Vinod Scaria
@vinodscaria
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Scientist | Former Doctor | Passionate about Genomics in Clinical Medicine #Genomics4Everyone | Occassional #MysteryDisease tracker | Views are personal
Bengaluru, India
Joined April 2010
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ANILPIN WE ARE THE ONE
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As a scientist, few things I can say
1) Rank has no correlation with research aptitude
2) Rank does not predict the career of a researcher
3) We should possibly stop giving too much importance to ranks, but start seeing things holistically , including passion in science.
Rank- 241
Result- Rejected
Rank- 60000
Result- Selected
Yes, 60000. No mistake in number of zeros.
This is admission criteria for Indian Institute of Science (IISc), one of India's best Research focused institute.
Who will do better Research? Someone with 241 rank or 60000?
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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.
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The migration map of India
The number of migrants from predominantly agricultural areas to megacities is stark.
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🔴Rise and Fall of SARS-CoV-2 lineages in India. Clearly BA.2.75 is growing to be the dominant lineage with ~50% prevalence in current week.
BA.5 seems to be declining and possibly on way out.
Data: INSACOG
Many thanks to
@r_karyakarte
for his efforts on characterizing BA.2.75
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🔘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.
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😡 This is what journalism (science journalism is not an exception) has stooped to in India.
@ndtv
if you don't, understand, at least don't mislead.
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3 calls today - from friends and their families in
#Delhi
prescribed
#Molnupiravir
& requesting advise
All young, all double vaxxed, 1 asymptomatic & 2 with mild symptoms, 1♀️ 2♂️, no comorbidities
None explained on risks.
This is negligence !!
Please stop this madness !!
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😢😡Sad and angry that the efforts of
@r_karyakarte
and many other researchers in India who ensured the genomes are sequenced and available for analysis dont even find a mention.
This is not done,
@Nature
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India lost a passionate scientist , Dr Milind Gore who was instrumental in understanding and controlling the
#JapaneseEncephalitis
and
#AcuteEncephalitisSyndrome
outbreaks in
#UttarPradesh
.
An unassuming and simple person, who touched many lives .
May his soul rest in peace.
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“You can quit your job, but you can’t quit your calling.” –
@Lissarankin
Now officially, former Senior Principal Scientist,
@IGIBSocial
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Brandolini's law : "The amount of energy needed to refute bullshit is an order of magnitude larger than to produce it."
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B.1.617 (blue) and B.1.1.7 (green) lineages seem to be edging out every other lineages which were prevalent in India.
Plot:
@Arvinden3
from
@GISAID
Data.
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A good example of what
#science
can do very quickly - says
@VirusesImmunity
, but it didn’t happen overnight.
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🔴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
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What do we know about the B.1.1.529 variant of SARS-CoV-2 with a very large number of mutations
An updated thread on emerging evidence.
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B.1.617 is the name
Find more information on the lineage at
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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
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Investment in
#Science
counts. A data snapshot of China, India and US in
@the_hindu
today.
🔴 What does this mean for India in the years ahead ? Would like to hear your thoughts.
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🔴Preprint on the A.2 cluster of
#Monkeypox
Genomes is now online.
@bani_jolly
1⃣Lineage A.2 is distinctly different from the predominant lineage B.1 linked to the 2022 outbreak
2⃣Suggest an early & cryptic spread of the virus across multiple geographies
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🔴
#NeoCoV
is not a new variant
🌕It is a bat coronavirus and does not infect Humans
🌕 Spillover events are rare from animals
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Kerala has been one of the first states to put a programme for systematic genomic surveillance of SARS-COV-2 variants to drive evidence based policies
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If this single chart does not wake us up from slumber and be prepared for the worst of
#OmicronVariant
, what shall?
Weekly hospital Admissions in
#Gauteng
🇿🇦 has been steadily growing, compared to the previous waves.
Data
@nicd_sa
Plot by
@jburnmurdoch
@FT
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First report of
#COVID19
#reinfection
from
#India
- two
#asymptomatic
health workers identified on routine
#surveillance
#CSIRfightsCOVID19
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Public Health England today declared the coronavirus variant B.1.617.2, which was first identified in India, would be classified as a variant of concern
#VoC
due to evidence it was more transmissible.
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Why are
#TravelBans
a bad idea ?
🔴 No evidence exists that they are effective
🔴 Viruses don't respect National Boundaries
🔴 I most cases, the virus transmission would have already happened before the ban was imposed
🔴 Hurts countries who are faithfully reporting variants.
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▶️ Are we flying blind on emerging infectious diseases ? How can we make a difference building affordable , accessible Diagnostics for India and for the world ?
@bani_jolly
and I write in
@the_hindu
today.
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When you see people commenting on how one state is doing better than another using
#COVID19
nos in isolation. 🤦
The real casualty in all of this - scientific interpretation of facts and data
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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
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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
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COVID19 vaccine disparity in
#India
in one chart
@indiainpixels
.
Nobody is safe until everyone is safe.
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SpiceHealth,
@IGIBSocial
set up genome testing lab at Delhi's IGI Airport . Read more :
@CSIR_IND
#CSIRfightsCOVID19
@Rakesh_IGIB
@taneja_bhupesh
@AnuragAgrawalMD
@RajeshPandey
@spice_health
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Why does India urgently need a Legal Framework for
#Genomics
I write in
@the_hindu
today.
Read online here
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Happy to share the recent paper on the
#Pharmacogenomic
landscape of clinically actionable variants in
#Indian
population from whole genomes in the
#IndiGen
programme.
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XBB.1.16 is evolving, as it is spreading.
1⃣Evolution by accumulation of genetic variants/mutations is a natural step of any organism.
2⃣The genetic mutations occur as the virus replicates in the cell
3⃣More infections would mean the virus has an increased chance of mutating
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🔴 Institute of Advanced Virology , a Kerala State institute announced rapid partial sequences of the
#Nipah
virus isolate from the outbreak. Kerala health minister announced on the news.
A great example for other states to emulate.
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An interesting abstract in the recent
@GeneticsSociety
meeting caught attention, primarily since
🔘was on the
#Indian
population
🔘there were no Indian organisation / investigators
🔘as published by a pharma company and a another which had(!) operations in India.
The abstract 👇
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#Bioinformatics
for Schoolers starts today.
#Bi4S
is an online education series on the fundamental concepts of genomics and bioinformatics for schoolers (12-18 years).
If you have missed out and would like to join in, please find more details at
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Preprint on the genomic analysis of vaccine breakthrough infections in collaboration with clinicians at the
@aiims_newdelhi
@CSIR_IND
@IGIBSocial
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The
#Diversity
of SARS-nCoV-2 genomes from
#India
.
Infographic :
@bani_jolly
Thanks to all who submitted sequences online
@virology_chitra
@IGIBSocial
@FollowDbtNibmg
@ICMRDELHI
@DBTIndia
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#Monkeypox
is not a new virus. It has been endemic in many countries in Africa.
The current attention in media highlights the deep bias in health reporting and the global health divide.
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Congrats
@bani_jolly
for defending her thesis successfully, and rightfully now Dr. Bani Jolly
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The proportions of B.1.618 has been growing significantly in the recent months in the state of West Bengal, India
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🔴Nipah Virus Disease /
#Bangladesh
🇧🇩
Child dies from
#Nipah
virus disease in Rajshahi. The patient was from Pabna. A week earlier, a 35-year-old woman died suffering from Nipah virus disease at the hospital after drinking date juice.
#EpidemicWatch
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The new emerging sublineages of
#SARSCoV2
#Omicron
and recombinants. What are they and why are they relevant?
@bani_jolly
and I write in
@the_hindu
today
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Some good news from
#Kerala
which apparently is flattening the COVID-19 curve.
Timely response and evidence based policies clearly seem to be the key.
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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, but do not have the full complement of variants as found in India
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So it is indeed XBB.1.16 in
#India
Data
@GISAID
and many thanks to
@r_karyakarte
and others for the active surveillance
Plot:
@Arvinden3
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COVID-19 Genome Surveillance Dashboard is now online integrating data from
#INSACOG
as well as the State Genomic Initiatives of
#Kerala
and
#Maharashtra
Credits:
@kavitapandhare
@bani_jolly
and NGS & analysis team at
@IGIBSocial
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🔴 A lot of discussions have come up on the BA.2.75 variant of
#SARSCOV2
. A continuously updated 🧵on emerging evidence on this variant.
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#NewDelhi
-based biotech startup Cellogen Therapeutics- working on cell based therapies - is planning to bring the new CAR-T cell cancer therapy to India and has inked an agreement with
@IGIBSocial
@CSIR_IND
#CancerTherapeutics
@DrGKharya
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Omicron sublineages dominate the current wave in China 🇻🇳 as per the new updates on
@GISAID
BF.7 in Beijing, BA.2.5 in multiple cities and previously known omicron sublineages in Shanghai.
So it is not a founder event, afterall. Omicrons are here to rule.
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B.1.617 and sublineages now constitute the majority of circulating viruses in the state of
#Maharashtra
Caveat- low nos of genomes from month of April. More genomes would provide a better picture.
Plot
@mercy_rophina
from data in
@GISAID
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🍅There has been a lot of chatter on
#TomatoFlu
In my opinion, a very wrong (and unscientific) way to name a disease, or even discuss about the disease in public media / communications.
My short 🧵on what this is all about.
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Yes, UK recorded 0 COVID-19 deaths today.
% adult pop vaccinated (74.9% 1 dose; 48.9% 2 doses)
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🔴Is
#OmicronVariant
the end of
#COVID19
evolution?
NO
ℹ️ Omicron continues to evolve, and and possibly accumulating mutations at a much higher pace as infections pick up across the world.
As an individual, you can stop the virus from mutating, by reducing infections >
#MaskUp
😷
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2024 Outbreaks in India and counting.
🔴 H5N1 - multiple states
🔴 Zika - multi state
🔴 Chandipura virus - Gujarat
🔴 Nipah - Kerala
🧬 Genomes in public domain - Zero
Can anyone explain why publications take precedence over public health for some scientists ?
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Recent preprint in collaboration with clinicians at Govt Medical College Kozhikode, Ernakulam and Idukki and
@SridharSivasub3
lab at
@IGIBSocial
on genomic survey of
#SARSCoV2
vaccine breakthrough infections from
#Kerala
#India
Read the preprint here
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E484K is a major immune escape variant - also found in a number of emerging lineages across the world.
E484K can escape multiple mAbs as well as panels of convalescent plasma.
The current evidence available on immune escape variants are compiled at:
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SARS-CoV-2 Variants and RT-PCR
Can RT-PCR Detect Omicron ?
A short thread on the topic. 👇
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To all who are discussing in
#America
today on the sidelines on
#ASHG
that there is no genomes and genomics from India.
@SridharSivasub3
@CSIR_IND
@IGIBSocial
@kapoormanav
@doctorveera
@anshulkundaje
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🔖How a team of doctors uncovered the recent Nipah outbreak in Kerala
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#Deltacron
🔴 Is it a variant ? NO
🔴 Why is it in news ? Because reported from
#Cyprus
🇨🇾 with mutations from Delta &Omicron VoCs
🔴 What should I do ? Keep Calm +😷+💉💉
🟡 Why ? Because it is likely due to an artefact in sequencing or contamination or even rarely co-infection
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Update of 200+ SARS-nCoV
#genomes
from
#India
now covering 19+ states/UTs
Infographics:
@bani_jolly
High-res / Interactive
Acknowledge all institutions who shared their genomes
#COVID2019
#COVID2019india
#IndiaFightsCoronavirus
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Excited to join the
@PLOSGPH
Editorial Board, a new
#OpenScience
journal for public health research that broadens the range of global perspectives we learn from to advance the health of all humankind.
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There are many unknowns for this lineage at this moment including its capability to cause reinfections as well as vaccine breakthrough infections. Additional experimental data is also required to assess the efficacy of vaccines against this variant.
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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
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At this moment, there is no conclusive evidence that the lineage drives the epidemic in West Bengal, apart from the fact that the nos and proportions have been significantly increasing in recent months. More focused epidemiological investigations would address these questions.
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4) Over simplification of a problem using a scoring system tends to ignore the nuances, and in many cases, undesirable outcomes .
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Some exciting news about COVID-19 vaccine from Novavax
▶️90.4% efficacy against symptomatic infection
▶️100% protection against moderate and severe disease.
➡️Diverse trial with ~44% non-White participants
🧬sequenced 70% of virus in infections
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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
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What is the JN.1 variant making headlines?
@bani_jolly
and I explain
🔟 points to understand in a short 🧵
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Calling motivated young researchers with a deep interest in
#Genomics
,
#Informatics
and Experimental
#Biology
to join our journey.
Medical graduates are encouraged to apply
Last date : 10th August 2021
Please share in your networks for wider reach.
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While E484K is in the Receptor Binding Domain, Y145 and H146 are not part of the residues interacting with the Human ACE2 receptor. The structural impact of the 2AA deletion causes to spike protein is yet to be understood completely.
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And along with B.1.617 forms a major lineage of SARSCOV2 in the state of West Bengal.
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For folks interested in phylogenetic analysis of
#SARSCoV2
genomes, here is a recent step-wise protocol by
@bani_jolly
Would indeed love to hear your feedback.
@IGIBSocial
#CSIRfightsCOVID19
@CSIR_IND
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5) Over reliance on a scoring system only promotes people to game the system.
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So the
#MysteryDiseaase
has reached Delhi too.
An Influenza like illness is doing the rounds in Delhi NCR . Typical symptoms are of fever , cough , cold , headache , body ache , extreme weakness .
Paracetamol, fluids , anti allergic medications and rest help.
Recovery is taking longer than the usual flu.
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