The South African scientists tracking the new coronavirus variant believe it probably evolved in a patient with HIV/Aids with a chronic Covid-19 infection.
If so, it will not be the first time a variant has emerged in a patient with a long-running Covid infection, scientists told the The Telegraph. In fact, many experts believe it could be how some of the other variants sprang up, including alpha, the first global "variant of concern", which emerged in Kent last autumn.
Across the world, scientists have traced the virus evolving in immunocompromised patients with months-long Covid infections.
Patients with untreated HIV or other conditions that weaken the immune system - such as cancer, for example - can struggle to see off Covid, leaving their body fighting the virus for prolonged periods. They effectively act as an evolutionary training gym for the virus to mutate to find new ways around their immune responses.
The difference in South Africa is the sheer numbers of people this potentially covers: 8.2 million South Africans are infected with HIV and only around 71 per cent of adults, and 45 per cent of children, are on treatment, leaving a large pool of people vulnerable.
Professor Richard Lessells, an infectious diseases expert at the KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), part of the team that first alerted the world about the spread of the new B.1.1.529 variant, said it is likely that the new variant was incubated in an untreated HIV/Aids patient.
"It doesn't seem to have emerged from a normal evolutionary process," Prof Lessells told The Telegraph. "There's been an evolutionary jump. This hasn't evolved from the delta variant."
Prof Sharon Peacock, Director of COG-UK Genomics UK Consortium, and Professor of Public Health and Microbiology, University of Cambridge, said this genetic difference was the clue - as it had also been with alpha.
“The genetic difference of B.1.1.529 has led to the hypothesis that this may have evolved in someone who was infected but could then not clear the virus, giving the virus the chance to genetically evolve (the equivalent of an evolutionary gym)," she said.
"The same hypothesis was proposed for the alpha variant, and studies have been done in individual immunocompromised patients that show changes occur in the virus over time, and in response to antibody therapy."
However, she added: "But the index (original) case of alpha was not determined – and trying to pinpoint the index case of a variant of concern does not aid the pandemic response, could be counterproductive by looking back rather than putting all efforts into looking forward, and is to be avoided."
Others said it was "certainly plausible" that this was how B.1.1.529 developed, although some scientists suggested that the gap between the existing virus and the new variant may instead represent a gap in sequencing data in countries lacking surveillance capabilities.
Professor Stuart Neil, a virologist at King's College London, told The Telegraph: "It's speculative, but it's something that has certainly been worrying people for a while, that persistent infection in immunocompromised people could be driving certain levels of viral diversity."
He said this route of viral evolution has been theorised before, for example for influenza.
The concern for many global health experts is that this has not fed into global vaccination strategies for Covid. It also shines a fresh light on the risks of the long-running inequality in HIV prevention, treatment and diagnosis globally.
It's ironic then that variants more likely appear in those who are immunocompromised continue to affect us globally, as COVID interrupts care for some with HIV. Continued commitments to HIV care, despite the disruptive nature of COVID, are crucial, alongside vaccination.
— Infectious Diseases (@InfectiousDz) November 26, 2021
In South Africa, only 24 per cent of people are fully vaccinated against Covid-19; although the gap seems to be more about hesitancy than supply. However, this is not the case in other African countries which also have high burdens of HIV. Scientists pointed out that it is feasible that B.1.1.529 came from one of these countries and was simply spotted in South Africa, which has strong viral surveillance networks.
"What we're seeing is exactly what we've warned about for the last year," said Prof Lessells in South Africa.
"If we leave parts of the world behind... then the disease will continue to evolve. We could have reduced the risk of this happening and we still can if we deal with the vaccine apartheid."
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