Omicron variant may have caught a piece of cold virus

The omicron variant of the virus that causes Covid-19 probably acquired at least one of its mutations by capturing a snippet of genetic material from another virus — possibly the one causing the common cold — present in the same infected cells, researchers say.

This genetic sequence does not appear in any previous version of the coronavirus, called Sars-CoV-2, but it is very present in several other viruses, including those that cause the common cold, and also in the human genome, researchers said.

By inserting that particular bit into itself, the omicron could be trying to appear “more human,” which would help prevent the onslaught of the human immune system, said Venky Soundararajan of data analysis firm nference in Cambridge, Massachusetts, who led the study published on Thursday (2) on the OSF Preprints website.

This could mean that the virus is more easily transmitted, although it causes only mild or asymptomatic illness. Scientists do not yet know whether omicron is more infectious than other variants, whether it causes more severe disease, or whether it will outperform delta as the predominant variant. It may take several weeks for us to have these answers.

Cells in the lungs and gastrointestinal system can harbor Sars-CoV-2 and common cold coronaviruses at the same time, according to previous studies. This joint infection sets the stage for viral recombination, a process in which two different viruses in the same host cell interact while making copies of themselves, generating new copies that have some genetic material from the two “parents”.

This new mutation may have first occurred in a person infected with the two pathogens when one version of Sars-CoV-2 captured the genetic sequence of the other virus, said Soundararajan and colleagues in the study, which has not yet been peer-reviewed.

The same genetic sequence often appears in one of the coronaviruses that cause colds in people — known as HCoV-229E — and in the human immunodeficiency virus (HIV), which causes AIDS, Soundararajan said.

South Africa, where omicron was first identified, has the world’s highest rate of HIV, which weakens the immune system and increases people’s vulnerability to infections with common cold viruses and other pathogens. In this region of the world, there are many people in whom the recombination that added this ubiquitous set of genes to the micron could have taken place, said Soundararajan.

“We probably lost many generations of recombinations” that occurred over time and that led to the emergence of the omicron, added the scientist.

More research is needed to confirm the origins of omicron mutations and their effects on function and transmissibility.

There are competing hypotheses that the latter variant may have spent some time evolving in an animal host.

Meanwhile, Soundararajan said, the new findings underscore the importance of people getting immunized with the vaccines currently available for Covid-19.

“You need to get vaccinated to reduce the likelihood that other people who are immunocompromised will encounter the Sars-CoV-2 virus,” Soundararajan said.