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The omicron variant might have originated in someone with a suppressed immune system

ARI SHAPIRO, HOST:

U.S. health officials said today that the omicron variant of the coronavirus is already in nearly two dozen countries. They emphasized that the full extent of the variant's spread is still unclear, and it's only a matter of time before it is detected in the U.S. This strain's high number of mutations has kicked off a frenzy of research. Scientists are racing to figure out how transmissible the variant is and how resistant it may be to vaccines. And they're also investigating this mystery - how did this heavily mutated variant get created? NPR global health correspondent Nurith Aizenman is here to bring us up to date.

Hi, Nurith.

NURITH AIZENMAN, BYLINE: Hi, Ari.

SHAPIRO: How can scientists actually determine where a given variant came from?

AIZENMAN: Well, the genetic code provides clues. It's kind of analogous to if a person wants to find out their own origin - were their ancestors from Ireland or from China? - they can find the traces of that ancestry in their genetic code. Well, scientists who track the coronavirus' evolution can determine a given strain's ancestry in one region of the world and then see, as they take samples over time and sequence them, how that particular strain, step by step, starts to pick up additional mutations until it morphs into a significantly different strain.

One of the premier researchers who does this kind of work is Trevor Bedford. He's a computational virologist and a professor at the Fred Hutchinson Cancer Research Center in Seattle. He says, when you look at the family tree for this new omicron variant, there's something surprising.

TREVOR BEDFORD: With omicron, your closest sequences are back from mid-2020 - so over a year ago, which, like - that is very rare to see.

AIZENMAN: In other words, while they can tell that this variant evolved from a strain that was circulating in mid-2020, there's been no trace of all the intermediate versions of it. And these mutations put it a long way from that 2020 strain.

SHAPIRO: Do scientists have any idea why that could be?

AIZENMAN: Well, one possibility is that the mid-2020 strain started circulating in some country or area where there hasn't been a lot of monitoring. So it was evolving under the radar all this time. But Bedford finds that hard to believe, as does another prominent scientist, Richard Lessells. He's an infectious disease specialist at the University of KwaZulu-Natal in Durban, South Africa. And he's part of the team that found omicron in South Africa and alerted the world. He says given how robust the surveillance network is in South Africa, it's improbable that precursors to omicron wouldn't have been found there. Instead, like Bedford, Lessells favors another hypothesis.

SHAPIRO: Tell us what that hypothesis is.

AIZENMAN: So Lessells says it's likely that omicron developed in the body of a single person, a person whose immune system was suppressed - say someone with uncontrolled HIV - and that all this time, omicron was lingering in their body. Here's how he says that process works.

RICHARD LESSELLS: Because of that immunosuppression, they can't clear the virus, and so they have a chronic infection. And the virus continues to replicate for several months. And of course, it evolves over that period of time.

AIZENMAN: Basically, getting better and better at evading the person's immune system with each mutation - and then eventually, by chance, omicron spreads from this person into others.

SHAPIRO: Is that just an educated guess, or is there evidence that that's what happened?

AIZENMAN: Yeah. I mean, there's not specifically evidence in the case of omicron of this, but Lessells' team has seen this process happen in a prior case. There was a woman infected with untreated HIV who then got the coronavirus. So the takeaway, he says, is that it's one more reminder that a key to ending this pandemic is to do a lot more for the millions of people in southern Africa who have HIV and are not getting medications.

SHAPIRO: NPR's Nurith Aizenman, thank you.

AIZENMAN: You're welcome. Transcript provided by NPR, Copyright NPR.