Thread by @vinodscaria

What do we know and don't about the Delta sub-lineage AY.4.2
ℹ️ AY.4.2 is a sub-lineage Delta (B.1.617.2) in the UK which has shown consistent increase over the past few months and has caught attention.
Plot: Sanger COVID-19 Genomic Surveillance Dashboard covid19.sanger.ac.uk/lineages/

The background:
Delta had significant advantage over other lineages, in almost all regions, practically eliminating all other lineages as they spread widely.
The continued evolution of delta provided a number of sublineages
There are now ~55 sublineages (AY.1 - AY.41) of Delta

Some of the AY.x sublineages have geographical preponderance, due to mutations present at the time of introductions. For example, UK has a AY.4 sublineage. More about the lineages and distribution is available at cov-lineages.org/lineage_list.h…

One need to keep in mind that the annotation of sublineages of delta by PANGO pango.network is still not a very accurate process, since the lineages are not very different from each other and continue to evolve.
(eg: early annotations of AY.4 in India had this issue)

The Delta spread in UK during the present wave was largely the sublineage AY.4
outbreak.info/location-repor…
The AY.4 sublineage has now diverged to 2 more sublineages AY.4.1 and AY.4.2 with specific genetic mutations.
AY.4.2 is charecterised by S:Y145H and S:A222V

While the rise of AY.4.2 is seen in UK this does not clearly mean significant advantage over delta
1. The time of emergence had alpha and beta which was much less transmissible than delta
2. Growth is not seen in any other regions
3. AY.4 does not seem to be replacing delta

@TWenseleers has a thread on the growth rate advantage of AY.4.2

https://twitter.com/TWenseleers/status/1450243269200424960?s=20

@chrischirp shared the comparison within regions

https://twitter.com/chrischirp/status/1450170379675316230?s=20

So until there is a significant advantage demonstrated, AY.4 is so sort of a 'scariant' . Keeping a close watch is possibly a prudent approach.