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NTUZUMA, South Africa — A few months ago, a community health worker in this sprawling hillside town on the edge of Durban city, Sizakele Mathe, was informed by a clinic that a neighbor had stopped taking his medication. It was a warning sign that he had stopped taking the antiretroviral tablet that suppresses HIV infection.

This was a threat to his own health and may have posed a risk to everyone else’s health during the Covid-19 era. The clinic sent Ms. Mathe to climb a hill, go down a narrow path, and try to get the woman back the pills.

Ms. Mathe is part of a national door-to-door nagging campaign that is as joyful as it is relentless. That’s halfway through a complex South African effort to prevent the emergence of new variants of the coronavirus, such as the Omicron strain described here that shook the world last week.

The other half takes place in a state-of-the-art laboratory 25 miles down the road. At the KwaZulu-Natal Research Innovation and Sequencing Platform in Durban, scientists sequence the genomes of thousands of coronavirus samples each week. The KRISP lab, as it’s known, is part of a national network of virus researchers who have identified both Beta and Omicron variants, drawing on the expertise developed there during the region’s decades-long battle with HIV.

This combination of hi-tech and grassroots represents one of the front lines in the world’s battle against the evolving coronavirus. On Friday, the research network in South Africa revealed that the new variant is spreading twice as fast as Delta, which is considered the most contagious version of the virus.

Researchers at KRISP are global leaders in viral phylogenetics, the study of the evolutionary relationship between viruses. They monitor mutations in the coronavirus, identify hotspots, and provide important data on who is infected with whom—which by tracing and inferring mutations in the virus between samples—helping curb spread.

Since the start of the pandemic, they have been taking a close look at how the virus has changed in South Africa because they are particularly concerned about one thing: the eight million people (13 percent of the population) living with HIV in the country.

When people with HIV are prescribed an effective antiretroviral and take it consistently, their bodies suppress the virus almost completely. But if people with HIV go undiagnosed, don’t get treatment prescribed, or don’t take or take their medication regularly every day, HIV weakens their immune systems. If they later contract the coronavirus, it can take weeks or months for the new virus to be cleared from their body.

When the coronavirus has lived in their systems for this long, it has a chance to mutate and mutate and mutate again. And if they pass on the mutated virus, a new variant would be in circulation.

“We have reason to believe that some variants that originated in South Africa could potentially be directly related to HIV,” said Tulio de Oliveira, principal investigator of the national genetic monitoring network.

In the early days of the pandemic, South Africa’s health authorities were prepared for the rise in the death rate of people with HIV, says epidemiologist Salim Abdool Karim, who heads the AIDS institute. Where KRISP is located. “But none of that happened.” The main reason for this is that HIV is most prevalent among the young and the coronavirus affects the elderly the most.

HIV infection makes a person about 1.7 times more likely to die from Covid – a high risk, but a paltry risk compared to the risk of people with diabetes who are 30 times more likely to die. Dr. “Once we realized that this was the case, we came to understand that our real problems with HIV in the midst of Covid is the possibility that severely immunocompromised people are likely to give rise to new variants,” said Abdool Karim.

Researchers at KRISP have shown that this has happened at least twice. Last year, they traced a virus sample to a 36-year-old woman with HIV who was on an ineffective treatment regimen and had not been helped to find medications she could tolerate. It took 216 days for him to clear the coronavirus from his system; At that time, viruses acquired 32 different mutations in his body.

In November, Dr. de Oliveira and team followed a case of a coronavirus with dozens of mutations in the Western Cape, a different part of the country where another patient also adhered poorly to his HIV medication regimen. The coronavirus remained in his body for months and produced dozens of mutations. When these women were prescribed effective drugs and given advice on how to take them properly, they quickly cleared the virus.

Dr. “We don’t have many people like her,” Abdool Karim said of the woman, who took 216 days to clear the coronavirus from her body. “But it doesn’t take a lot of people, it just takes a person or two.” And a single variant can shake the world like Omicron has.

The origin of this variant is still unknown. It’s not just people with HIV whose systems inadvertently give the coronavirus a chance to mutate: It can happen to anyone who is immunocompromised, such as transplant patients and those undergoing cancer treatment.

When the KRISP team identified a second case of a person with HIV-producing coronavirus variants, there were more than a dozen reports of the same phenomenon in the medical literature from other parts of the world.

Viruses also mutate in people with healthy immune systems. For people with HIV or another immunosuppressive condition, the difference is that because the virus stays in their systems for much longer, the natural selection process has more time to favor immune-evading mutations. The typical replication period in a healthy person would be only a few weeks rather than a few months; Less duplication means less opportunity for new mutations.

And because there are so many people with HIV in South Africa, and this new pandemic is disrupting life here in so many ways, there is a particular urgency to try to curb variants.

This is where the efforts of community health workers like Ms. Mathe come into play. On a typical workday, armed with an old cell phone and a mental list, he walks dirt roads past leaky standpipes and front-step hair salons. Recently in the clinic, who does not look well and who needs a visit. Ms. Mathe, who has been on HIV treatment for 13 years, is paid $150 a month.

Silendile Mdunge, a slim 36-year-old mother of three, stopped taking her antiretrovirals during the brutal third wave of Covid that hit South Africa between May and July. Medicines are no longer delivered to a nearby community collection point as many healthcare workers have been reassigned. Instead, he had to collect the pills at a central clinic about nine miles away. But he feared catching this new virus in a shared taxi or standing in the huge clinic queues he had heard of.

Ms. Mathe was drug-free for four months before arriving at the tiny scrap-wood house that Ms. Mdunge shared with seven family members.

“He told me that people who can’t be cured are no longer alive, that I should think of my children, that I might die,” said Mdunge, leaning against the hard door frame in a warm, light rain. . These were things he already knew in the abstract.

But Miss Mathe’s persistent presence made it difficult to ignore the warnings. Ms Mdunge shrugged and rolled her eyes, suggesting that she restart the treatment to stop bothering as much as anything else.

Miss Mathe listened with a grin to this account of her methods. “You wouldn’t be doing this job if you didn’t love people,” he said.

Of the eight million South Africans with HIV, 5.2 million are receiving treatment – ​​but only two-thirds of this group successfully suppress the virus with medication. The problem extends beyond the borders of South Africa: In sub-Saharan Africa, 25 million people live with the virus, of which 17 million are virally suppressed by treatment.

The KRISP lab is listing coronavirus samples from all over Africa to fill in some gaps for countries that don’t have the capacity. South Africa’s surveillance network and genomic sequencing are extensive enough that its researchers are the first to detect even cases not originating in the country.

The great fear is a variant with “immune evasion”: the ability to evade Covid vaccines or the immune response elicited by previous infection. As more and more people in South Africa are vaccinated against Covid, there is the potential for a variant to infuse in the body of a vaccinated person.

Leading South Africa’s Covid response, Dr. “You have a situation where you have the potential to create really bad variants,” Abdool Karim said. Previous variants emerged when few people had access to the vaccine, but now South Africa has delivered the vaccine to more than a third of its citizens. If people vaccinated with HIV do not have or are not taking their antiretrovirals, there may be an opportunity for the virus to mutate to evade the vaccine.

“Now, most of these HIV patients have been vaccinated, so they have immune responses. So if they’re going to create a new variant, that variant will have to evade these immune responses,” said Dr. Abdool Karim.

Dr. de Oliveira said he is less concerned about a vaccine-resistant variant emerging in South Africa, such as the United States pocket with untreated HIV, low vaccine coverage and a weaker surveillance network than South Africa.

“There’s a chance we’ll find him first,” he said with a cruel laugh.

The difference from the risk of the virus mutating in people with uncontrolled HIV pointed out that this is a problem with a ready-made solution – getting everyone with HIV treated – a transplant or cancer patient has no choice.

Above all, the answer to ending the variant threat is to contain the coronavirus transmission. Vaccinate, vaccinate, vaccinate Africa’s population,” he said. “My concern is vaccine nationalism or vaccine hoarding.” He added that people with HIV should be given priority for vaccine boosters to maximize the effectiveness of their immune response.

So far, South Africa’s efforts to address the volatile problem and be transparent about it have come at a high price in the form of flight bans and global isolation.

Dr. “As scientists, we’ve been discussing underestimating the HIV problem, especially in species that are at the forefront,” de Oliveira said in his lab last week. “If we raise our voices too loud, we also risk massive discrimination, border closures and economic measures. But if you don’t speak loudly, there are unnecessary deaths.”

Carl Zimmer contributing reporting.