Study maps immune system genes involved in resistance to SARS-CoV-2

In a study reported on Frontiers in Immunology, Brazilian researchers have taken the first steps toward understanding why some people are naturally resistant to infection by the novel coronavirus.

The researchers analyzed genetic material from 86 discordant couples in the sense that only the wife or husband was infected by SARS-CoV-2 although both were exposed to the virus. The results suggest that certain genetic variants found more frequently in the resistant subjects are associated with more efficient activation of defense cells known as natural killers (NKs). This type of white blood cell is part of the innate immune response, the first barrier against viruses and other pathogens. When NKs are correctly activated, they are able to recognize and destroy infected cells, preventing the disease from developing in the organism.

“Our hypothesis is that the genomic variants most frequently found in the susceptible spouse lead to the production of molecules that inhibit activation of NKs. However, this theory has yet to be validated by means of functional studies,” Mayana Zatz, last author of the paper, told. Zatz is a professor at the University of São Paulo’s Institute of Biosciences (IB-USP) and principal investigator of the Human Genome and Stem Cell Research Center (HUG-CELL), one of FAPESP’s Research, Innovation and Dissemination Centers (RIDCs).

After announcing to the press that they were recruiting volunteers for the project in mid-2020, the IB-USP scientists were contacted by some 1,000 couples with similarly intriguing stories. For example, a man aged more than 70 had to be hospitalized for treatment of complications from COVID-19, while his wife, who was about the same age, and his mother-in-law, aged 98 and living in the same house, displayed no signs of infection. Another curious case was that of a 100-year-old man who tested negative for the virus despite having been routinely in contact with his 90-year-old wife, who was infected.

“We thought cases like these were rare and were surprised to get so many reports. We selected 100 couples with comparable characteristics, including age and genetic ancestry, and took blood samples for detailed analysis,” Zatz said.

Couples were selected and material was collected by Mateus Vidigal, with the support of a postdoctoral scholarship from FAPESP. 

“The first step was a serological test to exclude asymptomatic cases [people who were infected but did not have symptoms] from the sample. That left 86 couples who were genuinely serodiscordant – only one spouse had antibodies against the virus in their blood,” Vidigal said.

While men were in the majority in the susceptible group (53 vs. 33), women predominated in the resistant group (57 vs. 29). Vidigal stressed that the study was conducted before novel variants of SARS-CoV-2 considered more transmissible were detected. “We can’t be sure the findings would be the same for people exposed to P.1, for example,” he said.

Complex inheritance

According to Zatz, the fact that resistance to SARS-CoV-2 is a relatively common trait in the population – unlike resistance to HIV, the virus that causes AIDS, for example – points to a complex genetic inheritance in which many genes are involved.

“That means that to find something significant when we look at the genome as a whole we would need to have a huge sample with more than 20,000 volunteers. So we decided to focus on two large groups of genes associated with immune response: the main histocompatibility complex [MHC] and the leukocyte receptor complex [LRC],” Zatz explained. “MHC genes determine whether two individuals are compatible in the case of a transplant, for example.”

Even with this filter, the task was far from trivial. Some of the genes in the MHC and LRC have more than 7,000 polymorphisms (different forms). “An example of polymorphisms is the different blood types. There are four genetic variants in the ABO system: A, B, AB, and O. In the case of MHC and LRC, some genes have thousands of variants,” she said.

To assist them in this daunting task, the IB-USP group established a collaboration with Erick Castelli, a researcher at São Paulo State University’s Botucatu Medical School (FMB-UNESP). Computational methods developed recently by Castelli with FAPESP’s support facilitated the study of MHC and LRC genes.

“Imagine you’re trying to assemble a jigsaw puzzle [the genome] with only one reference but many similar pieces and thousands of possibilities for each piece. The differences between them are very subtle so that it’s impossible to know where each one fits. The algorithm decides where to put each piece on the basis of an analysis of thousands of sequences that have been described. The method enables us to map the genome in great detail, to infer the sequence for each chromosome, and to predict which protein will be encoded by each gene,” Castelli told Agência FAPESP.

Analyzing the MHC, they found that variants of the genes MICA and MICB appeared to influence resistance to SARS-CoV-2. According to Castelli, their expression normally increases when cells come under some kind of stress, and this leads to the production of molecules that bind to NK receptors, signaling that something is wrong with the cells in question. 

“In the case of MICA, the most frequent polymorphism in infected subjects appears to increase production of the protein encoded by this gene, possibly in soluble form, inhibiting activation of NK cells,” he said. “In the case of MICB, a variant associated with reduced expression of the messenger RNA that encodes the NK-activating protein was 2.5 times more frequent among susceptible subjects. Both pathways, therefore, lead to lower activation of this immune system barrier.”

In the LRC, the analysis identified variants of interest in the genes LILRB1 and LILRB2. “In infected subjects, our analysis detected a fivefold increase in a variant of LILRB1 that appears to lead to augmented expression of receptors that inhibit the action of NK cells,” Castelli said.

Hypotheses regarding the role of each polymorphism in resistance or susceptibility to SARS-CoV-2 were worked out in partnership with researchers at Heart Institute (INCOR) of the University of São Paulo’s Medical School (FM-USP) led by Edécio Cunha Neto. 

“Generally speaking, we hypothesize that susceptible people have variants that result in a weaker response by NK cells, while in resistant people this response is more robust,” Cunha Neto said. “Several tests can be performed to verify this hypothesis. One would involve incubating SARS-CoV-2 with peripheral blood cells from susceptible and resistant individuals, and observing NK activation in each case.”

Even if the findings are confirmed, he added, other innate immune mechanisms must act in parallel to determine resistance to the virus. “One of them is certainly the capacity of defense cells to rapidly produce interferons [a protein class with a key role in anti-viral defenses],” he said.

The research was supported by FAPESP via six projects: 13/08028-1, 14/50931-3, 19/19998-8, 20/09702-1, 13/17084-2, and 17/19223-0.

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