Omicron keeps mutating as U.S. cases rise

BA.2 levels are particularly high (93% prevalence) in the New York/New Jersey region, and new sublineages have recently been identified in New York. Chart via the CDC.

As though it’s not already confusing enough to distinguish between Omicron BA.1 and BA.2, more sublineages have popped up in recent weeks as Omicron continues to spread and mutate. Here are two that I’m watching, though they don’t seem to be major causes for concern at this time.

BA.2 sublineages in New York

Last week, the New York State Department of Health announced that it has identified new sub-variants of BA.2, called BA.2.12 and BA.2.12.1, through testing and sequencing. The BA.2 lineage overall accounts for the vast majority of cases in New York, and these two new strains are causing over 90% of new cases in the central part of the state.

These two sublineages seem to be spreading even faster than original BA.2 in New York, with a growth advantage of about 25%—perhaps explaining in part why the state is once again seeing higher case rates than other parts of the country. It’s unclear so far whether these BA.2 offshoots will have any impact on severity or vaccine effectiveness; the health department is looking into this.

Also worth noting: New York has a more robust variant surveillance system than a lot of other states. It’s very possible that Omicron is mutating elsewhere in the country, too; but those potential sublineages haven’t been identified yet.

I appreciated this quote from a state health official in a New York Times update by Apoorva Mandavilli on the new sub-variants, as it sounds pretty similar to what I’ve been telling friends and family recently:

The number of cases so far may seem to be insignificant compared with the steep Omicron peak of the winter, but “we’re essentially back at levels of case rates back to the Delta wave,” said Eli Rosenberg, deputy director for science at the New York State Department of Health. “This would have been a very significant wave already by last year’s standards.”

XE recombinant in the U.K. and other countries

This new offshoot hasn’t been identified in the U.S. yet, but it deserves some attention. Essentially, BA.1 and BA.2 have combined—likely in regions or even in individual people that are experiencing simultaneous infections of both strains—and formed what scientists call a “recombinant” variant, with some genetic material from both. The BA.1/BA.2 conglomerate has been labeled XE.

According to research so far, XE may have a slight growth advantage over BA.2. The World Health Organization (WHO) estimated that XE is about 10% more transmissible than BA.2, but further study is needed to confirm this number. Over 600 XE cases have been identified in the U.K., according to TIME, along with smaller numbers in India, Thailand, and other countries.

Scientists aren’t particularly concerned about XE at this point because it hasn’t been spreading rapidly and outcompeting other variants, like the original Omicron did in the winter. But agencies like the U.K.’s Health Security Agency and the WHO are monitoring for any worrying signals.

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