Vinod Scaria Profile picture
Jun 13, 2021 10 tweets 6 min read Read on X
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.
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
The recent @PHE_uk report also has a mention of the variant in 36 cases in England.
assets.publishing.service.gov.uk/government/upl…

2 of the 36 were possible vaccine breakthrough infections
A dedicated nextstrain build for K417N is also now available .
@firefoxx66
There is a very informative thread on the evolution and phylogenetic context of AY.1 by @bani_jolly 👇

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More from @vinodscaria

Jul 8
#Zika virus outbreaks in #India. Should we be worried ?
A long 🧵 Image
#Zika is not a new virus.

🔴We have known it for decades, and India has seen previous, albeit small outbreaks in multiple states. Gujarat, Rajasthan, Kerala, Maharashtra and Uttar Pradesh, MP, TamilNadu , Delhi, Punjab, Telengana and Jharkhand in the previous years. Image
🔴This year, we have a multi-state outbreak with cases reported from Karnataka, Kerala and at least three districts in Maharashtra.

🔴The actual number of cases are unknown as there is no public tracker yet and the known is possibly just a small fraction of the disease burden. Image
Read 21 tweets
Jun 11, 2023
🔴 #Mpox aka #Monkeypox is spreading .
But not where you think it is.
A short 🧵 Image
The latest situation report on the multi-country outbreak of #mpox from @WHO has come out . In Summary:
▶️ 87,929 cases and 146 deaths from Jan 2022
▶️ 111 countries / territories affected as of date Image
▶️ The European and American Outbreak of #mpox which followed a super spreader event last year is pretty well under control.
There are few cases still being reported, but vaccination campaigns have brought the outbreak pretty well under control. Image
Read 13 tweets
Jun 10, 2023
🔴 Characterisation of #Influenza A #H3N8 with hallmarks of continued evolution, spread in poultry and occasional spillover to humans from #China 🇨🇳

journals.asm.org/doi/10.1128/jv…
▶️ Continued infection of poultry and spillover into humans could potentially accelerate evolution and adaptation to human to human tranmission
▶️ Adaptation to other mammals noted in the past, through evolutionary processes.
▶️ Genome analysis suggest the origin by reassortment of genomes from poultry H9N2 backbone
Read 7 tweets
Dec 21, 2022
#COVID19 in #China.
What we know and what we don't.
A long thread, summarizing my thoughts, which I hope to keep updated over the coming weeks. Image
To give a brief background:
The aggressive approach by #China to contain the virus following initial cases in Wuhan, has been seen with awe and admiration by man.
This included:
🔴Strict quarantine & lockdown
🔴Massive testing & surveillance
🔴Early vaccines
🔴Health Infra
While COVID19 spread across the rest of the world, infecting and killing millions of people, and putting healthcare infrastructure to the brim of their capacities, China remained isolated, contained the spread and remained an outlier in many aspects.
Data @WHO Image
Read 13 tweets
Oct 13, 2022
🔘Recombinant variants of SARS-CoV-2 and XBB/XBB.1 the recent and emerging recombinant variants with large immune evasive potential.
A short 🧵on emerging evidence. Image
Recombinant variants of viruses are generated when two or more viruses co-infect a cell at the same time. Chances for co-infection is rare, but nevertheless they occur.
Genomic surveillance can efficiently pick up such recombinant isolates. Image
There are 49 odd recombinant variants now catalogued for #SARSCoV2 by @PangoNetwork , an open collaboration of scientists across the world.
PANGO names recombinant variants of #SARSCoV2 with a name starting with 'X'. Image
Read 21 tweets
Jul 27, 2022
🔴The curious case of Indian #Monkeypox Genomes
Wonderful effort by clinicians in @KeralaHealth who diagnosed the disease and researchers at @icmr_niv, we now have sequences of MPX isolates in @GISAID .

This short 🧵is on what the early genomes say.
Analysis @bani_jolly
Briefly 4⃣ genome sequences have been deposited for two samples (EPI_ISL_13953610 and EPI_ISL_13953611) along with 2 re-sequenced genomes from isolates of one of the sample.
▶️Both the isolates were from early cases reported from Kerala
▶️Both cases have a travel history
The present sustained human-human transmission of the MPX virus is believed to have happened via superspreader events in Europe with 16000+ cases now spread across 70+ countries,
The initial cases seemingly were predominantly among gays/bisexuals and msm networks
Read 13 tweets

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