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/ Image
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… Image
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 Image
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
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.

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More from @vinodscaria

24 Jul
Closely tracking the delta+ lineages now across the world, one of the lineages AY.3 seems to be emerging in the United States of America. This tweetorial is to summarise the observations. I will be updating this thread as new evidence emerges.
Thanks Image
The interest in looking at this lineage closely comes from the fact that this lineage has been on the rise in USA in recent weeks.
Thanks @Unusual_Times for pointing this. Image
AY.3 seems to be localized to some states, like #Mississippi and #Missouri with nearby states slowly picking up. Image
Read 15 tweets
13 Jul
The recent outbreaks of #Zika Virus in #Kerala has renewed interest in this virus. This tweetorial explains some key aspects about the virus and why we should be actively using #genomics for #GeneticEpidemiology Image
The disease in most people is mild. Majority of people infected with Zika virus DO NOT develop symptoms. Symptoms are generally mild including fever, rash, conjunctivitis, muscle and joint pain, malaise, and headache, and usually last for 2–7 days.
Source: @CDCgov Image
Death is RARE
Infection during pregnancy can cause microcephaly & congential malformations.
Neurological complications like Guillain-Barré syndrome, neuropathy and myelitis are seen in some.
Read 13 tweets
8 Jul
Why are numbers in Kerala an anomaly ?
Here is my take on these numbers
No. of cases are not directly comparable across states, due to the large disparity in testing capacities. It is most likely that the high nos are just representative of the testing nos. Here is a comparison of some states. Data from covid19india.org
So are the COVID-19 deaths for the states. Of note and contrast would be Kerala and Bihar - see closely the no of tests and deaths
Read 8 tweets
13 Jun
As delta continues to evolve acquiring new mutations, there is a lot if interest in understanding these mutations. This tweetorial summarizes the emerging lineages of delta, otherwise named delta+

Data and analysis : @bani_jolly and @mercy_rophina
Understanding this continued evolution is of great importance in mapping the evolutionary landscape of emerging variants. Largely the virus has tried to optmise for transmission and immune escape by step-wise acquisition of new mutations.
One of the emerging variants is B.1.617.2.1 also known as AY.1 characterized by the acquisition of K417N mutation.

Thanks @bani_jolly for pointing out the mutation and lineage assignment.
Read 10 tweets
6 Jun
Interesting preprint on the antibody response after ChAdOx1-nCOV (Covishield) and BBV-152 (Covaxin) among Health Care Workers. (N=552 Covishield =456; Covaxin=96)
Both vaccines elicited👍immune response after 2nd dose. Seropositivity Covishield >Covaxin
medrxiv.org/content/10.110… Image
A number of factors include Age, Sex. Comorbidity including T2DM and Hypertension influence the antibody titres (Day 21-36 after 2nd dose) Image
More reasons why we should be eagerly looking forward to the Phase 3 data for Covaxin
Read 9 tweets
20 Apr
B.1.618 - a new lineage of SARS-CoV-2 predominnatly found in India and characterized by a distinct set of genetic variants including E484K , a major immune escape variant.
Initial sequences in the B.1.618 lineage were found in West Bengal, India.

Members of this lineage is also found in other parts of the world, cov-lineages.org/lineages/linea… but do not have the full complement of variants as found in India
This lineage is characterized by a 6 nt deletion (H146del &Y145del) , apart from E484K and D614G in spike protein
Other variants are in the ORF1ab, ORF3a, ORF7a, ORF7b and N genes
Read 9 tweets

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