A few months ago, Sizakele Mathe, a community health worker in Ntuzuma, South Africa, was notified by a clinic that a neighbor had stopped picking up her medication. It was a sign that she had stopped taking the antiretroviral tablets that suppress her H.I.V. infections.
That was a threat to her own health, and it might have posed a risk to everyone else. Ms. Mathe was dispatched by the clinic to climb a hill and try to get the woman back on her medication.
Ms. Mathe is part of a national door-to-door nagging campaign. The Omicron strain that was identified here and shook the world this past week is part of a sophisticated South African effort to stanch the emergence of new coronaviruses.
The other half is held at a state-of-the-art laboratory 25 miles away. Scientists at the KwaZulu-Natal Research Innovation and Sequencing Platform sequence the genomes of thousands of coronaviruses each week. The lab is part of a national network of virus researchers that identified both the Omicron variant and theBeta variant, drawing on expertise developed here during the region's decades-long fight with H.I.V.
One of the front lines in the battle against the coronaviruses is this combination of high tech and grassroots. The research network in South Africa reported on Friday that the new variant appeared to spread twice as quickly as Delta, which had been considered the most contagious version of the virus.
The study of the evolutionary relationship between viruses is done by the researchers at the KRISP. They provide crucial data on who is infecting whom and who has the coronaviruses in their samples, which they deduce by tracking the changes in the coronaviruses.
They are worried about the eight million people in South Africa who live with H.I.V. because they are concerned about how the virus changes in the country.
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The New York Times has a story about a scientist outside a lab in South Africa.
People with H.I.V. who are prescribed an effective antiretroviral are almost completely free of the virus. If people with H.I.V. aren't diagnosed, haven't been prescribed treatment, or can't take their medicines consistently, their immune systems are weakened. It can take weeks or months to clear the new coronaviruses from their bodies if they catch it.
The coronaviruses have the chance to change and change again when they live that long. A new variant of the virus is in circulation if they pass it on.
The principal investigator of the national genetic monitoring network said that there are reasons to believe that some of the variants that are emerging in South Africa could be related to H.I.V.
South Africa's health authorities were bracing for a big increase in deaths from H.I.V. in the first days of the Pandemic. The AIDS institute where the KRISP is housed created horror scenarios that Africa was going to be wiped out. None of that happened. The coronaviruses has hit older people harder than H.I.V.
An H.I.V. infection makes a person 1.7 times more likely to die of Covid, but it pales in comparison to the risk for people with diabetes, who are 30 times more likely to die. The real problem with H.I.V. was the prospect that people with severe immune problems would lead to new variant.
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The Centre for the AIDS Programme of Research in South Africa has a Covid-19 extraction room.
At least two times, researchers at KRISP have shown this. A woman with H.I.V. was traced to a virus sample last year because she was not being helped to find drugs that she could tolerate. She took 216 days to clear the coronaviruses from her system.
The coronaviruses sample was traced to a different part of the country, the Western Cape, where another patient was also poorly adhering to the H.I.V. drug regimen. She had the coronaviruses in her body for months. These women were prescribed effective drugs and counseled on how to take them, and they cleared the virus quickly.
The woman who took over two years to clear the coronaviruses from her system is not a lot of people like her. It just takes one or two people. Omicron has a single variant that can rattle the world.
The origin of this variant is unknown. People with H.I.V. are not the only ones whose systems can give the coronaviruses the chance to change.
There were more than a dozen reports of the same phenomenon in medical literature from other parts of the world when the second case of a person with H.I.V. was identified.
People with healthy immune systems can also be affected by Viruses. The natural selection process has more time to favor the more resistant genes for people with H.I.V. because the virus stays in their systems so long. A healthy person's typical replication period would be a couple of weeks, instead of many months, and fewer replications would mean less opportunities for new mutations.
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The real problem with H.I.V. was the prospect of people with compromised immune systems getting new versions.
South Africa has a lot of people with H.I.V., and this new Pandemic has hit hard here, disrupting life in many ways.
Ms. Mathe is a community health worker. On a typical workday, she walks dirt paths past leaking standpipes and front-step hair salons, armed with an ancient cellphone and a mental roster of people who need to be seen. Ms. Mathe has been on H.I.V. treatment for 13 years and is paid $150 a month.
Silendile Mdunge, a thin 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. Many health care workers were redeployed and her drugs were no longer being delivered to a nearby pickup point. She was supposed to collect the pills at the central clinic. She was afraid of contracting the new virus in a shared taxi or standing in a huge clinic line.
Ms. Mdunge was off the medication for four months before Ms. Mathe showed up.
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Economic recovery is at risk. The global economy is in a state of uncertainty as new restrictions on travel and trade are making consumers less confident.
Ms. Mdunge was leaning on the door frame in the rain, and she said that she could die if she didn't think of her children. She already knew those things.
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Ms. Mdunge said that Ms. Mathe told her that people who don't follow their treatment are no longer alive.
Ms. Mathe's presence made it difficult to ignore her warnings. With a shrug and an eye roll, Ms. Mdunge suggested that she restart treatment to end the pestering.
Ms. Mathe smiled as she listened to the recount of her methods. She said that if you didn't have love for people, you wouldn't do this job.
Only two-thirds of the eight million people with H.I.V. in South Africa are successfully suppressing the virus with medication. Sub-Saharan Africa has 25 million people living with the virus, of which 17 million are virally suppressed with treatment.
Some countries that do not have their own capacity to do coronaviruses can be filled by the lab. South Africa has a comprehensive network and researchers may be the first to detect cases that do not originate in the country.
The ability to escape Covid vaccines is a variant of the great fear. There is a chance that a variant of Covid could be found in the body of a person who has been vaccined.
The potential to create really nasty variant is what Dr. Abdool Karim said about the situation. South Africa has delivered the vaccine to more than a third of its citizens, which is a new variant. The H.I.V. could be able to evade the vaccine if people don't take their antiretrovirals.
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A woman and her baby are leaving a clinic in Hillbrow, a suburb of South Africa.
Many of these H.I.V. patients have received vaccinations so they have their immune responses. If they were to create a new variant, it would have to escape the immune responses.
Dr. de Oliveira said that he was not worried about vaccine-resistant H.I.V. in South Africa more than in the United States, where there is low vaccine coverage and a weak network.
He said with a laugh that the chances are we would find it first.
He pointed out that the risk of mutating H.I.V. is different for people with an uncontrollable H.I.V. and for transplant or cancer patients.
The best way to end the variant threat is to stop coronaviruses from spreading. He said to vaccine the population of Africa. My concern is vaccine nationalism or the over-consumption of vaccine. He said that people with H.I.V. should be prioritized for vaccine boosters.
Flight bans and global isolation have been the result of South Africa's efforts to tackle the variant issue.
The H.I.V. problem is debated by scientists in the kind of forefront. If we are very vocal, we risk discrimination and closing borders. We have unnecessary deaths if you are not very vocal.
Carl contributed to the reporting.
