One of the biggest lingering questions surrounding COVID-19 is why some people with the disease get sicker than others. While many factors are likely at play, numerous studies suggest a person’s genetics can predispose them to severe disease. Indeed, a genome-wide association study and a COVID-19 Host Genetics Initiative dataset specifically point to a 50 kilobase-sized genomic segment on chromosome 3 as a major genetic risk factor for severe COVID-19—a segment that, back in 2020, paleogenomicist Svante Pääbo and his collaborator Hugo Zeberg showed was inherited from Neanderthals some 50,000 to 70,000 years ago. However, the genetic variants on this segment—all strongly linked to each other—are legion, so the precise ones that drive its association with severe COVID-19 have remained elusive.
Now, Terence Capellini, a Harvard University human evolutionary biologist, and colleagues have systematically evaluated the more than 600 genetic variants in the region. Ultimately, they homed in on three variants that regulate two key chemokine receptor genes that play a role in mediating the cytokine storm that is often involved in the pathogenesis of severe COVID-19. The results, published February 10 in eLife, shed new light on the interplay between the host genome and COVID-19 outcomes and help unravel the molecular mechanisms that underpin severe COVID-19.
“From an evolutionary perspective, this work provides a beautiful example, all the way to the molecular level, of how a small part of our genome that was inherited from Neanderthals is impacting our health . . . to this day,” says Steven Reilly, a geneticist at the Yale School of Medicine, who wasn’t involved in the research. He adds that “the fact that this risk comes from DNA that originated in Neanderthals is very interesting and highlights how complex human ancestry is.”
To probe the specific genetic variants or alleles on chromosome 3 and their potential for driving severe COVID-19, Capellini’s team used population genetics and functional genomics techniques in tandem with a Massively Parallel Reporter Assay (MPRA). MPRA is a sophisticated functional genomics tool that allows scientists to test the potential impacts on gene regulatory function of thousands of genetic variants at a time.
The researchers first used computational analyses to understand how the genetic variants in the region overlapped with data on human immune cell function. They then used MPRA “to whittle down large blocks of linked variants to a few that are relevant,” explains Capellini. This allowed them to screen all 613 variants en masse in an immune cell line, which, in turn, enabled them to pinpoint the precise variants that altered the expression of key genes involved in mediating the immune response in COVID-19.
For those variants that did modulate gene expression, the researchers ascertained which of the two versions of the variant—the Neanderthal (or introgressed) allele, or the modern human one—did so. They thus pared down the 613 genetic variants in the region first to 20 variants that impacted gene expression, and then to four that showed activity differences between the introgressed and nonintrogressed versions. Specifically, they found on further experimentation that three of the four introgressed alleles significantly altered the expression of CCR1 and CCR5, genes that code for key receptors involved in immune signaling between cells in the presence of SARS-CoV-2.
The genomic region on chromosome 3 that is linked to severe COVID-19 houses a gene cluster encoding receptors for chemokines—proteins that attract immune cells to an infection. These chemokine receptor genes, such as CCR1, CCR2, CCR3, CCR5, and CCR9, are all located in close proximity to the variants on chromosome 3 that are associated with disease severity and are, thus, in turn, likely to confer risk for severe COVID-19—though they have not been among the genes most strongly associated with severe disease in previous studies.
Zeberg, an evolutionary geneticist at Karolinska Institutet in Stockholm who studies gene flow from Neanderthals and Denisovans into modern humans and who wasn’t part of the research, tells The Scientist that “the combination of experiments and bioinformatics” is praiseworthy. Furthermore, he says “the identification of the CCR5 gene is fascinating,” as he had previously found that this major genetic risk factor for severe COVID-19 protects against HIV.
The genetic basis of any complex disease is difficult to understand at the molecular level, Reilly says, as doing so involves pinpointing the small number of disease-associated genetic changes out of what is a massive genome. “The authors . . . bring in powerful population genetic tools to identify and characterize this locus,” he says, adding that the combination of population genetics and MPRA is more powerful than either approach on its own. He adds that he’s “particularly impressed” by the depth of the study—especially the researchers’ thought to test the variants’ function in the presence of SARS-CoV-2.
Michael Dannemann, an evolutionary geneticist at the University of Tartu in Estonia who also wasn’t part of the research, agrees, telling The Scientist that the application of MPRA to study Neanderthal DNA is a powerful approach and the paper’s discovery of the most likely functionally relevant variants “would not have been possible” using other approaches.
Capellini posits that the paper’s insights could have important therapeutic implications. But Zeberg isn’t so sure. Although there is “a great need to understand the major genetic risk factor for severe COVID-19,” Zeberg says, he tells The Scientist that he is “a bit surprised that the candidate causal variants identified . . . are not among the variants most strongly associated with severe COVID-19 in the genetic association studies.”
How these Neanderthal genes became prominent in the human genome remains to be uncovered. Capellini speculates that the variants could have been beneficial in the past, and therefore, selective pressures cemented their presence in the human genome.
Reilly concurs that the data would suggest that these alleles conferred some benefit to Neanderthals and ancient humans. “In a modern context it seems to confer risk, but it’s very interesting to think about what adaptive role it was playing earlier in human evolution.”