Where did Omicron come from? By all accounts it is a weird variant. Though highly mutated, it descended not from one of the other variants of concern, such as Alpha, Beta or Delta, but from coronavirus that was circulating maybe 18 months ago. So where has it been all this time? And why is it only wreaking havoc now?

Researchers are exploring a number of hunches. One is that Omicron arose in a remote region of southern Africa but failed to spread until now. Another is that it evolved in infected animals, such as rats, and then crossed back into humans. But a third explanation is gaining ground as more data come to light, that Omicron arose in a person with a weakened immune system: someone having cancer treatment perhaps, an organ transplant patient or someone with uncontrolled HIV.

Sub-Saharan Africa is home to two-thirds of the global population living with HIV. For a whole series of reasons, ranging from lack of access to clinics to fear of stigmatisation and disrupted healthcare, 8 million people in the region are not on effective HIV therapy.

Beyond the direct problems this causes with disease progression and vulnerability to Covid – people with advanced or uncontrolled HIV are far more likely to die from coronavirus – is the risk that uncontrolled HIV is driving the emergence of Covid variants.

“For me there are two key things,” says Dr Richard Lessells, an infectious diseases physician at the University of KwaZulu-Natal in Durban, who was part of the team that first reported Omicron. “First there is the science that needs to go on to get a better understanding of this. But more importantly, on a public health level, we don’t need to wait for the science. It is a reminder that while addressing the immediate challenge of Covid-19, we also need to intensify efforts to end HIV as a public health problem.”

The suspicion that variants of concern can evolve in patients with weakened immune systems is not new. The Alpha and Beta variants, first spotted last year in the UK and South Africa respectively, are widely thought to have emerged after long-term infections in patients.

The mechanism was laid out by Charles Darwin more than 150 years ago: evolution through natural selection. If a person is infected with Covid but mounts a weak immune response, the infection can persist for months. In that time, antibodies neutralise some of the virus, but not the versions they bind to less well. These surviving viruses proliferate, mutate and undergo further selection – potentially leading to variants that evade immune defences.

A preliminary study posted online this week reveals the process in action. Scientists in South Africa, Lessells among them, traced a particular sample of coronavirus to a 36-year-old woman who was not receiving effective antiviral therapy. Tests revealed that she had harboured the Covid virus for 216 days, in which time it accumulated 32 mutations, making it similar to the vaccine-evading Beta variant. If weakening of the immune system by HIV drives Covid evolution, the researchers say, then antiretroviral therapy must be ramped up to prevent it.

Writing in the journal Nature, Lessells and his colleagues make the case more strongly. They warn that the failure to tackle the Covid pandemic “with sufficient urgency” in countries with high rates of uncontrolled HIV “could lead to the emergence of variants of the coronavirus Sars-CoV-2 that spread more easily between people or render the vaccines less effective”. With Omicron, one possibility is that the virus lingered in an immunocompromised patient for months – explaining why it descends from such an old version – before it acquired the right mutations to break out and spread like wildfire.

The effort needed, then, is huge. Covid has caused massive disruption to healthcare services, with HIV patients among those badly hit. More than 1,300 healthcare workers have died of Covid in South Africa alone. Thousands more may leave the profession because of the unsustainable strain. The UK’s hefty cuts to international aid, including slashing funds for the UN agency focused on fighting HIV/Aids from £15m to £2.5m, will hardly help the situation.

Meanwhile, 70% of Britons are vaccinated against Covid, compared with 7.5% in Africa. What vaccine has arrived on the continent has been prioritised for the oldest, in line with strategies in many countries, but this means few of those with HIV are protected: about 80% of people with HIV in Africa are under 50 years old.

Prof Penny Moore at the University of the Witwatersrand and the National Institute for Communicable Diseases in South Africa said there was “good data” to indicate that immunocompromised people who could not clear Covid infections as quickly as others were a risk for new variants. “That includes HIV-positive people with uncontrolled viral replication, as well other groups like people on immunosuppressants,” she said. “But this is probably still a rare event.

“Increasing access to Covid-19 vaccines will reduce that risk, for sure, and there is a worrying overlap between areas where HIV prevalence is high and Covid-19 vaccine coverage is low,” she added. “I do think we need to translate our sense of urgency from Sars-CoV-2 to HIV prevention and treatment in parallel to tackling uneven vaccine coverage globally.”

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