A lucky few seem ‘resistant’ to Covid-19. Scientists want to know why

Her husband collapsed just before reaching the top of the stairs in their small one-bedroom house in São Paulo, Brazil. Frantic, Thais Andrade grabbed the portable pulse oximeter she had purchased after hearing that a low oxygen reading could be the first sign of the novel coronavirus. Erik’s reading was hovering eight points lower than it had that morning. He also looked feverish.

“When he hit 90% [on the oximeter], I said we can’t wait anymore,” Andrade recalled. “I called an ambulance.”

At the hospital that day in June 2020, a CT scan showed multiple lesions in her husband’s lungs — an indication of severe Covid-19 infection – which was later confirmed via a blood test. Erik, 44, had likely contracted the virus up to a week earlier, from a friend who had visited their home.

He spent the next several weeks on oxygen in the ICU, a stay that was complicated by blood clots before he was discharged. But it wasn’t his sudden decline and subsequent recovery that is notable: It’s that Andrade had been sharing the same close quarters with her husband while he was infected and able to transmit the virus. She never wore a mask in the home with him. They shared the same bed. They were physically intimate. Yet when tested for an active or past infection — twice — her bloodwork came up negative.

And that wasn’t the only time she was potentially exposed. As part of her research work as a veterinary neurologist, she went to a meeting at the University of São Paulo where an infected attendee set off a chain reaction of positivity – but Andrade dodged it. Her tests were again negative.

Both experiences suggest that Andrade may have won a sort of biological lottery — that she’s one of a lucky few “resistant” to the virus that has killed more than 4 million people. But how? That’s the mystery researchers around the world have set out to unravel.

The question of viral resistance has perplexed Mayana Zatz, a University of São Paulo genetics professor, for years, beginning with exploring the clinical variability of genetic diseases in patients who carried the same pathogenic mutation. She began with neuromuscular disorders like Duchenne muscular dystrophy, and then expanded to exploring why the Zika virus caused severe brain damage in some newborns while others were healthy.

In 2018, she published a study of nine sets of twins — seven fraternal and two identical — born to Zika-infected mothers; in each pair, one twin was born with microcephaly and developmental delay while the other was spared. Zatz suspected the answer to Zika resistance lay in their genes. To test this hypothesis, she collected blood from three of the pairs and reprogrammed their cells in the lab to generate induced pluripotent stem (iPS) cells and immature brain cells called neuroprogenitor cells (NPCs) that had genomes identical to those of the resistant and non-resistant infants. Then, her team infected the NPCs with Zika and found that the virus destroyed the NPCs of only those who were not resistant — supporting the idea that resistance is genetic.

It was a serendipitous moment in early February 2020, on her daily walk, that caused Zatz to turn her interest to exploring resistance to the Covid-19 virus.

Zatz often passed a middle-aged couple that lived nearby. After noticing the husband’s absence for several days, she stopped to ask after him. It turned out he had been gravely ill with Covid, yet his wife remained symptom-free. Zatz wondered: Along the same lines as the twin study, could discordant couples — where one is infected and the other not — be studied to potentially isolate gene associations for resistance?

Appearing on Brazilian TV a few days later, Zatz appealed for such couples to sign up for a study. “We received almost 3,000 emails of discordant couples, where one was infected and symptomatic while the partner was asymptomatic and seronegative,” Zatz told me.

After confirming the infection status of couples, her research team chose 100 of them to have their genes sequenced, in hopes of identifying mutations that are more frequent in key areas of the genomes of uninfected participants.

Zatz’s work is part of a growing effort to identify factors that may make people resistant to Covid, with the goal of finding clues to treatments, as well as understanding resistance against viruses more broadly. Other scientists have run lab experiments using CRISPR genome-editing technology to disable genes, in search of ones that could be manipulated to perhaps protect those of us not fortunate enough to have natural resistance against the coronavirus.

“The biological implications [of identifying a resistance gene] are important because it will provide one more piece in the assembly of the puzzle of the pathogenesis of Covid,” said pediatric immunologist Jean-Laurent Casanova of Rockefeller University, who has been studying the genes involved in Covid-19 severity, but is now shifting to look at elements of resistance. “Medically, if you knew you’re resistant, you know, you’d be relaxed. You would feel like King Kong right? The second possibility is that in people who are not genetically resistant, you can think of blocking the very same component on the surface of cells that you don’t have genetically.”

The first disease-resistance gene was discovered in 1905, when Cambridge University botanist Sir Rowland Biffen published a study isolating a single recessive gene for resistance to the fungus P. striiformis in wheat. The study has been pivotal in our understanding of genetically modified crops. A similar approach has since been applied to understanding children’s resistance to severe genetic diseases, and, more recently, to cancer. But when it comes to viruses, diseases that don’t arise within us but out of the environment and exposures, the picture becomes a bit more complex.

It’s hard to gauge how much you were exposed, and it’s not always clear when a virus makes someone sick. That’s especially true with SARS-CoV-2; the basic biology of how the virus attacks our bodies is still poorly understood, and its effects on people vary widely. Some people become infected but their immune systems spontaneously clear the virus, keeping them from developing the actual disease. These individuals may be asymptomatic, but this is not the same as resistance; an antibody test would generally detect evidence of a prior infection. Instead, resistance is broadly understood as having cleared a virus before it enters cells and gets a foothold – preventing infection, in other words, not just disease.

Resistance has been demonstrated against other viruses. In 1994, doctors found that a man named Stephen Crohn, despite having been exposed to numerous HIV-positive partners, was found to have no signs of HIV infection during multiple rounds of testing. Researchers later discovered he had a “delta 32” genetic mutation, which prevented HIV from entering his cells. However, later studies have suggested that resistance to HIV is rarely as simple as one mutation – there may be several genes and proteins that confer resistance, as found in research among sex workers in Kenya.

A team of scientists at New York University and the Icahn School of Medicine at Mount Sinai were the first to report finding genes possibly tied to resistance to Covid-19. In early 2020, Benjamin tenOever, a professor of microbiology at Mount Sinai, along with Neville Sanjana, an assistant professor of biology at NYU, and colleagues at the New York Genome Center set out to sort through the potential genetic factors underlying Covid resistance. To do this, they used CRISPR genome editing technology to disable each of the 20,000 human genes in lung cells and then exposed them to SARS-CoV-2. Most of the cells died within a few days. “Anything that lives,” tenOever explained, “is clearly missing something essential for a virus, and so potentially has a significant gene mutation.”

In January 2021, the group published a paper in Cell, reporting that RAB7A, a gene important for the movement of cargo from inside the cell to the cell surface, topped their quantitative ranking of genes the coronavirus can’t do without. Inhibiting RAB7A reduces SARS-CoV-2 infection by ensuring ACE2 receptors are retained inside the cell, making them unavailable as the required point of attachment for the spike protein of SARS-CoV-2 (which attaches and then enters the cell).

Although mutations in RAB7A are very rare, according to Sanjana, drugs that inhibit this gene or others required for viral infection could, in theory, be used as a treatment or even be used as a post-exposure prophylactic.

“Amazingly,” Sanjana said, “we found many genes whose loss reduces viral infection. For a subset of these, we identified existing drugs that can be repurposed to inhibit these genes. Some of them are already FDA-approved.”

But tenOever isn’t so sure their results will translate to therapies, noting that despite identifying the mutation that blocked HIV infection years ago, and spending billions of dollars since, we haven’t come up with a workable way to make people resistant to HIV. “Even if you found an inert protein that could be erased from our biology without major impact,” he said, “it doesn’t [necessarily] translate to any meaningful therapeutic.”

Casanova disagrees, believing that identifying mutations governing resistance can have a meaningful impact on therapeutics, but it involves re-imagining exactly where to target drugs.

In a paper accepted for publication in Nature Immunology, Casanova, Zatz, and colleagues with the COVID Human Genetic Effort propose several potential sites in the genome that could govern resistance to SARS-CoV-2, and suggested undertaking large genome-wide association studies that screen large populations for gene variants associated with resistance to SARS-CoV-2.

Casanova points to a limitation in the field of microbiology, which explains why therapeutics for infectious diseases have focused primarily on the disease-causing organism, instead of the host.

“The history of infectious diseases is essentially characterized by the idea that the microbe [alone] is causal, and you can prevent disease by vaccinating against the microbe, or by interfering with the microbe (via drugs). In my work, we see we can prevent or treat infectious diseases, not [just] by hammering the microbe, or playing with adaptive immunity (via vaccines or monoclonal antibodies), but by restoring deficient immunity, which accounts for life-threatening disease,” Casanova said.

This is the core reason why studying those who appear “resistant” to SARS-CoV-2 is of interest, he said.

This point underlies Zatz’s focus as well: In her Covid studies, she’s looking for mutations in genes that regulate the immune response to viruses. She hypothesized that two main biological pathways could be involved in resistance. The first is the major histocompatibility complex (MHC), which includes various genes that govern how the immune system recognizes and latches on to viral proteins. Another factor is the leukocyte receptor complex (LRC), which is involved in how various types of white blood cells – such as natural killer (NK) cells — respond to pathogens.

In April 2021 Zatz’s team published the initial results of the discordant couples study in a preprint posted to medRxiv. Contrary to the lab’s hypothesis, no single gene mutation in these pathways was responsible for Covid-19 resistance. In July, Zatz’s lab re-analyzed the results. Among the genes related to immune modulation, 46 variants in the MICA and MICB genes were associated with symptomatic infections, all which influenced NK cell activity in infected individuals but not in their resistant partners. Zatz found that NK activity was less efficient in symptomatic individuals. The resistant individuals were mostly women, with professions ranging from physicians to teachers to the trades. In other words: the ‘super-resisters’ could be anyone. This study has been peer-reviewed and is awaiting publication in the journal Frontiers in Immunology.

Overall, the findings echo that of the Kenyan sex worker study for HIV: Several gene mutations, working together, may confer resistance. Zatz hopes that this research, and the studies that follow, will shed light on future Covid treatments.

Her earlier Zika work, she says, illustrates how understanding resistance can lead to novel therapeutic approaches. Using the findings from the study of twins’ neuroprogenitor cells, and knowing that certain brain tumors of embryonic origin are largely comprised of the same NPCs, her team decided to test whether the Zika virus might be used to attack cancer cells. Hence a new experiment was born: Brain tumors in mice, “treated” with Zika, showed significant shrinkage — and in one-third, the cancer cells disappeared completely. When Zatz’s team repeated the experiment in dogs, the reduction in tumor size extended their lives for many months without side effects.

“Our enemy — the virus — became our ally,” Zatz said.

While Zatz and other researchers pursue ways to make all of us — as Casanova put it — feel like King Kong, Andrade doesn’t see herself as being endowed with superhuman abilities to combat the pandemic.

“It’s still not clear if I can spread Covid or carry the virus to someone, even though I am ‘resistant’ to it. Erik is clearly vulnerable, so it doesn’t feel like much of an advantage if my loved ones are not resistant,” Andrade wrote in an email. “And with new, more contagious variants complicating the slow rate of general population vaccination in Brazil, it’s really hard to be more relaxed about it.”