune disorders like rheumatoid arthritis, or keep transplanted organs from being rejected.

Researchers have seen coronaviruses with frightening mutations arise in Covid-19 patients whose natural defences have been suppressed. Photo: AFP

De Oliveira has been warning for months that the people mostly likely to spawn such mutations in Sub-Saharan Africa are the roughly 8 million with unrecognised or poorly treated HIV. Largely young, unvaccinated and with debilitated immune systems, these people could “become a factory of variants for the whole world”, he said.

In June, his team chronicled the emergence of more than 30 genetic changes in Sars-CoV-2 specimens taken from a single South African woman with advanced uncontrolled HIV. The mutations they saw – including several that could erode vaccine protection and boost disease transmission – appeared over a period of six months.

Now de Oliveira worries that a similar scenario might have given rise to Omicron. Last week, he alerted the World Health Organization that his team had detected a variant with dozens of new mutations that was circulating in Gauteng, South Africa’s most densely populated province, and in neighbouring Botswana. The samples the scientists studied were collected between November 12 and November 20.

More than 30 of the mutations they saw were in the code for the crucial spike protein of the virus – the key that picks the lock to human cells and initiates an infection. Many of the changes were familiar to de Oliveira from his study of HIV patients with prolonged coronavirus infections.