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+
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.
The context of the K417N mutation is shown in figure below. The mutation maps to the receptor binding domain and has also been associated with immune escape
Ref: clingen.igib.res.in/esc
Schema: @mercy_rophina
A number of genomes are now available for the lineage AY.1 / B.1.617.2.1 from across the world. The sequences are mostly from Europe, Asia and America. The travel histories are not readily available to make assumptions.
In fact the sequences come from a number of countries across the globe
One important point to consider regarding K417N is evidence suggesting resistance to mAbs Casirivimab and Imdevimab. The mAb cocktail incidentally has received an EUA from @CDSCO_INDIA_INF in India.
The variant freq for K417N is not much in India at this point in time
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…
A number of factors include Age, Sex. Comorbidity including T2DM and Hypertension influence the antibody titres (Day 21-36 after 2nd dose)
More reasons why we should be eagerly looking forward to the Phase 3 data for Covaxin
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
This lineage is defined by 15 genetic variants including 6 Spike protein variants.
Two variants of these 6 (E484Q and L452R) are involved in immune escape as well as increased infectivity. More about these variants and immune escape can be found at ESC clingen.igib.res.in/esc
This lineage is also now found in a number of countries including UK, USA, Australia, Singapore and Germany
#Genome sequencing of the #SARSCoV2 isolates from both the episodes suggest distinctly different virus , confirming reinfection.
Since the individuals were #asymptomatic during both episodes, and identified on regular #surveillance suggest asymptomatic #reinfections could be an under-reported entity. 2/2
High throughput approaches for detection and genetic epidemiology of SARS-CoV-2 holds key as we open up economic hubs & cities. #COVIDseq provides the way forward.
@IGIBSocial in #India is one of the initial centres to evaluate this approach globally and suggesting high sensitivity for detection, along with the opportunity to do genetic epidemiology to understand dynamics.