Covid-19 mutation risk is huge as role of HIV complicates strategy

The world’s biggest number of HIV cases is complicating SA’s efforts to fight the coronavirus pandemic, raising the risk of more mutated versions emerging and spreading across the globe. 

Many of the country’s 8.2-million HIV-infected people are immunocompromised and scientists say they can harbour the coronavirus for longer, allowing it to mutate as it reproduces. A study of an HIV positive 36-year-old woman showed that Covid-19 stayed in her body for 216 days and mutated rapidly.

“There is good evidence that prolonged infection in immune-compromised individuals is one of the mechanisms for the emergence of SARS Covid-19-2 variants,” Tulio de Oliveira, a bioinformatics professor who runs gene-sequencing institutions at two SA universities, said at an August 30 immunology conference. “You have this massive virus evolution, really the virus accumulating over 30 mutations.” 

As the world struggles to stay ahead of rapidly emerging variants, getting SA’s HIV-infected people vaccinated has become critical. The recent discovery of another mutation in the country after the virulent Beta variant late last year shows the risk to everyone of not urgently pushing vaccinations through. 

The trouble is most of SA’s HIV-infected people are poor and marginalised. Many live in remote areas and have been largely left out of vaccination drives. Awash in vaccines — with more than enough doses to inoculate the country’s 40-million adults — SA’s problem now is getting them into the arms of people who desperately need them.

“Speed and coverage is important to make sure that people who are HIV-positive are getting vaccinated,” said Glenda Gray, president of the SA Medical Research Council and co-lead of the SA arm of Johnson & Johnson’s vaccine trial. 

The country’s vaccination drive has been patchy, at best. In northern Johannesburg, vaccine stations can be found at every kilometre or two, and pop stars and talk-show hosts extol the virtue of getting shots, on radio stations targeted at the rich and the urban. In the rural and impoverished Northern Cape, it’s a very different story. 

A 400km drive over two days from the provincial capital of Kimberley across an arid semi-desert to Upington found vaccines available at only one location. That’s because clinics in most towns can only administer shots on certain days and for limited hours. It’s little different in the impoverished townships that sit on the periphery of the biggest cities.

The health system is up against not just the difficulty of getting vaccines to remote areas, but also a lack of information and awareness. 

“The young people are scared; they hear rumours that people die after getting the vaccine,” said Lee-Ann Montse, an HIV counsellor, as she sat outside the refurbished shipping containers that serve as a clinic in Schmidtsdrift, a village 80km west of Kimberley. It doesn’t help that some people live as far as 15km from the clinic, and in an area with rampant unemployment, transport is a challenge, Montse said. Some days, only two or three people arrive to register for shots, she said. 

The extent of the disinformation and its effects are demonstrated by the experience of Schalk van der Merwe, who grows raisins and nuts and rears livestock near the town of Groblershoop in the Northern Cape.

When he encouraged his workers to register for vaccination, only three were willing. After bringing a nurse from the town clinic to his farm to answer questions, ranging from whether people can get vaccinated if they are HIV positive to if it will affect fertility, 93 people came forward. 

“We’ve had a strategy of taking the people to the vaccine, but given the demographic break-up of our country, with 25-million to 26-million people who are largely sitting in townships or remote areas of the country,” vaccines need to be taken to them, said Stavros Nicolaou, head of the health-work unit at Business for SA, an industry group that’s working with the government. “They don’t have all the information or digital access.”

SA has been hit the hardest in Africa by the coronavirus, with about 2.9-million confirmed cases. Excess death numbers show that more than 250,000 people who wouldn’t normally have died have perished during the pandemic — or one in 240 South Africans. 

Even in the face of such numbers, people like Themba Maseko say their main preoccupation is unemployment — at 34.4%, SA has the highest rate of joblessness among the 82 countries tracked by Bloomberg.

“I don’t see how getting vaccinated will help me solve some of the immediate problems facing me and my family,” said the 43-year-old father of two in Mabopane, a township near Pretoria. Like other impoverished townships, Mabopane counts a sizeable number of people who are HIV-positive, making it a high-risk area.

SA has struggled with HIV and the disease it causes, Aids, for more than three decades. In 2020, 13.7% of South Africans were estimated to be infected with HIV, according to Stats SA. While deaths have been capped thanks to the world’s biggest antiretroviral treatment programme, Covid-19 has added a new wrinkle to their plight. 

The Beta variant, which cut the efficacy of the AstraZeneca shot and led to dozens of countries banning travel from SA, emerged after a surge of cases in Nelson Mandela Bay. That region has the lowest uptake of antiretrovirals used to treat HIV, meaning that many people there may be immunocompromised, according to De Oliveira. 

And while the newer mutation recently noticed in SA is being studied by the World Health Organisation to determine if it is a variant of interest, its emergence shows the risks of large swaths of unvaccinated people. Only about 7.4-million people, or about 18.5% of the adult population in the country, are fully vaccinated. 

“SA really risks becoming one of the mutation factories of the world,” De Oliveira said.

Bloomberg News. More stories like this are available on bloomberg.com