Vinod Scaria Profile picture
Scientist at @IGIBsocial, Former Doctor Co-founder GUaRDIAN https://t.co/J5eN3vAG3L for #RareDisease #Genomics Pathogen Genomics & Surveillance Views are personal.
Singh M.K. Profile picture 1 added to My Authors
Jan 4 8 tweets 3 min read
A lot of discussion about B.1.640.2 reported from Southern France 🇫🇷 and a preprint on the variant medrxiv.org/content/10.110…
This 🧵is to summarize what we know. 👇 🔴14 changes including N501Y and E484K, & 9 deletions in Spike
🔵B.1.640 (now renamed B.1.640.1) had been in the @WHO watchlist for quite some time (Nov 2021)
🔵Index case seemingly was from Cameroon (doesn't mean it originated there)
🔴Many of the mutations are shared with VoCs
Dec 3, 2021 9 tweets 5 min read
🔴Transmissibility or Virulence : What should really worry us ?
Since these two have been widely discussed, given #omicron is around. A short explainer 👇.
3 plots below - from ~2x of Rt value and 1/2 of hospitalization rates (less virulent) to basal value (~ Delta wave) Rt is the effective reproductive no.
One could clearly see why 2x Rt would create a sharper and ⏫rate of hospitalizations.
For a less virulent and highly transmissible variant, assuming 1/2x hospitalization rate, this would still create a significant wave of hospitalizations.
Nov 30, 2021 4 tweets 2 min read
and now this !
bbc.com/news/world-eur… Scotland outbreak cases had no apparent travel history to Southern Africa.
theguardian.com/uk-news/2021/n…
Nov 29, 2021 10 tweets 3 min read
SARS-CoV-2 Variants and RT-PCR
Can RT-PCR Detect Omicron ?
A short thread on the topic. 👇 RT-PCR is a sensitive molecular method widely used for the detection of SARS-CoV-2 in biological samples. This is based on the principle that short pieces of DNA (aka primers) can specifically target DNA/RNA and amplify them using a polymerase protein
Nov 25, 2021 28 tweets 16 min read
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. Image B.1.1.529 is a newly designated variant of SARS-CoV-2 github.com/cov-lineages/p…
This would not have been possible without the exemplary work of researchers in Africa who have sequenced and deposited the genomes in public domain which forms the basis of this variant designation.
Nov 24, 2021 4 tweets 3 min read
Real-world data on effectiveness of BBV152 / Covaxin whole inactivated #COVID19 vaccine against symptomatic infection
👥Healthcare Workers at @aiims_newdelhi
🗓 Coincided with the 2nd wave in #Delhi majorly driven by VoCs
thelancet.com/journals/lanin…

#MedTwitter #vaccines #India Adjusted effectiveness of BBV152 against symptomatic COVID-19 after 2 doses adm at least
🔸️14d before testing was 50% (95% CI 33–62; p<0·0001).
🔸️28d before testing was 46% (95% CI 22–62) 
🔸️after excluding previous COVID19 cases, 14d before testing was 47% (95% CI 29–61)
Nov 3, 2021 8 tweets 4 min read
Insights on the recent wave of COVID-19 infections in @Singapore
The present wave in Singapore is of interest since a significant large proportion (82.7%) of population has received 2 doses of #COVID19 #vaccines but nevertheless have a wave of infections and deaths. With respect to COVID-19 variants and VoCs, clearly Delta (and 2 prominent sublineages AY.23 and AY.23.1) dominate the present wave of infections.
Data: @DiseaseOutbreak
Oct 20, 2021 9 tweets 4 min read
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
Jul 24, 2021 15 tweets 8 min read
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
Jul 13, 2021 13 tweets 9 min read
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
Jul 8, 2021 8 tweets 3 min read
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
Jun 13, 2021 10 tweets 6 min read
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.
Jun 6, 2021 9 tweets 4 min read
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
Apr 20, 2021 9 tweets 3 min read
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
Apr 10, 2021 9 tweets 5 min read
B.1.617 is the name
Find more information on the lineage at cov-lineages.org/lineages/linea… Image 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 Image
Sep 23, 2020 5 tweets 7 min read
First report of #COVID19 #reinfection from #India - two #asymptomatic health workers identified on routine #surveillance
academic.oup.com/cid/advance-ar…

#CSIRfightsCOVID19 #Genome sequencing of the #SARSCoV2 isolates from both the episodes suggest distinctly different virus , confirming reinfection.
Aug 24, 2020 4 tweets 2 min read
Image Facebook live in #Malayalam at facebook.com/INDIA.CSIR on 28th August 2020 from 3.00PM to 4.00PM
Aug 12, 2020 5 tweets 4 min read
High throughput approach to detection and genetic epidemiology of SARS-CoV-2 using Next Generation Sequencing #CSIRfightsCOVID19 @IGIBSocial @CSIR_IND

thehindu.com/sci-tech/healt… 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.