Delta AY Sub-Variant, Which Requires 'Urgent Research', Found in These U.S. States

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A new COVID Delta offshoot that scientists have voiced concerns about as it spreads through the U.K. has also been detected in the U.S.

© Christophe Archambault/AFP / Getty Scientists work on COVID genome sequencing in a laboratory at the Pasteur Institute in Paris on January 21, 2021. The Delta variant has split into dozens of offshoots.

However, there have only been six U.S. cases reported and it does not appear to have been spreading recently in the states.

Delta has branched off into dozens of different types that are referred to with the ‘AY’ label.

One particular Delta AY variant has sparked calls for investigation after rising sharply in the United Kingdom from July onwards, as seen in the following GISAID virus sampling data chart from Outbreak.info.

© Outbreak.Info An Outbreak.Info chart showing sample detection of AY.4 with Y145H (AY.4.2) in the U.K. Outbreak.Info

It’s a version of the AY.4 Delta variant that already accounts for around 80 percent of recent cases in the U.K. Now, scientists have noticed an offshoot of the AY.4 variant—an offshoot of an offshoot—that includes a spike mutation known as Y145H.

In the U.K. it has accounted for around eight percent of new sequenced cases in recent days and about one percent of total cases, Outbreak.Info shows.

Dr. Scott Gottlieb, former commissioner of the U.S. Food and Drug Administration (FDA) from 2017 to 2019, took note of the variant in a tweet on Sunday and said it had been increasing in prevalence since about July.

He wrote: “We need urgent research to figure out if this Delta plus is more transmissible, has partial immune evasion?

“There’s no clear indication that it’s considerably more transmissible, but we should work to more quickly characterize these and other new variants.”

UK reported its biggest one-day Covid case increase in 3 months just as the new delta variant AY.4 with the S:Y145H mutation in the spike reaches 8% of UK sequenced cases. We need urgent research to figure out if this delta plus is more transmissible, has partial immune evasion?

— Scott Gottlieb, MD (@ScottGottliebMD) October 17, 2021

Cornelius Roemer, a bioinformatics scientist, has suggested labeling the new Delta offshoot with the name AY.4.2.

AY.4.2 remains very rare in the U.S., where only six sequences have been recorded. In the U.K. by comparison, there had been 14,385 sequences as of October 16.

It has only been detected in four states altogether, Outbreak.Info shows – Oregon, where there have been three cases, and North Carolina, Washington, and Washington D.C., where there has only been one case in each.

Professor Christina Pagel from the Department of Mathematics at University College London (UCL) has noted on Twitter that the AY.4.2 is “not growing anywhere near as fast as Delta did” and said the variant is “something to keep an eye on but not panic over.”

That was 10 days ago, so hopefully it will start showing up in COG & Sanger tracking soon.

It’s not growing anywhere near as fast as Delta did & even the *worst* case is only a very moderate advantage (maybe 10%) vs 50% that alpha had over wildtype and delta had over alpha 4/6

— Prof. Christina Pagel (@chrischirp) October 14, 2021

She added that continuing high cases of Delta in countries like the U.K. are giving it “plenty of opportunities” to keep mutating into new subtypes.

Professor Francois Balloux, director of the genetics institute at UCL, tweeted on Saturday that the Y145H mutation is not an obvious candidate for COVID advantages like immune escape or increased transmissibility but “it feels worthwhile keeping an eye on it.”

To summarise, the recent rise in the UK of AY.4.2 would be compatible with a transmissibility advantage of ~10%. As such, it feels worthwhile keeping an eye on it. Though, based on its genetic make-up, it is not a priori an obvious VoC candidate.

8/

— Prof Francois Balloux (@BallouxFrancois) October 16, 2021

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