Thread by @vipintukur

A short thread on sub-lineages of #Omicron & their current epidemiology

Now, we know the Omicron (BA.1) has got 3 sub-lineages: BA.1, BA.2 & BA.3.

1/

https://twitter.com/vipintukur/status/1482183923027562496

-BA.1 is known as Omicron, the parent variant.
-BA.2 is sub-variant that shares many but not all mutations with BA.1. >5000 cases so far
-BA.3 probably antigenically similar to BA.1 as it shares mutations at 417, 446, 484 & other key sites. Only 42 cases are reported so far 2/

-Both BA.1 & BA.2 carry almost all spike RBD mutations 1st noted for Omicron & both furin cleaveage adjacent mutations
-BA.1 & BA.2 have NSP6 deletion seen in other VOC
-BA.2 does not carry spike:69/70del deletion & will thus not be detectable by SGTF (S-gene target failure) 3/

-BA.2 less antigenic escape than BA.1 because it lacks G446S.

-Another sublineage is BA.1 + R346K that is more escape because site 346 is major antigenic site. 4/

It was noticed that a number of genomes whilst having many of the defining mutations of Omicron do not have the full set and also have a number of their own unique mutations. 5/

Figure showing diff in mutations: The yellow column gives the mutations unique to the new 'BA.2' lineage, blue column the mutations unique to the original 'BA.1' lineage of Omicron & the green column those shared by both - i.e. inferred to have arisen prior to the split 6/

Here are calculated binding scores by @jbloom_labs

BA.2 calculated to have *less* antigenic escape than main BA.1 lineage. BA.1 + R346K has *more* escape 7/

Here are site-wise plots that explain why BA.2 is less antigenic escape than BA.1 because it lacks G446S.

BA.1 + R346K is more escape because site 346 is major antigenic site. 8/



BA.2 in Indian context:

Apart from Denmark, BA.2 is increasing in #India & South Africa also.

In India, BA.2 has become the dominant Omicron variant towards end of December. Growing from ~5% in mid December to >50% by beginning of January. 9/

In most other countries, BA.1 remains dominant, though BA.2 seems to slowly growing in share everywhere. 10/

An interactive data site by @corneliusroemer where you can type the name of your country to know the exact prevalence of diff sublineages 👇. 11/

https://twitter.com/corneliusroemer/status/1482833651276697612?s=21

Apart from some predictions based on BA.2 sequence by @jbloom_lab not much is known about BA.2

You may get some interesting videos on the impact of mutations on antibodies evasion here 👇

https://twitter.com/jbloom_lab/status/1470442863108362240?s=21