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"
2. The Letter Chosen by the WHO
"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'
news18.com/news/world/why…
3. The Omicron variant has been found in nearly every province of South Africa, as well as Botswana, Belgium, Israel, UK and Hong Kong.
This month, Israel held an exercise, The “Omega Exercise”, meant to prepare for a hypothetical, new COVID-19 variant
jpost.com/health-and-wel…
4. Omicron Infographic
(appeared in Germany and Italy now)
breakingnews.ie/world/pharmace…
5. Overview of Omicron (B.1.1.529) from @nicd_sa
6. Timeline of Omicron from @nicd_sa
Note:
@Clucky92864053 points out that this variant of the virus itself was first identified back in July 2021
threadreaderapp.com/thread/1464592…
7. Minimal FAQ from @nicd_sa (26 November 2021)
nicd.ac.za/frequently-ask…
9. Opinion of Trevor Bedford @trvrb
He considers that the extremely long branch (>1 year) indicates continual evolution in a chronically infected individual before spilling back into the population.
Archived thread:
threadreaderapp.com/thread/1464353…
10. Opinion of @trvrb (2)
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
11. Spreading quickly
with a doubling time of 4.8 Days
12. Opinion of @ydeigin
"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"
13. Some facts from Dr Emma Hodcroft @firefoxx66
"making it hard with current sequences to tell much about the evolutionary history"
and
14. Phylogenetic analysis of SARS-CoV-2 clusters in their international context - cluster 21K
Maintained by Emma Hodcroft @firefoxx66
nextstrain.org/groups/neherla…
15. Krammer @florian_krammer asks a question
"Do you think it is plausible that this variant was mostly generated within one host with a persistent infection?"
16. Rewind to the South African HIV patient
17. Earlier Concerns
Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection
and
As COVID-19 collides with HIV/AIDS, the pandemic may be taking an ominous turn
https://t.co/RMZ2y9i23I
18. Rumours abound - Molnupiravir (1)
@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
and
19. But according to Daily Maverick (SA) (18/11/21)
"New antiviral pills to treat Covid unlikely to be made available in South Africa for some time"
dailymaverick.co.za/article/2021-1…
and the trials took place at 170 sites in many countries not just South Africa.
merck.com/news/merck-and…
20. Also rumours of Lab Leaks ;)
University of Pretoria BSL3
up.ac.za/centre-for-vir…
21. BSL3 and BSL4
nicd.ac.za/wp-content/upl…
22. The Mutations
Page 18:
SARS-CoV-2 variants of concern and variants under investigation in England
Technical briefing 29 - 26 November 2021
assets.publishing.service.gov.uk/government/upl…
23. Significance of the Mutations
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"
24. Others Disagree, for example @_b_meyer
25. Comments
26. @_b_meyer rightly chastised by @notoriousFIL
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"
We def need more people like @notoriousFIL in #DRASTIC
27. Two specific tweets
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
2.
28. Back to Omicron (Opinion of @JCPEREZCODEX )
Fibonacci Sins!
He identifies a "RUPTURE" that no longer follows a pattern of virus-to-host adaptation, and thus suspects lab manipulation
and
https://t.co/fU5L8xNPoB
29. @jcbarret dissects the "Omicron" mutations
30. @jbloom_lab on the "Omicron" Mutations
He explains how mutations in #SARSCoV2 Nu variant (B.1.1.529) will affect polyclonal and monoclonal antibodies targeting RBD.
31. @theodora_nyc responds to @jbloom_lab
(experiments in Sep 2021 were with VLPs)
SARS-CoV-2 polyclonal neutralizing antibody escape
nature.com/articles/s4158…
"Nature performed the same experiment as we did with a lot more samples"
33. @florian_krammer is a worried virologist
"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"
34. But is Omicron just a "storm in a teacup"?
South African Medical Association Says Omicron Variant Causes 'Mild Disease'
sputniknews.com/20211127/south…
35. Short Video Interview with Angelique Coetzee
(Medical Health "Chief" of South Africa)
36. From a storm in a teacup to a blessing?
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?
37. Keep up to date with Omicron @nytimes
Great graphics by Jonathan Corum @13pt
and @carlzimmer
Tracking Omicron and Other Coronavirus Variants
nytimes.com/interactive/20…
unroll Omicron @threadreaderapp
Update 1
People currently arguing about the positive outlook
Update 2 via @phil_aussie and a great idea
Update 3 Thanks @AGHuff
The "UK " Diplomatic Connection...
thailandmedical.news/news/this-is-g…
Update 4
Opinion of Geert Vanden Bossche @GVDBossche
Quite a short opinión piece ;) mostly looking at ADE and vaccines
voiceforscienceandsolidarity.org/scientific-blo…
Update 5 by Moritz Gerstung @MoritzGerstung
A thread on Omicron mainly focusing on HIV
threadreaderapp.com/thread/1464287…
Update 6 from Mia Malan @miamalan
early look at the identified mutations
Update 7
Although some conclude that accumulation of mutations in a single immunocompromised patient (perhaps AIDS) is plausible, @Daoyu15 disagrees
and
and
Update 8 - @P_J_Buckhaults is surprised
Update 9 - @ydeigin moves further to a lab leak
Update 10 - @NPRGoatsandSoda
npr.org/sections/goats…
Update 11 - "Weird" Omicron by @EricTopol
Update 12 - Mega Omicron Thread by...
Hans Kristian "Lazarus" Andersen @K_G_Andersen2
Thinks it's "odd" and suspects "reverse zoonosis" possibly from rodents...
Update 13 - @mroliverbarnes
Update 14 - Reinfections surging?
"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"
who.int/news/item/28-1…
Update 15 - Reinfections (2)
"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.
reuters.com/world/africa/s…
Update 16 - Reinfections (3)
"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"
news24.com/news24/southaf…
Update 17 - Rodents?
Humanised Mice and Rodents with HIV?
Interestingly, Anderson mentions similar mutations in rodents as supporting his reverse zoonosis hypothesis:
But stops there.
Update 18 - Rodent and other animal Mutations
by Robert Garry and Bill Gallaher
Mutations arising in SARS-CoV-2 spike on sustained human-to-human transmission and human-to-animal passage
virological.org/t/mutations-ar…
Update 19 - Updated Mutations including Omicron
Rats and Mice abound!
Note hACE2 mice in grey
virological.org/uploads/short-…
Update 20 - HIV Rodents?
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
ncbi.nlm.nih.gov/labs/pmc/artic…
Update 21 - Humanised Mouse Models (2)
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
Update 22 - Sample HIV Mouse papers
1. A mouse model for study of systemic HIV-1 infection, antiviral immune responses, and neuroinvasiveness (USA 2005)
pnas.org/content/102/10…
Update 23 - Sample HIV Mouse papers
2. Rectal Transmission of Transmitted/Founder HIV-1 Is Efficiently Prevented by Topical 1% Tenofovir in BLT Humanized Mice (UNC, 2013)
journals.plos.org/plosone/articl…
Update 24 - Sample HIV Mouse papers
3. Mucosal HIV-1 transmission and prevention strategies in BLT humanized mice (UNC)
cell.com/trends/microbi…
Update 25 - Rats and HIV (2007)
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"
archive.ph/zbHwn
Update 26. SARS COV 2 in Mice
As is known, unlike the first identified strain, new SARS-CoV-2 VOCs are capable of infecting animal models (mice) in the lab.
pasteur.fr/en/press-area/…
Paper
B1.351 & P.1 variants extend SARS-CoV-2 host range to mice
biorxiv.org/content/10.110…
Update 27 - ABSL2, University of Cape Town
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
ncbi.nlm.nih.gov/labs/pmc/artic…
Update 28 - HIV Research with Mice (Cape Town)
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
pubmed.ncbi.nlm.nih.gov/?term=Williams…
Update 29 - Groundhog Day (2020)
"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"
medrxiv.org/content/10.110…
Update 30 - December 22, 2020
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"
Update 31 - Garry & Gallaher - Rodent Mutations
"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"
statnews.com/2021/12/02/som…
Update 32
Oh my Cron, this will be the never ending thread!
Update 33 - @DrJlieberman
1. Key mutations in Omicron (NTD deletions around 144, 478K, 484A, 501Y) emerged independently in an immunosuppressed patient
2. Mapping of viral mutations that escape antibodies used to treat COVID-19
Update 34 - Bloom Lab @jbloom_lab
Update 35 - Finland (double vaccinated + booster)
A man in the COVID ward of Landspítali with the omicron variant of the coronavirus is fully vaccinated and has received a booster dose.
ruv.is/frett/2021/12/…
@THAILANDMEDICA1 puts the boot in again
thailandmedical.news/news/breaking-…
Update 36 - First of many preprints on Omicron
A bleak picture? (Posted Yesterday)
Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa
medrxiv.org/content/10.110…
Update 37 - Omicron Origins by @WmHaseltine
Discusses 3 theories:
1. immunocompromised patient
2. Reverse Zoonosis
3. Molnupiravir-induced
archive.ph/MuTGu
Update 38 - Fishing for Silent Omicron Mutations
"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
Update 39 - it gets worse, says @tony_vandongen
"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.
Update 40 - Explosive Thread by @VBruttel
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
threadreaderapp.com/thread/1466919…
Update 41 - Targeted Manipulation
"only logical explanation is targeted manipulation"
Update 42 - Risky Research in Durban BSL3
Update 43 - Omicron first detected in Durban?
Update 44 - Frozen in Time (Further Evidence)
Update 45 - The Durban Paper
Affiliations listed
pubmed.ncbi.nlm.nih.gov/33780970/
Full paper: Published: 29 March 2021
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
nature.com/articles/s4158…
Update 47 - Inconvenient Truths?
Rambaut @arambaut shuts down the discussion
github.com/cov-lineages/p…
h/t @ydeigin
Update 48 - Updated Omicron Mutation Graphic
(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."
virological.org/uploads/short-…
Update 49 - Spike mutations & Epitope Effects
Report on Omicron Spike mutations on epitopes and immunological/epidemiological/kinetics effects from literature
virological.org/t/report-on-om…
Update 50 - Monkey Cells
"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"
discovery.co.za/corporate/heal…
Update 51 - Sandile Cele
KZN scientist finds new way of growing new Covid-19 variant in groundbreaking research
iol.co.za/dailynews/news…
Update 52 - BSL3 Lab Durban via @WhereIsYanLing
edition.cnn.com/videos/world/2…
Update 53 - Interview with Sandile Cele
The Scientist Working Towards a COVID-19 Breakthrough
Update 54 - Compare Dates
Image A
Startling new variant raises urgent questions (long new branch)
science.org/doi/epdf/10.11…
Image B (Durban Paper) noted by @VBruttel
nature.com/articles/s4158…
Experiments using plasma from donors with 1st wave variant B.1.351 (501Y.V2 VOC)
Update 55 - Suart Neil's Opinión
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,
Update 56 - Durban Cases?
The two Durban cases likely travelled through Gauteng
Gauteng cases earlier than Durban
Update 57 - Omicron Battered Kids?
Mainly unvaccinated for obvious reasons of course
thedailybeast.com/omicron-varian…
Update 58 - Kids, Good, Bad and Ugly
Most cases are incidentally diagnosed SARS-CoV2
SARS-CoV2 found in admission screen
less Covid-19 pneumonia
Hospitals not made to handle mass paediatric casualties
Update 59 Strange Mutation Ratios @P_J_Buckhaults
Non Synonymous Versus Synonymous mutations
33:1...!
threadreaderapp.com/thread/1465739…
Update 60 - Explained by Recombination?
Missing intermediates explained?
Update 61 -Recombination with other Coronaviruses?
Omicron variant of SARS-CoV-2 harbors a unique insertion mutation of putative viral or human genomic origin
osf.io/f7txy/
Same genetic sequence appears in HCoV-229E and in the human immunodeficiency virus (HIV)
Update 62 - Deja Vu
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
archive.ph/LvJcb
Update 63 - The Man from Boston - Deja Vu
Extraordinary Patient Offers Surprising Clues To Origins Of Coronavirus Variants (Feb 2021)
wbur.org/npr/964447070/…
Paper:
Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host
nejm.org/doi/full/10.10…
Update 64 - The Boston Spike Protein Mutations
What One 'Extremely Unusual' COVID-19 Case Tells Us About New Variants
wbur.org/hereandnow/202…
Update 65 - Related Durban Paper (2)
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
medrxiv.org/content/10.110…
Update 66 - @EthicalSkeptic Omicron Opinión
Although I disagree with his theory, he has certainly done a great deal of background research
Update 67 - Super Spreading Omicron Christmas?
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!
inews.co.uk/news/health/om…
Update 68 - Similar Event in Norway
analogartistdigitalworld.com/2021/12/norway…
and
dailymail.co.uk/news/article-1…
it seems all were double vaccinated and all mild cases of illness.....so far.
Update 69 - A herd of virologists at work
Selection analysis identifies significant mutational changes in Omicron likely to influence both antibody neutralization & Spike function
Part 1
virological.org/t/selection-an…
Part 2
virological.org/t/selection-an…
Spoiler: They are confused
Update 70 - The above paper tries hard to explain
"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
Update 71 "escape calculator" thread by @jbloom_lab
archived:
threadreaderapp.com/thread/1468001…
Update 72 - A sister lineage to Omicron ;)
"Nothing to worry about" says @theosanderson
Update 73 -The contrarian point of view of @Daoyu15
"VSV based directed evolution explains this almost flawlessly"
threadreaderapp.com/thread/1467638…
Update 74 - A quite tedious paper on Omicron
(one of the many to come)
Genome Characterization and Potential Risk Assessment of the Novel SARS-CoV-2 Variant Omicron (B.1.1.529)
scienceopen.com/hosted-documen…
Update 75 - Twitter as usual way ahead of academia
Scroll up from last tweet in discussion on the possibility of Omicron emerging via an HIV patient
with contributions from:
@Daoyu15
@roadjull
@VBruttel
@TonyBurnetti
@pathogenetics
@P_J_Buckhaults
Update 76 - Opinion of Dr Fareed Abdullah
Discussion | SAMA: Tshwane epicentre of Omicron
Update 77 - CEZPD scrubbing web pages a la WIV?
1. OK
Introduction to the Centre for Emerging Zoonotic and Parasitic Diseases (CEZPD) in Johannesburg (BSL3 and 4)
nicd.ac.za/centres/centre…
2. Scrubbed?
web.archive.org/web/2021081819…
Can @nicd_sa explain?
Update 78 - A more innocent explanation
Maybe CEZPD has a virus?
Update 79 - Morons!
Thailand medical news loses its patience..
thailandmedical.news/news/morons-ha…
Update 80 - The Arrival of Omicron
via @Onorpik
Update 81 - Omicron Cartoons (1)
Sources:
1 cartoonmovement.com/cartoon/omicron
2 archive.ph/0znaH
3 dailymaverick.co.za/article/2021-1…
4 newframe.com/cartoon-knee-j…
Update 82 - Omicron cartoons (2)
5 baltimoresun.com/opinion/editor…
6
journal-news.net/journal-news/t…
7
cincinnati.com/story/opinion/…
8 twitter.com/i/lists/134320…
Update 83 - Omicron cartoons (3)
9
slguardian.org/2021/11/omicro…
10
9gag.com/tag/omicron-pe…
11 fredericknewspost.com/terms/special/…
12
startribune.com/editorial-cart…
Update 84 - Omicron now avoiding detection
How dare you try to detect me, says Omicron on a trip to Australia (Queensland).
1. msn.com/en-us/news/wor…
2. theguardian.com/world/2021/dec…
3. theguardian.com/world/2021/dec…
Update 85 - Two Lineages within Omicron
@BallouxFrancois says:
There are two lineages within Omicron, BA.1 and BA.2, that are quite differentiated genetically. The two lineages may behave differently.
Update 86 - Welcome Omicron's Sister!
Proposal to split B.1.1.529 to incorporate a newly characterised sibling lineage
List of mutations found in Omicron's sister
github.com/cov-lineages/p…
and image
github.com/cov-lineages/p…
Update 87 - @arambaut busy deleting comments & closing discussions
"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"
github.com/cov-lineages/p…
Update 88 - Transmission to a second person?
"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"
Update 89 - One BIG uncertainty
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"
ft.com/content/d315be…
Update 90 - Thread by @jburnmurdoch
(explaining aspects of FT article linked in last tweet)
Update 91 - AB Neutralisation of Omicron Variant
The Good (Pfizer Spin)
The Bad:
Average loss of neutralization potency was lower than feared
The Ugly:
Up to 37 times reduction in Delta vs. Omicron
threadreaderapp.com/thread/1468465…
Update 92 - The Ugly (reasons)
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
Update 93 - The "Ugly" Paper @CiesekSandra
Reduced Neutralization of SARS-CoV-2 Omicron Variant by Vaccine Sera and monoclonal antibodies
medrxiv.org/content/10.110…
Update 94 - The opinion of @BallouxFrancois
on the antibody neutralisation results for Omicron
Update 95 - Big One straight from the Horse's Mouth
@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
medrxiv.org/content/10.110…
h/t @mouth_madness
Update 96 -Shape shifting Omicron?
Update 97 - Omicron Lab Leak Hypothesis (Thread)
Update 98 Surely some revelation is at hand?
Surely the Omicron is at hand.
Update 99 - Lab Leak 2.0 (worth a read)
Summarised many anomalies discovered to date
bprice.substack.com/p/lab-leak-20
via @capitolsheila
unroll Omicron @threadreaderapp
save Omicron @buzz_chronicles
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