The mystery of where omicron came from — and why it matters

NURITH AIZENMAN

The discovery of omicron — the new variant of coronavirus with a high number of concerning mutations — has kicked off a frenzy of research. Scientists are racing to figure out how transmissible this variant is and how resistant to vaccines.

They’re also grappling with a mystery: How did omicron get created?

NPR spoke with two scientists in the thick of this research. Trevor Bedford is a computational virologist and professor at the Fred Hutchinson Cancer Research Center in Seattle. Richard Lessells is an infectious disease specialist at the University of KwaZulu-Natal in Durban, South Africa, and part of the team that identified omicron in South Africa and alerted the world. Here’s what they have to say.

Omicron’s genetic family tree contains a big surprise

One of the key tools that scientists use to puzzle out the origin of a particular coronavirus variant is to look at its genetic code. Just as a person who wants to find out their ancestry — were their forebears Nordic? Mongol? — can find traces of that lineage in their genes, the virus’s genome contains clues.

“It’s been very common to use an evolutionary tree — or a family tree — of these SARS-CoV-2 viruses to catch introductions in places like Australia and Taiwan that have not had a lot of local spread,” says Bedford. “You can figure out where the importations are coming from by looking at the viral genome and checking, ‘Is it close in its sequence characteristics to [strains] that are circulating elsewhere that have been sequenced and shared with the database?’ ”

Scientists can then see, as they continue to take samples in the new region over time, how each particular strain starts to pick up additional — often benign — mutations step-by-step until it morphs into a significantly different strain.

But Bedford says that when you look at the family tree for this omicron variant there’s something surprising: “With omicron, your closest sequences are back from mid-2020 — so over a year ago. That is very rare to see.”

In other words, while scientists can tell that this variant evolved from a strain that was circulating in mid-2020, in the intervening months there’s been no trace of all the intermediate versions that scientists would have expected to find as it morphed into its current form.

“It doesn’t tie into anything that was circulating more recently,” says Bedford.” Yet its mutations put it a long way from that 2020 strain.