Vipin M. Vashishtha Profile picture
May 2 7 tweets 5 min read Twitter logo Read on Twitter
Some more info on XBB.2.3. Aka #Acrux

➡️ XBB.2.3 has 4 defining mutations:

-Spike mutations: S:D253G & S:P521S
-ORF mutations: ORF1a:G2091S & ORF7a:A13V
-Beyond XBB.2, #Acrux XBB.2.3 has the Spike P521S & S486P mutations 1/

H/T: @T_Brautigan
➡️ Acrux XBB.2.3 was first spotted in India (Karnataka) & then in the USA—origin is somewhat unclear.

Here is the animated map by @Mike_Honey_ showing the spread of the XBB.2.3.* "Acrux" variant around the world. 2/

➡️ Singapore (26%) and India (22%) are still the hotspots.

Spain (11%) and Australia (8%) are also showing recent growth.

Spotted in many other countries including Japan, South Korea, China, the UK & the US. 3/ Image
Though it is present in China & Japan, but still trying to find its way through some other dominant XBBs like XBB.1.5, XBB.1.16, XBB.1.9 etc 4/ ImageImage
➡️ #Acrux is evolving fast in to many offsprings, and one of its descendants, XBB.2.3.2 is considered to be the fastest.

According to @LongDesertTrain, XBB.2.3.2 also has an interesting mute ORF1a:R2159W (NSP3_R1341W) that has shown up in several fast-growing lineages 5/
➡️ In India, the share of #Acrux XBB.2.3 is increasing, but still it is not able to outcompete currently dominant #Arcturus. However, its offspring XBB.2.3.2 may have some edge over it 6/

H/T: @siamosolocani Image
➡️ Another offspring of the XBBB.2.3 aka #Acrux, XBB.2.3.8 +478R is worth monitoring.

Here is the latest table of currently dominant, some key subvariants by @siamosolocani 7/ Image

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More from @vipintukur

May 3
A great work by @yunlong_cao & colleagues

Their study in both mice & humans suggests that repeated Omicron infections can diminish the adverse impact of immune imprinting and generate high neutralizing titers against XBB.1.5 and XBB.1.16 in both plasma and nasal mucosa. 1/
In mice, the efficacy of single Omicron-boosting is heavily limited by immune imprinting, especially when using variants antigenically distinct from WT, like XBB. However, this situation could be largely mitigated by a second Omicron booster. 2/ Image
Similarly, in humans, Omicron infections could also alleviate WT-vaccination-induced immune imprinting and generate high neutralizing titers against XBB.1.5 and XBB.1.16 in both plasma and nasal mucosa. 3/ Image
Read 12 tweets
May 3
The SARS-CoV-2 surface Spike protein binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. 1/
In a new study, the researchers combine these two binding properties in a simple fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein. 2/
The ACE2-antibody selectivity change caused by mutation (i.e., the change binding to ACE2 minus the change in binding to immunity-inducing Abs) is proposed to be a key metric of virus fitness, which furthermore enables substantial systematic error cancelation when evaluated. 3/ Image
Read 6 tweets
Apr 30
How long population immunity induced by natural infection, primary-series vaccination, and booster vaccination against SARS-CoV-2 lasts?

A new study from Qatar offers some clues. 1/
Using a test-negative study design,
population immunity against infection of each of previous infection, primary-series vaccination, and booster vaccination were characterized at the national level month by month for 2 calendar years 2/ Image
The 3 forms of population immunity showed rapid variation over time driven by waning of protection. Vaccine-derived population immunity declined by 1 absolute percentage point every 5 days! 3/
Read 13 tweets
Apr 21
XBB.1.16 #Arcturus Covid surge in India: How it is affecting young children & infants.

Here are the key findings based on our study of 25 children from April 4-16’ 23:

1-Current outbreak is causing a mild febrile illness
2-Total duration of illness is only 1-3 days. 1/
3-Young infants are disproportionately more affected than older children.

4-The youngest infant was 13 day old neonate!

5-infants below one year had a significantly higher positivity rate than older children (40.38% versus 10.5%, p=000816). 2/ Image
6-Unlike the previous BA.2 Omicron wave, respiratory symptoms are predominating in young infants

7-Cycle threshold values for nucleocapsid and ORFlab genes on positive RT-PCR vary from 18 to 23. 3/
Read 6 tweets
Apr 14
A plethora of respiratory viruses, including SARS-CoV-2, strategically manipulate the host's splicing machinery to circumvent antiviral responses. 1/
What is RNA splicing? ....a form of RNA processing in which a newly made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). During splicing, introns (non-coding regions) are removed, & exons (coding regions) are joined together 2/ ImageImage
According to a new study, SARS-CoV-2 exploits the host splicing machinery to bolster viral replication & subvert the immune response by selectively upregulating unproductive splicing isoforms from antigen presentation & antiviral response genes. 3/

biorxiv.org/content/10.110…
Read 13 tweets
Apr 13
When is the Indian Covid surge driven by XBB.1.16 going to peak?

Y’day India reported >7500 cases. Early trends point the tally would def cross 8500 today. However, there is a lot of speculations on when the current peak of the surge would peak. Let’s look for the answers 1/ Image
There are three different views:

1-According to @JPWeiland as far as weekly growth is concerned, it is already peaked. But the outbreak is still growing & the positivity rate is at the highest since Jan’21 BA.2 peak! 2/ ImageImage
2-As per the @MoHFW_INDIA’s ‘unusual’ claim, the COVID in India is moving towards the endemic stage. They expect the cases to rise for the next 10-12 days, and will gradually come down to become endemic 3/

Read 5 tweets

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