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Vinod Scaria Profile picture
@vinodscaria
Jul 24, 2021 • 15 tweets • 8 min read • Read on X
Scrolly
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
While the epi-trends are not very clear, the number of genomes of AY.3 seem to be increasing faster than Delta B.1.617.2 . This could be potentially due to cluster testing also, but surely needs epi data to confirm. Image
AY.3 does not have the K417N mutation in the spike protein unlike their delta+ counterparts AY.1 and AY.2 Image
And is largely charecterised by non-spike mutations. Specifically ORF1a mutation I3731V . This is clearly of interest since nothing is pretty much known about ORF1a and role in viral transmission or fitness. Image
A dedicated build for AY.3 phylogeny has been made available by @firefoxx66 . The tree can be browsed here nextstrain.org/groups/neherla… Image
Continued evolution is observed in this lineage with a new sublineage AY.3.1 now assigned github.com/cov-lineages/p… and charecterised by additional mutations ORF1a:D1127Y and ORF1b:H1550Y Image
Interesting clues on what is really happening can come from the fact that the nonstructural proteins NSP6 and NSP14 both are involved in #autophagy
sciencedirect.com/science/articl…
tandfonline.com/doi/abs/10.108…
and NSP6 is also involved in IFN antagonism
sciencedirect.com/science/articl…
The estimated current advantage of AY.3 wrt delta in US is ~40%
cov-spectrum.ethz.ch/explore/United… Image
And now growing in proportions in the USA
@TWenseleers suggest possible founder effect and insignificant advantage compared to delta B.1.617.2
Updated analysis from @TWenseleers
Spread of AY.3 in #SouthAfrica.
At least this does not look like a founder effect to me.
@alchemytoday @TWenseleers Image
With the new sub-lineage AY.3.1 now a significant number of #Mississippi, #UnitedStates genomes are reclassified.
Thanks @alchemytoday for adding this sublineage Image

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More from @vinodscaria

Vinod Scaria Profile picture
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
Vinod Scaria Profile picture
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
Vinod Scaria Profile picture
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
Vinod Scaria Profile picture
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
Vinod Scaria Profile picture
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
Vinod Scaria Profile picture
Jul 2, 2022
🔴 A lot of discussions have come up on the BA.2.75 variant of #SARSCOV2. A continuously updated 🧵on emerging evidence on this variant.
This variant was highlighted for designation recently. Majority of genomes have come from India 🇮🇳, apart from many other countries. github.com/cov-lineages/p…
Why is this lineage interesting?
⚪ Interesting because it has 9 unique changes in the spike protein incl. a reversion compared to the BA.4 and BA.5 subvariants of omicron now spreading widely across the globe.
Schema @mercy_rophina
Read 11 tweets

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