How HIV and COVID-19 Variants Are Connected

It’s a matter of time until an even more dangerous coronavirus variant emerges if we fail to vaccinate the world’s most vulnerable populations.

Garrett-Laurie-foreign-policy-columnist9
Garrett-Laurie-foreign-policy-columnist9
Laurie Garrett
By , a columnist at Foreign Policy and former senior fellow for global health at the Council on Foreign Relations.
Paramedics assess a COVID-19 patient in Johannesburg
Paramedics assess a COVID-19 patient in Johannesburg
Paramedics assess a COVID-19 patient in Johannesburg on Jan. 4. MICHELE SPATARI/AFP via Getty Images

The troubling arrival of a new form of the COVID-19 virus that is rife with mutations—around 50 of them—has world leaders, stock markets, and scientists scrambling in anticipation of a global coronavirus tsunami that some fear could outstrip today’s delta variant pandemic. It’s still too early in the study of the new omicron variant to have dissected all those mutations, deciphering their likely impacts on viral spread, illness severity, the reliability of diagnostic tests, vaccine protection, and the utility of dozens of drugs and treatments. South Africa was the first country to identify the variant, based on cases that had been detected in Botswana. There are indications it was circulating in Europe even earlier, but a genetic analysis of some 200 South African omicron samples by well-known computational biologist Trevor Bedford of the Fred Hutchinson Cancer Research Center in Seattle pushes the date of first emergence in that country possibly back to September.

The evolution of potentially dangerous variants like omicron has been ensured by the wealthy world’s decision not to protect vulnerable populations outside its borders. Put simply, strategies rich countries have implemented to limit the carnage from COVID-19 inside their borders have not been mirrored at a global scale. In European countries, Canada, Japan, and the United States, for example, great pains have been taken to prioritize treatment and vaccination for people with weakened immune systems. But globally, one of the world’s largest concentrations of immunocompromised people—the untreated HIV-positive people of southern Africa—has been all but ignored.

In addition to omicron, two other significant variants may have emerged in South Africa—the so-called beta variant, which surfaced in 2020, and a newer form labeled C.1.2. Late in 2020, as manufacturers rolled out COVID-19 vaccines, the beta form proved challenging. It had mutated into a variant that partially evaded the immune responses conjured by the Moderna, Pfizer, and Johnson & Johnson products. South Africa’s genomic surveillance network tracked the near-disappearance of beta, overwhelmed by the delta variant that was first detected in India—by June, delta was taking a devastating toll across southern Africa.

The troubling arrival of a new form of the COVID-19 virus that is rife with mutations—around 50 of them—has world leaders, stock markets, and scientists scrambling in anticipation of a global coronavirus tsunami that some fear could outstrip today’s delta variant pandemic. It’s still too early in the study of the new omicron variant to have dissected all those mutations, deciphering their likely impacts on viral spread, illness severity, the reliability of diagnostic tests, vaccine protection, and the utility of dozens of drugs and treatments. South Africa was the first country to identify the variant, based on cases that had been detected in Botswana. There are indications it was circulating in Europe even earlier, but a genetic analysis of some 200 South African omicron samples by well-known computational biologist Trevor Bedford of the Fred Hutchinson Cancer Research Center in Seattle pushes the date of first emergence in that country possibly back to September.

The evolution of potentially dangerous variants like omicron has been ensured by the wealthy world’s decision not to protect vulnerable populations outside its borders. Put simply, strategies rich countries have implemented to limit the carnage from COVID-19 inside their borders have not been mirrored at a global scale. In European countries, Canada, Japan, and the United States, for example, great pains have been taken to prioritize treatment and vaccination for people with weakened immune systems. But globally, one of the world’s largest concentrations of immunocompromised people—the untreated HIV-positive people of southern Africa—has been all but ignored.

In addition to omicron, two other significant variants may have emerged in South Africa—the so-called beta variant, which surfaced in 2020, and a newer form labeled C.1.2. Late in 2020, as manufacturers rolled out COVID-19 vaccines, the beta form proved challenging. It had mutated into a variant that partially evaded the immune responses conjured by the Moderna, Pfizer, and Johnson & Johnson products. South Africa’s genomic surveillance network tracked the near-disappearance of beta, overwhelmed by the delta variant that was first detected in India—by June, delta was taking a devastating toll across southern Africa.

Lurking in the background, first detected in May, was the highly mutated C.1.2 variant, bearing significant mutations in the spike protein that initiates infection of human cells and in the so-called furin cleavage site—an area key to the coronavirus efficiently injecting itself into targeted human cells. The South Africans identified it as a new lineage of the virus that showed increased transmissibility, and by August reported it was perhaps the most mutated virus to date—already then found in nine countries.

Following the emergence of the C.1.2 and other variants that were first seen in Africa, and the global spread of delta, the World Health Organization’s director-general issued a stern warning in July: “The virus continues to evolve, resulting in more transmissible variants.”

In the wealthy world, each new major variant has been greeted with greater mass vaccination efforts and added doses. Much attention has been given to provision of third shots for individuals undergoing chemotherapy to treat cancer, radiation treatment, transplants, and other medical procedures that necessarily undermine immune systems.

One reason for this nearly universal effort in wealthy countries to bring cancer and transplant patients up to par with their healthier counterparts—a rationale beyond human decency—is recognition that some of the variants likely arose in the bodies of people with cancer or other conditions. Indications are, for example, that the alpha form of the coronavirus that swept across the United Kingdom last Christmas may have arisen in an immunocompromised patient, such as one undergoing lymphoma treatment.

Of course, the sorts of costly treatments and care that keep angioblastoma or heart transplant patients alive in Luxembourg or Scotland aren’t available for most citizens of poorer nations. Few, if any, residents of Bulawayo, Zimbabwe, have the opportunity to replace a cancer-ravaged lung with a transplanted one, undergoing months of costly immunosuppressive drug treatment to prevent their immune system from rejecting the foreign tissue. So, an advanced-stage Zimbabwean lung cancer victim is unlikely to survive long enough to harbor a coronavirus infection for weeks, allowing the virus to evolve inside their body, acquiring mutations that make the microbe better adapted to spreading among humans.

If humanity wanted to give a coronavirus a golden opportunity to circulate, adapt, and evolve inside the bodies of human beings, eventually taking on a form that threatens all—rich and poor alike—it couldn’t do better than to ignore the estimated 38.7 million people living with HIV, especially the roughly 10 million who remain untreated, most of them residing in sub-Saharan Africa. In 2020 it is estimated another 1.5 million people were newly infected with HIV, almost 700,000 of them in eastern and southern Africa. More than 600,000 people died of AIDS-related illnesses around the world in 2020, while international attention was focused on COVID-19.

The great HIV/AIDS pandemic is rarely mentioned these days. Now that very efficient, minimally toxic, and inexpensive treatments are available, along with prophylactic drugs that can block infection altogether, HIV has become the out-of-sight, out-of-mind virus. But it’s far from disappeared.

In wealthy countries, it’s relatively rare today to see AIDS—the immune-system-ravaging terminal disease state—take hold in individuals. That’s because HIV tests and treatments are generally available, and drug company ads for medicines that block or treat the virus are staples of late-night TV. It also seems that one of the most widely used anti-HIV drugs, tenofovir, has some effect on the coronavirus, dampening the impact of COVID-19. Appropriately treated, HIV-positive individuals maintain robust immune systems that appear to tolerate COVID-19 vaccines and infection. (Although a New York study found higher death rates to COVID-19 among HIV-positive people in the first half of 2020.)

In the United States, meanwhile, access to testing and treatment for HIV is remarkably lower among African American and Latino men, accounting for their higher death rates due to HIV and possibly some of the racial disparity in COVID-19 mortality. From March to September 2020, in the early months of the COVID-19 pandemic and well before vaccines were available, the number of HIV tests at a single major lab plummeted by more than 600,000, and the number of viral load tests performed to monitor HIV-positive patients’ treatment fell by more than 60,000. Gay men of color were most effected by the downturn in access to HIV testing and treatment in America, according to an October study: “People with HIV in the USA, particularly those with pronounced immunodeficiency, seem to be at elevated risk of COVID-19 hospitalisation and mortality. The exacerbated COVID-19 outcomes in Black or African American and male people with HIV suggest profound health inequities faced during the COVID-19 pandemic.”

A Spanish study also found higher death rates in HIV-positive men in most of 2020. A study from February through June 2020 found that it’s possible HIV-positive Black men in Britain were also more likely in to suffer severe COVID-19 and to die of the disease if infected.

In countries where access to HIV medications, testing, and prevention tools were already limited before COVID-19 emerged, the pandemic is proving devastating. Speaking on Nov. 30 to the United Nations General Assembly, Anthony Fauci, the director of the U.S. National Institute of Allergy and Infectious Diseases, warned that personnel and supply chain burdens on health systems were impeding HIV tracking and treatment. “We also must assure that people with HIV in all countries have early access to effective COVID-19 vaccines and therapeutics while their supply of anti- HIV drugs also is maintained,” he said.

Thanks to the U.S. President’s Emergency Plan for AIDS Relief program, which has since 2003 expended more than $100 billion to prevent, test, and treat HIV infection in poor countries, and thanks to mass-scale generic manufacturing of HIV tests and treatments, an estimated 27.5 million HIV-positive people living in poorer countries are undergoing HIV treatment, making them better able to withstand COVID-19 disease or immunization—if vaccines are available. While individuals with advanced HIV disease may not be able to muster an immune response against COVID-19 despite full vaccination, those who are well treated for their HIV gain clear benefit from the vaccines.

But there are still more than 10 million people in poor countries who carry HIV and either do not know it or refuse to seek care because of the tremendous stigma attached to being HIV-positive. Millions more suffer periodic treatment interruptions due to stock-outs of local drug supplies or their inability to get transport to a clinic or dispensary. Lockdowns and supply chain issues related to the COVID-19 pandemic have severely exacerbated these problems. It is estimated that 296,000 people in sub-Saharan Africa could die as a direct result of HIV treatment interruptions and exposure to COVID-19. “A chilling pattern of inequity shapes the burden of COVID-19 and HIV,” the British medical journal the Lancet said in November 2020.

For those too young to have lived through the late 20th-century HIV epidemic, never witnessing the results of the virus’s voracious appetite for white blood cells and other crucial components of the human immune system, it’s worth recalling that individuals in the throes of the disease are overwhelmed by a long succession of so-called opportunistic infections of fungi, bacteria, and viruses that, unchecked by the cells and antibodies of immunity, devour one organ after another. The same COVID-19 lockdowns and supply chain interruptions that have stymied HIV testing and care for millions of HIV-positive people have also undermined treatment of their key opportunistic killer, tuberculosis. WHO announced in October that TB control efforts were falling apart all over the world amid the strains COVID-19 has put on public health systems, leading to an 18 percent drop in testing for the disease between 2019 and 2020, a 19 percent decline in those under treatment for drug-resistant TB, and, most disturbingly, a 37 percent fall in treatment of extremely drug resistant TB—not because the numbers of TB cases are down but because far fewer people are accessing testing and treatment. The added burden of COVID-19, atop HIV and TB, leads to higher mortality. According to WHO’s report, some 1.5 million people died from TB in 2020; 214,000 of them were HIV-positive.

COVID-19 is an opportunistic infection. For the under- or untreated HIV-positive individual, the coronavirus is an invader that can take up residence in lung tissue, the lining of blood vessels, the brain—and smolder. With time, the virus can adapt to human cells through mutation and selection—and eventually be passed on to other individuals. In July, for example, South African researchers agreed, suggesting that there is “growing evidence that the beta SARS-CoV-2 variant first identified in South Africa is leading to more severe disease in people living with HIV, and that failure to clear SARS-CoV-2 infection in a patient with advanced HIV creates conditions that can lead to evolution of dangerous mutations in SARS-CoV-2.”

At the Nelson Mandela School of Medicine in Durban, South Africa, doctors treated an HIV-positive woman for COVID-19 who had been on HIV treatment since 2006. Though her COVID symptoms resolved after eight days in hospital, constant PCR testing showed the coronavirus persisted in her body and mutated considerably, for 216 days—a discovery, the researchers argue, “may provide justification for prioritising people living with HIV for COVID-19 vaccination.”

There is currently no evidence to indicate that omicron arose through southern Africa’s millions of HIV-positive people. But few aspects of the international response to COVID-19 are as idiotic, stupid, and ultimately self-destructive as the failure, born from wealthy-nation selfishness, to make Africa’s HIV-positive population a top vaccination target, just as their cancer and transplant counterparts are in the rich world.

As the threat of omicron now rises to the level of an emergency G-7 summit, a one-day Dow Jones Industrial Average plummet of more than 900 points, and even some social panic wafting across the internet, the rich-world response is to isolate southern Africa in its time of need. It is an obscene gesture—or, as WHO characterizes rich-world hoarding of COVID-19 vaccines, it is “self-defeating” and “morally indefensible.”

As WHO Director-General Tedros Adhanom Ghebreyesus said at a special session of the World Health Assembly on Monday, “The emergence of the highly mutated omicron variant underlines just how perilous and precarious our situation is. South Africa and Botswana should be thanked for detecting, sequencing, and reporting this variant, not penalized.”

Of the more than 8 billion doses of vaccines administered worldwide to date, only 26 million have gone into arms in South Africa, or 0.3 percent of global supply. While 54.5 percent of the world population has received at least one dose of a COVID-19 vaccine, only 6 percent of the population of poor countries have. One of the wealthiest nations in sub-Saharan Africa, South Africa, has managed to fully vaccinate around 24 percent of its population. Kenya has fully vaccinated about 5 percent of its people; Nigeria, less than 2 percent. South Africa now has a stockpile of 16 million doses, and it has asked J&J and Pfizer to hold off sending more until this supply is dispersed: That’s great news. But neighboring countries with large HIV-positive populations are still waiting. Malawi has fully vaccinated only 3 percent of its population; Namibia, 12 percent; Zambia, 4 percent.

Omicron concern may be having an impact on rich countries’ vaccine hoarding. On Monday, a coalition of organizations, including the African Union’s African Vaccine Acquisition Trust (AVAT), issued a plea to the world for steady, consistent supplies: “Donations to COVAX, AVAT, and African countries must be made in a way that allows countries to effectively mobilize domestic resources in support of rollout and enables long-term planning to increase coverage rates.”

Many issues are at play in the immoral skewing of vaccine resources, including patent protections that prohibit generic manufacturing, shortages of syringes and chemical supplies that are essential for production and distribution of immunization, and the incompetence of the multilateral global health system, to name a few.

Excuses can, and have, been made.

But omicron signals that these barriers—all of them—must be torn down. While we have no indication that this variant arose in the immunocompromised body of an HIV-positive individual, humanity’s egregious refusal to prioritize those in southern Africa who have been infected by the 20th-century’s second great pandemic is likely to continue providing the coronavirus with fertile ground for spread, growth, and evolution. We are aiding and abetting the virus by hoarding vaccines and by categorizing one group of rich-world immunocompromised as top priority, while ignoring a significant group in Africa with HIV-weakened immune capabilities.

The racial component in this seems inescapable. Black African nations are singled out for travel bans, despite circulation of omicron in white European countries. And black African people in great need are denied access to full immunization against the COVID-19 virus.

Shame on all of us.

Laurie Garrett is a columnist at Foreign Policy, a former senior fellow for global health at the Council on Foreign Relations, and a Pulitzer Prize-winning science writer. Twitter: @Laurie_Garrett

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