"It's amazing that the Xi variant seems to have somehow managed to evade detection..."
Why 'Omicron', Not 'Nu' or 'Xi'?
WHO Says Two Letters in Greek Alphabet Jumped to 'Avoid Stigma'
Here is how B.1.1.529 (#Omicron #B11529) compares to Alpha, Beta, Gamma, Delta variants.— nference (@_nference) November 27, 2021
Omicron has highest novel Spike mutations including striking cluster on the "crown" suggesting significant selection pressure & antigenic distinction from prior strains
(Credits: nference) pic.twitter.com/4oZQbjhbG8
There have been a number of overview threads on the emerging variant designated as @PangoNetwork lineage B.1.1.529, @nextstrain clade 21K and @WHO Variant of Concern Omicron. I'm not going to attempt to be comprehensive here, but will highlight a few aspects of the data. 1/16— Trevor Bedford (@trvrb) November 26, 2021
The @nextstrain https://t.co/wVE7ubYBoy focal build for 21K (B.1.1.529) is now live.https://t.co/UD1WPcJphP— Dr Emma Hodcroft (@firefoxx66) November 26, 2021
As previously, the long branch leading to 21K is clearly visible, making it hard with current sequences to tell much about the evolutionary history. https://t.co/dQSPFv2lwm pic.twitter.com/hoxllKKTho
What a coincidence that a variant with an extraordinary number of significant mutations appears shortly after the mutagenic drug molnupiravir is licensed for broad generic distribution.— Adam Gaertner \U0001f1fa\U0001f1f8 (@veryvirology) November 26, 2021
Merck just announced that it's much less effective than thought, too.https://t.co/hTCcvlbgBC
Ok so to put it very simply, you\u2019re saying given the large steps in evolution this virus has shown over the last 2 years, proving it is highly adaptive, lessens the theory it leaked from a lab?— Eyedeas (@eyedeas604) November 26, 2021
@_b_meyer has made important contributions to the corpus of knowledge about SARS-CoV-2, but this thread, provides a very good opportunity to demonstrate why even very good scientists should not be considered generally authoritative on matters of virus evolution. https://t.co/41q1vTupS0— notoriousFIL (@notoriousFIL) November 26, 2021
The argument that the 681 Proline was somehow "suboptimal" relies on misunderstanding about the conditionality its presence given the rest of the Spike protein structure, as well as persistent misunderstanding about the mutational capacity of these viruses to rapid adaptation.— notoriousFIL (@notoriousFIL) November 26, 2021
WAS #OMICRON #Variant LAB. MANIPULATED?— jean-claude perez (@JCPEREZCODEX) November 27, 2021
Evidence for #Omicron of an abnormal BUG in continuity of human host #Fibonacci #spikes adaptation of #variants ==> see these charts @xazalbert @andrebercoff @Beatrice_Rosen @edgarmorinparis @AlexandraJAlva4 @AldoSterone111 @ivanrioufol pic.twitter.com/h6irybIVYx
Here's how mutations in #SARSCoV2 Nu variant (B.1.1.529) will affect polyclonal and monoclonal antibodies targeting RBD. These assessments based on deep-mutational scanning experiments; underlying data can be explored interactively at https://t.co/uP3IKvnDw0 (1/n)— Bloom Lab (@jbloom_lab) November 25, 2021
I wish I was as optimistic @jbloom_lab— Theodora (@theodora_nyc) November 26, 2021
Our polymutant spike has 20 aa substitutions and is almost completely resistant to neutralization by almost all vaccinated and convalescent plasma we tested. This new one has more in overlapping regions. https://t.co/0MKyr4lQ57
3) The mutations in Omicron which seem to wipe out the majority of neutralizing antibody epitopes are very worrisome. Combined with the apparent fitness of the virus, this could be a problem. There is now a lot to do to get a better idea of the risk this virus variant poses.— Florian Krammer (@florian_krammer) November 27, 2021
\U0001f1eb\U0001f1f7 Le #docteur #AngeliqueCoetzee, #m\xe9decin-chef de l'Afrique du Sud, a r\xe9v\xe9l\xe9 qu'elle n'avait \xe9t\xe9 t\xe9moin que de cas tr\xe8s, tr\xe8s l\xe9gers" du nouveau variant depuis qu'il a \xe9t\xe9 signal\xe9. Elle a ajout\xe9 que ce n'\xe9tait rien de plus qu'une "temp\xeate dans une tasse \xe0 th\xe9#Omicron #3emeDose pic.twitter.com/0TX1UcZlCK— BLF.TV (@blf_tv) November 27, 2021
Stronger binding works inside the body. Faster, meaning more severe, and new tissue pathologies because of the stronger binding.— Jonathan Mesiano-Crookston /Denial Is Bad Strategy (@jmcrookston) November 27, 2021
Let's kill this myth of increased transmissibility equals decreased severity because it's not true.
Omnicron is too long, how about we all just call it Xi\U0001f44d— Aussie Phil (@phil_aussie) November 28, 2021
Some thoughts about the punctuated evolution of variants of concern including B.1.1.529 in Southern Africa. \U0001f9f5— Moritz Gerstung (@MoritzGerstung) November 26, 2021
A shared characteristic of all known VOCs is that they appeared suddenly with a large number of mutations, many more than the incremental changes we see normally. pic.twitter.com/b0HQJZa42I
[Thread] What is the potential impact of the new B.1.1.529 #COVID19 variant? @rjlessells:— Mia Malan (@miamalan) November 25, 2021
1. It's relatively simple to detect some B.1.1.529 cases, as it's possible to use PCR tests to do this in some cases
2. B.1.1.529 = has many mutations across different parts of the virus pic.twitter.com/ytktqLzJUi
Also, HIV patients usually give line lengths that are about half this length. The line length lead to other VOCs were less than 1/4 that lead to 21K. Not likely a single patient can cause this. It takes more plasma selection using VSV-SARS-CoV-2 S to achieve this.— Daoyu (@Daoyu15) November 28, 2021
Omicrons (B.1.1.529) most recent common ancestor is AV.1. Relative to this MRCA, Omicron has 25 nonsynonymous and 1 synonymous mutation in Spike, and 13 nonsynonymous and 6 synonymous mutations in the entire rest of the genome. This is very strange & I don't understand.— Dr B. (@P_J_Buckhaults) November 30, 2021
Come on, how can you dismiss the potential lab origin of Omicron out of hand? The first SARS escaped from labs at least 4 times. And Omicron looks very much like a strain would look like if it was passaged repeatedly in the presence of antibodies. https://t.co/jIgXJ90gIM— Yuri Deigin (@ydeigin) December 2, 2021
The Omicron genome is "weird" (as my colleague @K_G_Andersen has noted) and there's much uncertainty about how and when it originated, by @kakape @ScienceMagazine w/@arambaut @firefoxx66 @c_drosten @MichaelWorobey @DirtySci @rjlessells @ArisKatzourakishttps://t.co/BwtbtwA40V— Eric Topol (@EricTopol) December 2, 2021
The Omicron variant:— Oliver Barnes (@mroliverbarnes) November 26, 2021
\U0001f518~50 mutations that alter its amino acid
\U0001f518 32 spike protein mutations. Spike is outer layer of virus that interacts with human cell
\U0001f518 15 receptor binding domain mutations. RBD is grappling hook that attaches to human cell
Visuals from @jburnmurdoch /1 https://t.co/R4Sx0b2nlN pic.twitter.com/63nYL2lfOp
The Spike gene of Omicron has 25 mutations that change an amino acid.— Tony VanDongen (@tony_vandongen) December 3, 2021
Because of the codon redundancy you would expect ~2 times as many silent mutations: 50.
And there is apparently only 1 silent (\u201csynonymous\u201d) mutation.
Random mutagenesis can not generate such statistics. https://t.co/QKh6jTiJFK
5) The only plausible explanation how this huge number of mutations could have been acquired completely below the radar is:— valentin bruttel (@VBruttel) December 4, 2021
- scientists enabled SARS2 samples to escape antibody responses by passaging them in presence of diluted convalescent serum on human/humanized cell lines.
6) Exactly this extremely risky research, which could render all of world wide vaccination efforts useless, was done in South Africa.https://t.co/kpqQW5ORNV— valentin bruttel (@VBruttel) December 4, 2021
And not even at their BSL4 lab, no, in Durban, which only has a BSL3 lab\U0001f631. pic.twitter.com/XD6owjkx4J
7) Durban, as you mentioned above @ydeigin, is exactly the city where omicron was first detected in one of the patients.— valentin bruttel (@VBruttel) December 4, 2021
Where they "trained" SARS2 variants to become resistant to neutralizing antibodies by slowly and carefully increasing covalescent plasma concentrations... pic.twitter.com/QDqDneazmG
1.There is unsurprisingly a lot of speculation about where omicron has come from. There are several hypotheses \u2013 personally I lean towards evolution as an immune escape variant in an immunocompromised host.— Stuart Neil (@stuartjdneil) December 4, 2021
A batch of samples from KwaZulu-Natal province (including Durban) has just been shared, for samples collected up to 27 Nov. Omicron is at a lower frequency there: ~30%.— Mike Honey \U0001f489\U0001f489\U0001f489 (@Mike_Honey_) December 3, 2021
The latest from Gauteng (centre of the Omicron outbreak) are for 22 Nov, showing sustained frequency ~90%. pic.twitter.com/RbUOjM8sqF
Important update from Steve Biko Hospital in Tshwane. Tho the numbers of hospitalized patients with #Omicron has been high, rates of COVID pneumonia are low. Most cases are incidentally diagnosed SARS-CoV2. Pediatric cases too. We need to wait, but these data not alarming, https://t.co/kQdh0O0AcJ— Emily Wong, MD (@emilybethwong) December 4, 2021
Spike is 3819 coding nucleotides. It has 33 NS and 1 S changes. The neighboring ORF3A-E-M-ORF6-ORF7A-ORF8-N-ORF10 genes have 4000 coding nucleotides. They have eight NS and three S changes. Spike is smaller and has four times the NS changes. pic.twitter.com/emqNEgp0FC— Dr B. (@P_J_Buckhaults) December 4, 2021
This is a virus that recombines. So its genes can evolve separately, in different genomes, and be combined in a co-infection. Given that thousands of particles are produced per infected cell, a cell infected by two different lineages can test many combinations simultaneously.— Atila Iamarino *ainda de licen\xe7a paternidade (@oatila) December 5, 2021
OK, through examining the latest Omicron sequence sample QLD-2568 from 2 Dec 2021, & using a well vetted rate of sustained mutation - parsing this genetic distance into the lineages of Alpha and Omicron - I get a divergence (Last Common Ancestor) date of— Ethical Skeptic \u2600 (@EthicalSkeptic) December 5, 2021
\U0001d541\U0001d552\U0001d55f\U0001d566\U0001d552\U0001d563\U0001d56a \U0001d7da\U0001d7d8\U0001d7d9\U0001d7e0 pic.twitter.com/12BXvusLCE
1/18 "Selection analysis identifies significant mutational changes in Omicron that are likely to influence both antibody neutralization and Spike function" https://t.co/5OxhwEt7mL @DarrenM98230782 @Tuliodna @jbloom_lab @robertson_lab @nekrut @LemeyLab and many others.— Sergei Pond (@sergeilkp) December 5, 2021
We\u2019ve created calculator that aggregates deep mutational scanning data to estimate how mutations to #SARSCoV2 RBD affect recognition by human polyclonal antibodies. The calculator emphasizes extensive antigenic change in #Omicron variant. https://t.co/hFhwcKED0o (1/n)— Bloom Lab (@jbloom_lab) December 6, 2021
A sister lineage to Omicron has been designated BA.2, and the main lineage named BA.1. BA being an alias for B.1.1.529, now redefined to encompass both groups.— Theo Sanderson (@theosanderson) December 7, 2021
(Just taxonomy changing to encompass the full phylogeny, BA.2 is not cause for concern.)https://t.co/AqgRKXcnPP
Closely resembles that of SARS-CoV-2 during isolation and culturing in VERO E6 cells), and traits are unlikely to be lost (Sarbecoviruses that are isolated from wild samples are highly stable in cell cultures, such as WIV1, Rs4874, WIV16, SARS-CoV or GX/P2V).— Daoyu (@Daoyu15) December 6, 2021
We are experiencing technical issues with our website. Our teams are working on it. We apologize for the inconvenience.— NICD (@nicd_sa) December 7, 2021
Okay folks, still lot of uncertainty around severity of disease, but here\u2019s what I\u2019ve gleaned from latest data and many chats that @mroliverbarnes and I have had with the brilliant, tireless doctors & public health officials in South Africa https://t.co/u4VJzy6671— John Burn-Murdoch (@jburnmurdoch) December 7, 2021
A third set of results about neutralisation of the omicron variant, this time also including 'boosted individuals', i.e. 3x doses of vaccine in various combinations. This set of results does not bode particularly well for the neutralising efficacy of boosters against omicron.— Prof Francois Balloux (@BallouxFrancois) December 8, 2021
The best journalists lack all conviction,— Billy Bostickson \U0001f3f4\U0001f441&\U0001f441 \U0001f193 (@BillyBostickson) December 16, 2021
while the worst Virologists
Are full of passionate intensity.
Surely some revelation is at hand;
Surely the Omicron is at hand.
The Omicron! Hardly are those words out
When a vast image out of Spiritus Mundi
Troubles my sight: pic.twitter.com/it0LssRjp5
The PEPTIDES again!— Billy Bostickson \U0001f3f4\U0001f441&\U0001f441 \U0001f193 (@BillyBostickson) October 21, 2020
"Such a peptide commonality is unexpected and highly improbable from a mathematical point of view"
Molecular mimicry between SARS-CoV-2 spike glycoprotein and mammalian proteomes: implications for the vaccinehttps://t.co/yLQoUtxtv2
via @gerdosi https://t.co/lsCv2j4gf9 pic.twitter.com/hdgM5KZd39
Warnings ignored, and the stunning fact that the wealthiest country in the world is short of masks and gowns and ventilators - and possibly, hospital beds. Dr Dennis Carroll says it's time to rip off the bandaid on harsh #coronavirus\xa0measures. #COVID19 pic.twitter.com/ZNZnhZnmPs— Michael Holmes (@holmescnn) March 21, 2020
1/4 From an obscure PhD thesis by Aleksei Avery CHMURA, now chief of staff at @EcoHealthNYC & author of:— Billy Bostickson \U0001f3f4\U0001f441&\U0001f441 \U0001f193 (@BillyBostickson) May 11, 2020
2013 WIV paper: https://t.co/ISK9ltN7h6
Evaluating Risks of Paramyxovirus and Coronavirus Emergence in China
1/ I like the— Gilles Demaneuf (@gdemaneuf) November 24, 2020
"Since the United States forswore offensive bioweapons research back in 1969, presumably DARPA's disease program is now aimed at preventing, not creating strategic surprises of the epidemiological sort".