“In trying to find what makes some people more vulnerable to severe COVID-19, several groups identified mutations in a region of chromosome 3 as a likely culprit. Around the same time, a study in 2020 showed that region was inherited by modern humans through breeding with Neanderthals¹. But it remained unclear which specific gene variants increase the risk of severe symptoms, and why. Now a new study involving Italian scientists has narrowed the search to four variants of Neanderthal origin related to functional genes².

The study began as a computational analysis that compared samples from modern humans from a biobank in Estonia with genomic sequences from Neanderthals, to understand which genes were conserved across evolution. Using ad-hoc software, researchers at Tartu University had found that a region of chromosome 3 comprising of multiple genes was included in our DNA from reproducing with Neanderthal ancestors, thus coming independently to the same conclusion published in 2020. “We started this project before COVID-19 and found several polymorphisms in the region that matched the Neanderthal samples,” says Davide Marnetto, previously at Tartu, and now at the University of Turin. When the association with severe disease became clear, Marnetto and colleagues decided to dissect their results further.

To investigate which Neanderthal-inherited variants directly affect gene expression, the scientists performed a massive parallel reporter assay (MPRA) in collaboration with a group from Harvard University. This technique allows to test the expression of a specific variant in human cell lines to assess their functionality and relevance for the gene function. They also tested variants either present in the human population before Neanderthal mixing or new variants that appeared at a later stage in human evolution, to consider any possible combination for the variants of interest. The scientists used cell lines expressing ACE2, the receptor for SARS-CoV-2. In the presence and absence of SARS-CoV-2, they found four variants on the “Neanderthal” section of chromosome 3 which strongly modulate the regulation of CCR1 and CCR5 genes, two critical receptors for chemokines, small proteins that play a major role in the activation of immune response. Cytokine storms are characteristic of severe COVID-19 reactions, and the study implies that those four specific ancestor variants the CCR1 and CCR5 are involved.

“Differently from similar studies, this work went all the way, demonstrating experimentally what they saw computationally,” says Hauke Busch, Professor at the University of Lübeck, who was not involved in the study. Using a three-way approach (evolutionary, computational, and molecular biology), the researchers were able, for the first time, to correlate specific variants of the genes inherited from the Neanderthal with the causative effects observed in response to the COVID-19 infection.

The authors point out that though the Estonian genomic collection used in the study is a good representative of Europeans with Neanderthal origins, it does not represent the wider human population. More studies will be needed to confirm the role of those variants and other genetic risks in the response to COVID-19 at a global level.