The Omicron variant of the virus that causes COVID-19 likely acquired at least one of its mutations by taking pieces of genetic material from another virus, possibly the one that causes the common cold, that was in the same infected cells.
This genetic sequence did not appear in an earlier version of the coronavirus, called SARS-CoV-2, but is ubiquitous in many other viruses including those that cause the common cold, as well as in the human genome, the researchers said.
"By inserting this particular snippet into itself, Omicron might make itself look 'more human', which would help it evade attacks by the human immune system," said Venky Soundararajan of Cambridge, a Massachusetts-based data analytics firm.
This could mean the virus is more contagious, but causes only mild or no symptoms. Scientists don't yet know whether Omicron is more contagious than the other variants, whether it causes more severe disease or whether it will overtake Delta as the most common variant. It can take several weeks to get answers to these questions.
According to previous research, cells in the lungs and digestive system can host both SARS-CoV-2 and the common cold coronavirus at the same time. Such coinfection regulates viral recombination, a process in which two different viruses in the same host cell interact while making copies of themselves, then producing a new copy that has some genetic material from both "parents".
"This new mutation was first able to occur in people infected with both pathogens when the SARS-CoV-2 version took the genetic sequence from another virus," said Soundararajan.
The same genetic sequence appears many times in one of the coronaviruses that causes the common cold in humans, known as HCoV-229E and in the human immunodeficiency virus (HIV) that causes AIDS.
South Africa, where Omicron was first identified, has the highest rates of HIV in the world, which weakens the immune system and increases a person's susceptibility to infection with the common cold virus and other pathogens. In that region, there are many people who allow the recombination that adds gene sequences to the Omicron.
"We probably missed the many generations of recombination that happened over time and that led to the emergence of the Omicron," Soundararajan said.
Further studies are needed to confirm the origin of the Omicron mutation and its effect on function and transmissibility. There are many competing hypotheses that the newest variant may have spent some time evolving in an animal host.
Meanwhile, Soundararajan said, the new findings underscore the importance of people getting the currently available COVID-19 vaccine.
"You have to vaccinate to reduce the chance that other people, whose immunity is compromised, will encounter the SARS-CoV-2 virus," Soundararajan said.