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Genetic variant linked to both Covid risk and HIV protection

A new study published in the journal Proceedings of the National Academy of Sciences describes a genetic risk factor for severe COVID-19 that some humans seem to have inherited from the Neanderthals – a prehistoric population of hominids that lived in Eurasia between 200,000 and 35,000 years ago. The experts report that this particular genetic variant may offer a certain degree of protection against HIV and possibly other infectious diseases.

According to study author Hugo Zeberg, a researcher at the Max Plank Institute for Evolutionary Anthropology, this major genetic risk factor for severe COVID-19 – located on chromosome 3 in a genomic region encompassing a gene cluster encoding chemokine receptors – has been introduced into modern human populations through gene flow from Neandertals 50,000 to 70,000 years ago. While there was no clear evidence why this genetic variant was adaptive, it has nevertheless increased in frequency over time and is unusually common today, with 16 percent of Europeans, and 50 percent of South Asians carrying it in their genomes.

In a previous study published in 2021, Professor Zeberg and Professor Svante Pääbo, a colleague from the Max Plank Institute, have found that hospitalized COVID-19 patients presenting this genetic variant were 70 percent more likely to develop a severe form of the disease. But why would such a dangerous DNA variant persist for such a long time and spread so widely in human populations?

“This major genetic risk factor for COVID-19 is so common that I started wondering whether it might actually be good for something, such as providing protection against another infectious disease,” Professor Zeberg said.

Further analyses revealed that people who carried this genetic risk factor for COVID-19 had fewer CCR5 receptors, which are known to be used by another virus to infiltrate into and infect white blood cells: the notorious human immunodeficiency virus (HIV). By analyzing patient data from three major biobanks (FinnGen, UK Biobank, and the Michigan Genomic Initiative), Professor Zeberg discovered that carriers of the risk variant for COVID-19 had a 27 percent lower risk of contracting HIV. 

“This shows how a genetic variant can be both good and bad news: Bad news if a person contracts COVID-19, good news because it offers protection against getting infected with HIV,” he said.

However, since HIV emerged only in the 20th century in human populations, protection against AIDS cannot be an explanatory factor for why this genetic variant persisted through natural selection for so long. “Now we know that this risk variant for COVID-19 provides protection against HIV. But it was probably protection against yet another disease that increased its frequency after the last ice age,” Professor Zeberg concluded.

Further research is needed to find out which other diseases may be modulated by this genetic variant and in what ways (smallpox seems to be a possibility, though further data is needed). Clarifying this might offer new therapeutic pathways in the case of already established human diseases, and perhaps even against pathogens that may emerge in the future and cause massive outbreaks.

By Andrei Ionescu, Staff Writer

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