"It's amazing that the Xi variant seems to have somehow managed to evade detection..."
via @readomain
Why 'Omicron', Not 'Nu' or 'Xi'?
WHO Says Two Letters in Greek Alphabet Jumped to 'Avoid Stigma'
https://t.co/xnGR9XK2tF
1. Omicron Thread - A Compilation of Opinions
"finally, the time has slip and slid its slimy course through to us - and we're the vicious bastards of the new generation. we do not relent, and we should not be held to account for our ancestral faults"
https://t.co/mhJO6yOQRE
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
"It's amazing that the Xi variant seems to have somehow managed to evade detection..."
via @readomain
Why 'Omicron', Not 'Nu' or 'Xi'?
WHO Says Two Letters in Greek Alphabet Jumped to 'Avoid Stigma'
https://t.co/xnGR9XK2tF
This month, Israel held an exercise, The “Omega Exercise”, meant to prepare for a hypothetical, new COVID-19 variant
https://t.co/c2PoTfJiIE
https://t.co/HN9csJqK0z
Prof @Tuliodna is giving an insightful overview of the #NewVariant #B11529 pic.twitter.com/VnFBrj2pOT
— NICD (@nicd_sa) November 25, 2021
Note:
@Clucky92864053 points out that this variant of the virus itself was first identified back in July 2021
https://t.co/13V16t1V4u
He considers that the extremely long branch (>1 year) indicates continual evolution in a chronically infected individual before spilling back into the population.
https://t.co/uIDzJH65vO
Archived thread:
https://t.co/eOelixoKeF
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
He highlights the striking accumulation of mutations in the S1 domain of the spike protein.
He concludes that the presence of host derived RNA insertion from TMEM245 gene points to evolution within humans rather than spillback from animal population
https://t.co/YgG1J7z6sc
with a doubling time of 4.8 Days
https://t.co/CP5TUo5ffy
Just now! pic.twitter.com/gCchtzT6Ko
— Andr\xe9s Posada (@APosadaO3) November 26, 2021
"Looks like the new strain was either incubated in an immunocompromized person for months or serially passaged in a lab in the presence of convalescent plasma"
https://t.co/Jbf1f1rkIF
Oh and they actually were doing similar experiments in South Africa:https://t.co/52h0VkXDwg
— Yuri Deigin (@ydeigin) November 27, 2021
"making it hard with current sequences to tell much about the evolutionary history"
https://t.co/4Cht9WLzS8
and
https://t.co/kut28XyFh3
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
Maintained by Emma Hodcroft @firefoxx66
https://t.co/IP5CxFROa5
"Do you think it is plausible that this variant was mostly generated within one host with a persistent infection?"
https://t.co/P11iawQReP
1. A woman with HIV had the coronavirus for 216 days. The virus mutated at least 30 times inside her. https://t.co/Y5TBBtiGDR via @businessinsider
— Billy Bostickson \U0001f3f4\U0001f441&\U0001f441 \U0001f193 (@BillyBostickson) August 29, 2021
Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection
https://t.co/lqffiIAyNI
and
https://t.co/RMZ2y9i23I
As COVID-19 collides with HIV/AIDS, the pandemic may be taking an ominous turn
https://t.co/RMZ2y9i23I
2. Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infectionhttps://t.co/tafjp9Hd29
— Billy Bostickson \U0001f3f4\U0001f441&\U0001f441 \U0001f193 (@BillyBostickson) August 29, 2021
@veryvirology and @marc_g_wathelet point to a possible connection to recent trials with Merck and Ridgeback’s Investigational Oral Antiviral "Molnupiravir" in South Africa
https://t.co/g8kyKdDxek
and
https://t.co/jFUTPw5pur
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
"New antiviral pills to treat Covid unlikely to be made available in South Africa for some time"
https://t.co/UJcDqDCpCl
and the trials took place at 170 sites in many countries not just South Africa.
https://t.co/5GybZu9aHE
Page 18:
SARS-CoV-2 variants of concern and variants under investigation in England
Technical briefing 29 - 26 November 2021
https://t.co/vgoktp62Ly
For some, these mutations support lab leak theory (Wuhan), for example @zhiyanle
"the mutations again proves SARS-2 is lab-made. Natural Cov needs 50 years for 1100BP mutation; but lab-made nCov can have 5 times more mutation just in a year"
https://t.co/6MyarZHKfy
Lab leak theory folks: but the FURIN Site
— Bj\xf6rn Meyer (@_b_meyer) November 26, 2021
Viral Evolution in less than 2 years: what, that crappy thing? Hold my beer... pic.twitter.com/PTuxM9ubDM
https://t.co/HkOAxcCWb6
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
in a complex but very interesting thread related to the argument that "the 681 Proline before the FCS of SARS-COV-2 was somehow "suboptimal"
https://t.co/n9CBtpL9gP
We def need more people like @notoriousFIL in #DRASTIC
@_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
1. 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
https://t.co/880zuh33Pp
2.
https://t.co/Wn523bt9nu
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
Fibonacci Sins!
He identifies a "RUPTURE" that no longer follows a pattern of virus-to-host adaptation, and thus suspects lab manipulation
https://t.co/fU5L8xNPoB
and
https://t.co/fU5L8xNPoB
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
https://t.co/GtnsW4FOTZ
Took a look at the spike mutations in B.1.1.529 this evening, and colour coded them (details below)...there is...not much green.\U0001f9f5 pic.twitter.com/yNHM55oTTH
— Jeffrey Barrett (@jcbarret) November 25, 2021
He explains how mutations in #SARSCoV2 Nu variant (B.1.1.529) will affect polyclonal and monoclonal antibodies targeting RBD.
https://t.co/a6kap9CFtt
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
https://t.co/3nUrKzSJOv
(experiments in Sep 2021 were with VLPs)
SARS-CoV-2 polyclonal neutralizing antibody escape
https://t.co/OhHsjPhJxg
"Nature performed the same experiment as we did with a lot more samples"
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
"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"
https://t.co/6NaGupsEpm
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
South African Medical Association Says Omicron Variant Causes 'Mild Disease'
https://t.co/qPsfZeVRfx
(Medical Health "Chief" of South Africa)
https://t.co/XRgw2xyqYA
\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
via @DMoffin
"Wouldn't artificially creating a highly infectious virus with very low pathogenicity, & therefore outcompeting more deadly variants, be most genius thing researchers could do to end the pandemic?
https://t.co/hDYkUAxsSv
Just a thought: Wouldn't artificially creating a highly infectious virus with very low pathogenicity, and therefore outcompeting the more deadly #coronavirus #variants, be the most genius thing researchers could do to truly end the pandemic? #Omicron
— DeMoffin (@DMoffin) November 27, 2021
Great graphics by Jonathan Corum @13pt
and @carlzimmer
Tracking Omicron and Other Coronavirus Variants
https://t.co/dnV79zYAgy
People currently arguing about the positive outlook
https://t.co/PlyVbxzE4g
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.
https://t.co/2unHFeVJhT
Omnicron is too long, how about we all just call it Xi\U0001f44d
— Aussie Phil (@phil_aussie) November 28, 2021
Opinion of Geert Vanden Bossche @GVDBossche
Quite a short opinión piece ;) mostly looking at ADE and vaccines
https://t.co/INWSQpwbds
A thread on Omicron mainly focusing on HIV
https://t.co/v5fQDRQxF3
https://t.co/TwinU53oDe
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
early look at the identified mutations
https://t.co/es8ARBwBaW
[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
Although some conclude that accumulation of mutations in a single immunocompromised patient (perhaps AIDS) is plausible, @daoyu15 disagrees
https://t.co/Ml4Ribsi1q
and
https://t.co/ovY4nSVPqD
and
https://t.co/ZcRa4vzkcd
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
https://t.co/WmHXxn2SuR
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
https://t.co/i2P1Kp0goU
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
https://t.co/tK9yVPcsnO
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
Hans Kristian "Lazarus" Andersen @K_G_Andersen2
Thinks it's "odd" and suspects "reverse zoonosis" possibly from rodents...
https://t.co/NlhSgz1D6j
\U0001f9a0 Omicron - on a scale from 1-10, how bad is this going to be? This one's a weirdo, so I'm a 3, a 10, or anything in-between.
— Kristian G. Andersen (@K_G_Andersen) November 30, 2021
A thread below with my take on some of the key questions.https://t.co/c7byYwPeHb
1/ pic.twitter.com/vjteCSrrhh
https://t.co/QO237D88Uj
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
"there may be an increased risk of reinfection with Omicron (ie, people who have previously had COVID-19 could become reinfected more easily with Omicron), as compared to other variants of concern"
https://t.co/zZrPal1cF1
"Previous infection used to protect against Delta but now with Omicron that doesn't seem to be the case," said Anne von Gottberg, microbiologist at South Africa's National Institute for Communicable Diseases.
https://t.co/hcOVwrEhIY
"We monitored these reinfections for Beta & Delta wave & we didn't see increase in reinfections above what we expect when the force of infection changes - when the wave stops. However, we are seeing an increase for Omicron"
https://t.co/3XkPmnuvLZ
Humanised Mice and Rodents with HIV?
Interestingly, Anderson mentions similar mutations in rodents as supporting his reverse zoonosis hypothesis:
https://t.co/a4GhCIIETW
But stops there.
3. Several of the mutations in Omicron have been observed in animals, including rodents:https://t.co/JFLR532zv1
— Kristian G. Andersen (@K_G_Andersen) November 30, 2021
18/
by Robert Garry and Bill Gallaher
Mutations arising in SARS-CoV-2 spike on sustained human-to-human transmission and human-to-animal passage
https://t.co/LiduigHlC7
Rats and Mice abound!
Note hACE2 mice in grey
https://t.co/daNwvmArj8
Now as is well known, HIV cannot infect mice, rats..
BUT
Humanized mouse models currently available are capable of replicating both HIV-1 & 2 exclusively in human immune cells that are present both in the periphery & in tissues
https://t.co/owQ8TeuElE
Humanized mouse models like the T cell only mouse or the myeloid only mouse permit the analysis of HIV biology in individual cell types.
systemic reconstitution of humanized mice with human cells permit in vivo analysis of HIV persistence
1. A mouse model for study of systemic HIV-1 infection, antiviral immune responses, and neuroinvasiveness (USA 2005)
https://t.co/KPCj2KOOpi
2. Rectal Transmission of Transmitted/Founder HIV-1 Is Efficiently Prevented by Topical 1% Tenofovir in BLT Humanized Mice (UNC, 2013)
https://t.co/hUFGtMKjy7
3. Mucosal HIV-1 transmission and prevention strategies in BLT humanized mice (UNC)
https://t.co/u8fZhWgoT1
By @sciencecohen
"now scientists have shown that a genetically engineered rat is susceptible enough to HIV infection that it may be able to help evaluate some AIDS drugs"
https://t.co/OeCW6YK4ZD
As is known, unlike the first identified strain, new SARS-CoV-2 VOCs are capable of infecting animal models (mice) in the lab.
https://t.co/SHhnbGx3Gb
Paper
B1.351 & P.1 variants extend SARS-CoV-2 host range to mice
https://t.co/SHZWjXntWk
Research on HIV vaccines & helminth parasite infested Mice (2018)
Note:
In this specific study the BALB/c mice did not have HIV
Chronic schistosomiasis suppresses HIV-specific responses in a mouse model
https://t.co/ye13mpwHRW
Anna-Lise Williamson
Department of Pathology, Faculty of Health Sciences, University of Cape Town
Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town
https://t.co/dkMEuywLUG
"One hypothesis for emergence of this lineage, given the many mutations relative to background mutation rate of SARS-CoV-2, is that it arose via intra-host evolution in 1 or more people with prolonged viral replication"
https://t.co/hH5d6yMkh1
immunosuppressed patient hypothesis discarded
multiple individuals?
"If evolution within long-term infections were the explanation for the evolution of this lineage then it supposes a transmission chain that passes through multiple individuals"
"7 (mutations) are associated with rodent adaptation — changes that allow the virus to infect mice, rats & related species. All 7 of those mutations are in Omicron"
https://t.co/HT04EcDp5B
1. Key mutations in Omicron (NTD deletions around 144, 478K, 484A, 501Y) emerged independently in an immunosuppressed patient https://t.co/lwBXDJYfNv
2. Mapping of viral mutations that escape antibodies used to treat COVID-19
https://t.co/d6N7wIfh9k
Interesting to note that several of the key mutations in omicron (NTD deletions around 144, 478K, 484A, 501Y) emerged independently in the immunosuppressed patient that we studied together https://t.co/uNxoekIwT4
— Jonathan Li (@DrJLi) December 1, 2021
https://t.co/C90cEovQeu
I have gotten multiple e-mails in last few hours asking about theories of *how* the #SARSCoV2 Omicron variant evolved. In the interest of simplicity, my thoughts are pasted below (1/2): pic.twitter.com/CPYEmiYUmC
— Bloom Lab (@jbloom_lab) December 1, 2021
A man in the COVID ward of Landspítali with the omicron variant of the coronavirus is fully vaccinated and has received a booster dose.
https://t.co/gJQ3zvH8l1
@THAILANDMEDICA1 puts the boot in again
https://t.co/sXwrW9RBXR
A bleak picture? (Posted Yesterday)
Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa
https://t.co/w3jZjMVs0h
Discusses 3 theories:
1. immunocompromised patient
2. Reverse Zoonosis
3. Molnupiravir-induced
https://t.co/FQp8kjo0NF
"To produce those 25 selected mutations, evolution would also have produced ~50 silent ones which would persist, since they are not selected against"
But did not happen, says @tony_vandongen
https://t.co/ts5S1k9t4V
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
"The large concentration of silent mutations would have to occur anywhere in the 30k genome sequence"
But there only 7 silent mutations in total (instead of the expected 300)
Whoever designed this failed to make it look natural.
So to sum this up:
SARS2 Omicron genome looks like it was "separated/frozen" between June 2020 and late summer 2021 -
This has never before been seen in nature, only in lab leaked pandemics
https://t.co/zwa0I9ZRBS
"only logical explanation is targeted manipulation"
https://t.co/IYejXk7lNn
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.
https://t.co/9nJG2geEPJ
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
https://t.co/dvbOpLmbfV
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
https://t.co/2BjK8CqD1L
9) of course they used cell lines transfected for human ACE2, and froze their viral samples, which still is the only logical explanation for omicron completely splitting off from all other variants of in June 2020. pic.twitter.com/N9lNbB41Q2
— valentin bruttel (@VBruttel) December 4, 2021
Affiliations listed
https://t.co/Dl5FqjnQoz
Full paper: Published: 29 March 2021
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
https://t.co/FwaFzw5ZCp
Rambaut @arambaut shuts down the discussion
https://t.co/uqyDE75L11
h/t @ydeigin
(Animals) By robert Garry
"This version makes corrects mutations sustained at Q493 and Q498 in humans (Omicron) and mice plus adds a few mink mutations."
https://t.co/UiuFb2U1qk
Report on Omicron Spike mutations on epitopes and immunological/epidemiological/kinetics effects from literature
https://t.co/SFJWS2xzgU
"in an otherwise deserted lab. Cele & de Oliviera chanced their luck on using human saline to infect monkey cells, which until then had proved unresponsive to weeks of experimentation. The outcome was best Christmas gift ever"
https://t.co/thvhlcvy5M
KZN scientist finds new way of growing new Covid-19 variant in groundbreaking research
https://t.co/x5sZMlLBM9
The Scientist Working Towards a COVID-19 Breakthrough
https://t.co/FMNvAxin23
Image A
Startling new variant raises urgent questions (long new branch)
https://t.co/7lQTJvchji
Image B (Durban Paper) noted by @VBruttel
https://t.co/5BSOzdo3FQ
Experiments using plasma from donors with 1st wave variant B.1.351 (501Y.V2 VOC)
I don't usually RT Threads by @stuartjdneil but will make an exception this time as his thread presents some quite valid counter arguments against certain recent leaking suggestions,
https://t.co/gbaOfeaYG3
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
The two Durban cases likely travelled through Gauteng
Gauteng cases earlier than Durban
https://t.co/PvWHzxkzGa
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
Mainly unvaccinated for obvious reasons of course
https://t.co/mHhr8m5s2C
Most cases are incidentally diagnosed SARS-CoV2
https://t.co/MNMtgAZZZq
SARS-CoV2 found in admission screen
less Covid-19 pneumonia
https://t.co/QJq4AMqwja
Hospitals not made to handle mass paediatric casualties
https://t.co/sr4MuoCzsD
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
Non Synonymous Versus Synonymous mutations
33:1...!
https://t.co/xq1hcOlYyH
https://t.co/HYMoBxpD8s
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
https://t.co/J8AfX1HI9O
Missing intermediates explained?
https://t.co/s8q5eYxoGr
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
Omicron variant of SARS-CoV-2 harbors a unique insertion mutation of putative viral or human genomic origin
https://t.co/vHgkmMVfLs
Same genetic sequence appears in HCoV-229E and in the human immunodeficiency virus (HIV)
B.1.1.7 variant first detected in UK had 12 + mutations that appeared suddenly. Recombination may merge mutations from different variants that arose spontaneously within same person over time or that co-infected someone simultaneously
https://t.co/AEakq2GMT9
Extraordinary Patient Offers Surprising Clues To Origins Of Coronavirus Variants (Feb 2021)
https://t.co/juanmyH8JE
Paper:
Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host
https://t.co/9VgREsLzxY
What One 'Extremely Unusual' COVID-19 Case Tells Us About New Variants
https://t.co/M7yop2xmxW
Advanced HIV drives SARS-CoV-2 evolution?
Divergence of delta and beta variants and SARS-CoV-2 evolved in prolonged infection into distinct serological phenotypes
https://t.co/ZqwuZkaqvB
Although I disagree with his theory, he has certainly done a great deal of background research
https://t.co/owqYx9qido
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
Party in UK where 14 of 18 guests tested positive for the new variant despite everyone being double jabbed & some with booster, all guests had taken a lateral flow test 24 hours beforehand that was negative!
https://t.co/C23vh1w5ek
https://t.co/uzXj5M9drC
and
https://t.co/YoCsE6luM8
it seems all were double vaccinated and all mild cases of illness.....so far.
Selection analysis identifies significant mutational changes in Omicron likely to influence both antibody neutralization & Spike function
Part 1
https://t.co/AvIMY7TwBe
Part 2
https://t.co/8GVcVYBu2Z
Spoiler: They are confused
"the extensive time period of undetected replication"
1. surveillance failure hypothesis
2. chronic infection hypothesis
3. reverse-zoonosis hypothesis
4. Combination of above
An analysis by @sergeilkp
https://t.co/kEnRmFTDhR
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
https://t.co/EOTzBTAK5P
archived:
https://t.co/zRBjc1LDe8
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
"Nothing to worry about" says @theosanderson
https://t.co/VCiJJOtL1O
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
"VSV based directed evolution explains this almost flawlessly"
https://t.co/LYCYQ5VRyX
(one of the many to come)
Genome Characterization and Potential Risk Assessment of the Novel SARS-CoV-2 Variant Omicron (B.1.1.529)
https://t.co/FKLm1iORi0
Scroll up from last tweet in discussion on the possibility of Omicron emerging via an HIV patient
https://t.co/bVFqm0RQno
with contributions from:
@daoyu15
@roadjull
@VBruttel
@TonyBurnetti
@pathogenetics
@P_J_Buckhaults
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
Discussion | SAMA: Tshwane epicentre of Omicron
https://t.co/VR2PZXtnTi
1. OK
Introduction to the Centre for Emerging Zoonotic and Parasitic Diseases (CEZPD) in Johannesburg (BSL3 and 4)
https://t.co/mkalJm3tpX
2. Scrubbed?
https://t.co/uR49CDWpz8
Can @nicd_sa explain?
Maybe CEZPD has a virus?
https://t.co/tIAB2K2Dvg
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
Sources:
1 https://t.co/Yn6TIU5S6H
2 https://t.co/KvOA52WX5m
3 https://t.co/SwVAEMmv12
4 https://t.co/JsfuSp4ot8
5 https://t.co/IsIheuVazt
6
https://t.co/H8PfMwq47E
7
https://t.co/lGc3Gf3NFo
8 https://t.co/Dv4N0JXUgL
9
https://t.co/yuNgyImfQC
10
https://t.co/yIKflZ6pul
11 https://t.co/YM8ITI6GQ7
12
https://t.co/UGFy9mUobm
How dare you try to detect me, says Omicron on a trip to Australia (Queensland).
1. https://t.co/XG7gSaxPo6
2. https://t.co/wbkDFiQWrG
3. https://t.co/xokuQXHw45
@BallouxFrancois says:
There are two lineages within Omicron, BA.1 and BA.2, that are quite differentiated genetically. The two lineages may behave differently.
Proposal to split B.1.1.529 to incorporate a newly characterised sibling lineage
List of mutations found in Omicron's sister
https://t.co/LdHOHR931q
and image
https://t.co/GZDVeLYrTn
"There are B.1.1.529 lineages that do not have the N440K & K417N mutation (336 GISAID entries) & form a separate clade when analysed with other sequences that do contain these mutations"
https://t.co/7q4OVyjmF1
"Either an intermediate that didn't acquire all defining mutations or it is consensus of a mixture of 2 lineages"
"If chronic infection hypothesis is true, no reason to believe patient zero would only have transmitted to one other"
Omicron’s less severe cases prompt cautious optimism in South Africa
"However, potential for Omicron to result in less severe symptoms may be more a consequence of immunity than the virus evolving to become less virulent"
https://t.co/1n02xgs5ZH
(explaining aspects of FT article linked in last tweet)
https://t.co/hGQA5RCfeU
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
Thread follows
The Good (Pfizer Spin)
https://t.co/vIgMF0Of9A
The Bad:
Average loss of neutralization potency was lower than feared
https://t.co/HRVHRqBj6m
The Ugly:
Up to 37 times reduction in Delta vs. Omicron
https://t.co/ZVqXwItBwP
Briefing on Pfizer/biontech neutralisation studies has begun. 19 or 20 seras (why don't they know which?!)
— Tom Whipple (@whippletom) December 8, 2021
1/x pic.twitter.com/fBay0uA6oT
monoclonal AKs imdevimab and casirivimab are - as expected - ineffective with Omicron
experiments were carried out with a virus isolate (infectious virus), not with pseudoviruses.
Question about different results
https://t.co/EXZymWYFGb
Thanks for sharing! Do you know how many in your sample have received a vaccination after infection? You report higher neutralisation values than https://t.co/ue4smsJzYt who only had double-vacc after infect. and I am wondering if this may be due to vaccination.
— TBA (@knigotnik) December 8, 2021
Reduced Neutralization of SARS-CoV-2 Omicron Variant by Vaccine Sera and monoclonal antibodies
https://t.co/3QYSjyp3Az
on the antibody neutralisation results for Omicron
https://t.co/95iYlyoJgg
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
1/ https://t.co/nOyL7wq1NI
@Sandile_Cele22 @Tuliodna So, pay attention!
SARS-CoV-2 evolved during advanced HIV disease immunosuppression & has Beta-like escape of vaccine & Delta infection elicited immunity
https://t.co/1yDnZ7JNtz
h/t @mouth_madness
https://t.co/enR1ucg5Hd
4. Shape Shifting Omicron?https://t.co/shwk5JJXMd
— Billy Bostickson \U0001f3f4\U0001f441&\U0001f441 \U0001f193 (@BillyBostickson) January 4, 2022
Cathepsin Cell Entry Paper from Glasgow here:https://t.co/4ey0EVd35h
PDFhttps://t.co/07dqv75MI0
https://t.co/WV7IBrzk80
The Omicron Mouse Hypothesis gains legs
— Billy Bostickson \U0001f3f4\U0001f441&\U0001f441 \U0001f193 (@BillyBostickson) January 2, 2022
Evidence for a mouse origin of the SARS-CoV-2 Omicron varianthttps://t.co/PoUCgJfm6X https://t.co/MPH0iqNZ1h pic.twitter.com/pEDJsj6SKi
Surely the Omicron is at hand.
https://t.co/uLFIIA8K3D
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
Summarised many anomalies discovered to date
https://t.co/654LCTQTml
via @capitolsheila
More from Billy Bostickson 🏴👁&👁 🆓
1. WIV Research groups (archived pages) for Reference
dsRNA viruses molecular biology
https://t.co/lwrQoo6ygG
2. Emerging Viruses Group
https://t.co/ND56gVGOAn
3. Structural Biology of Viral Genome Replication
https://t.co/wUqc0YIP3X
4. Molecular Biology of hepatitis Viruses & Gene Therapy
https://t.co/snBbxkhNsC
5. Insect Virus Genetic Engineering Lab
https://t.co/S68mVOA2Ob
dsRNA viruses molecular biology
https://t.co/lwrQoo6ygG
2. Emerging Viruses Group
https://t.co/ND56gVGOAn
3. Structural Biology of Viral Genome Replication
https://t.co/wUqc0YIP3X
4. Molecular Biology of hepatitis Viruses & Gene Therapy
https://t.co/snBbxkhNsC
5. Insect Virus Genetic Engineering Lab
https://t.co/S68mVOA2Ob
1. Thread: RaTG13 Real or Fake?
A Norwegian Scientist @Vehuardo recently claimed RaTG13 is an "authentic virus"
https://t.co/tAXMNTwdhA
This failed to take into account the work of our DRASTIC colleagues & other published analyses.
This thread is a polite attempt to educate.
2. https://t.co/tw606vgHwp
which says RaTG13 doesn't make sense on how it was sequenced, or how the data got so messed up in the lab as to include copy paste mistakes, bat dna, pangolin dna, rice dna, mice dna, & nobody should use it to form conclusions until it's properly vetted
2 (cont)
"sequence is incomplete & provided segment doesn't function. The identified markers suggest partial match basis & actual virus itself as described by the sequence can't functionally exist due to incoherent structures that appear to be the result of sample contamination"
3. RaTG13 integrity is further attacked here:
The Validity of critical pieces of evidence for the natural origin of SARS-CoV-2 is Dubious, and needed to be
4. and here:
Major Concerns on the Identification of Bat Coronavirus Strain RaTG13 and Quality of Related Nature
A Norwegian Scientist @Vehuardo recently claimed RaTG13 is an "authentic virus"
https://t.co/tAXMNTwdhA
This failed to take into account the work of our DRASTIC colleagues & other published analyses.
This thread is a polite attempt to educate.
2. https://t.co/tw606vgHwp
which says RaTG13 doesn't make sense on how it was sequenced, or how the data got so messed up in the lab as to include copy paste mistakes, bat dna, pangolin dna, rice dna, mice dna, & nobody should use it to form conclusions until it's properly vetted
2 (cont)
"sequence is incomplete & provided segment doesn't function. The identified markers suggest partial match basis & actual virus itself as described by the sequence can't functionally exist due to incoherent structures that appear to be the result of sample contamination"
3. RaTG13 integrity is further attacked here:
The Validity of critical pieces of evidence for the natural origin of SARS-CoV-2 is Dubious, and needed to be
4. and here:
Major Concerns on the Identification of Bat Coronavirus Strain RaTG13 and Quality of Related Nature
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Hello!! 👋
• I have curated some of the best tweets from the best traders we know of.
• Making one master thread and will keep posting all my threads under this.
• Go through this for super learning/value totally free of cost! 😃
1. 7 FREE OPTION TRADING COURSES FOR
2. THE ABSOLUTE BEST 15 SCANNERS EXPERTS ARE USING
Got these scanners from the following accounts:
1. @Pathik_Trader
2. @sanjufunda
3. @sanstocktrader
4. @SouravSenguptaI
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Everything covered in this thread.
1. Management
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4. Examples
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Hello!! 👋
• I have curated some of the best tweets from the best traders we know of.
• Making one master thread and will keep posting all my threads under this.
• Go through this for super learning/value totally free of cost! 😃
1. 7 FREE OPTION TRADING COURSES FOR
A THREAD:
— Aditya Todmal (@AdityaTodmal) November 28, 2020
7 FREE OPTION TRADING COURSES FOR BEGINNERS.
Been getting lot of dm's from people telling me they want to learn option trading and need some recommendations.
Here I'm listing the resources every beginner should go through to shorten their learning curve.
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2. THE ABSOLUTE BEST 15 SCANNERS EXPERTS ARE USING
Got these scanners from the following accounts:
1. @Pathik_Trader
2. @sanjufunda
3. @sanstocktrader
4. @SouravSenguptaI
5. @Rishikesh_ADX
The absolute best 15 scanners which experts are using.
— Aditya Todmal (@AdityaTodmal) January 29, 2021
Got these scanners from the following accounts:
1. @Pathik_Trader
2. @sanjufunda
3. @sanstocktrader
4. @SouravSenguptaI
5. @Rishikesh_ADX
Share for the benefit of everyone.
3. 12 TRADING SETUPS which experts are using.
These setups I found from the following 4 accounts:
1. @Pathik_Trader
2. @sourabhsiso19
3. @ITRADE191
4.
12 TRADING SETUPS which experts are using.
— Aditya Todmal (@AdityaTodmal) February 7, 2021
These setups I found from the following 4 accounts:
1. @Pathik_Trader
2. @sourabhsiso19
3. @ITRADE191
4. @DillikiBiili
Share for the benefit of everyone.
4. Curated tweets on HOW TO SELL STRADDLES.
Everything covered in this thread.
1. Management
2. How to initiate
3. When to exit straddles
4. Examples
5. Videos on
Curated tweets on How to Sell Straddles
— Aditya Todmal (@AdityaTodmal) February 21, 2021
Everything covered in this thread.
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2. How to initiate
3. When to exit straddles
4. Examples
5. Videos on Straddles
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