2021-09-06: updated with the sub-variant AY.25. The situation is changing rapidly. This article is not being updated
The CDC uses W.H.O’s classification of the SARS-COV2 variants. W.H.O has failed to elevate Delta sub-variants into full variants when such a classification is more than warranted. Consequently, what has been called Delta (B.1.617.2) since May 2021 is a mix of many sub-variants with different properties. This confused clinicians and the CDC added to this confusion.
For the last couple of weeks, the prevalent coronavirus variant is not Delta (B.1.617.2), but its sub-variants AY.3, AY.4, and AY.25 (B.1.617.2.3, B.1.617.2.4, B.1.617.2.25, respectively). AY.25 is very similar to AY.4 AY.3-AY.4 sub-variants represented 25%-30% of sequenced samples in the US from early July to late August, and are therefore likely responsible for higher severity of the cases. Now these two sub-variants represent more than 60% of cases in the US. AY.4 is on its way to becoming the dominant variant.
Initially, the CDC identified significant sub-variants AY.1, AY.2, and AY.3, and tracked them separately. It failed to identify and track AY.4. When the percentages of AY.1 and AY.2 cases dropped, the CDC stopped tracking AY.3, and only continued to track AY.1 and AY.2. This created the false impression that the Delta sub-variants had nearly disappeared.
The mutation S:G142D in the N-terminal domain (NRD) of the spike, which was not present in the original Delta variant, rapidly rose to ~50% of all sequences in late June through mid-August, and then dropped to <15%.
Among the mutations present in AY.3 and AY.4, but not in the original Delta (B.1.617.2), are ORF1a:T3255I and ORF1a:P2287S, also present in the dreadful Lambda variant (C.37). Curiously, the frequency of this pair of mutations has jumped from 2% in May to more than 80% of all sequenced samples by the end of August.
This graph is from September 2. See https://outbreak.info/location-reports?loc=USA for the live updates.
The original B.1.617.2 and all the sub-variants have the spike mutations P681R (thought to be responsible for turbocharged transmission) and L452R (the strongest vaccine immunity breaker).
AY.3 and AY.4 are distinguished from the original Delta mainly by a large set of mutations in ORF1ab. The speed with which these two sub-variants have displaced all other Delta sub-variants and other variants of concern shows their significance.
Originally published on Sep 2, 2021. Updated over Sep 3-5. Corrected with variant AY.25 on Sep 6.