2hats
Dust.
#torymutantviruscfy
Covid Mutations
- Thread starter Supine
- Start date
elbows
Well-Known Member
8ball
Maximum Facepalm
Sounds like a brand of toning mist.
elbows
Well-Known Member
How about purga?
I can almost hear people now, talking about how rough it was when they caught the purga rona.
8ball
Maximum Facepalm
Well, it goes well with Tory, just the wrong way round.
2hats
Dust.
Turns out to have been speculation by Birx, apparently.
False Reports of a New ‘U.S. Variant’ Came From White House Task Force (Published 2021)
Reports of a highly contagious new variant, published on Friday by multiple news outlets, were based on speculative statements made by Dr. Deborah Birx.
elbows
Well-Known Member
Turns out to have been speculation by Birx, apparently.
False Reports of a New ‘U.S. Variant’ Came From White House Task Force (Published 2021)
Reports of a highly contagious new variant, published on Friday by multiple news outlets, were based on speculative statements made by Dr. Deborah Birx.www.nytimes.com
Its not good for credibility when authorities that failed to control their outbreaks and are suffering badly in the middle of winter tries to explain their nasty curves by blaming a new variant without any proper evidence. The curve simply looking much worse than they'd have liked to see is entirely insufficient, but apparently its just too tempting for them to resist seeding such narratives.
I'm hoping my own thoughts on the UK side of things are helped along by the s gene dropout figures over the next few weeks. So far I consider that there are a few compelling nuggets in such data, but also some contrary indicators, especially recently.
2hats
Dust.
New mutation, related to B.1.1.248 lineage, identified in Japan, apparently an import from Brazil (4 cases). Features N501Y and E484K mutations in common with 'SA' variant but with other mutations ('UK' variant doesn't feature E484K).
www3.nhk.or.jp
Somewhat related preprint - a case of a B.1.1.248 reinfection (after 5 months) in Brazil - DOI: 10.20944/preprints202101.0132.v1
New variant of coronavirus detected in Japan | NHK WORLD-JAPAN News
Japan's health ministry says four people who arrived at Tokyo's Haneda Airport earlier this month were infected with a coronavirus variant different from those found in Britain and South Africa.
www3.nhk.or.jp
2hats
Dust.
Confirmed reinfection in the UK by a different variant (B.2 first, then B.1.1.7), after just over 8 months. Patient was a 78 year old with type 2 diabetes, no immunosuppression. First episode mild, second critical/life threatening. The patient's antibody levels were regularly monitored after the first infection and antibodies to SARS-CoV-2 were present shortly before the onset of the second infection. Raises questions about immune and vaccine escape and possibility of reinfection.
DOI: 10.1093/cid/ciab014
DOI: 10.1093/cid/ciab014
elbows
Well-Known Member
That link didnt do much for me, gave me a useless empty pdf. Here is another Confirmed Reinfection with SARS-CoV-2 Variant VOC-202012/01
2hats
Dust.
LSHTM analysis (not yet peer reviewed) of the 501Y.V2/B.1.351 variant through modelling the South African pandemic. Either it is 1.50 (95%CI: 1.20-2.13) times as transmissible as previously circulating variants, or if it is as equally transmissible as previous variants then it evades 21% (95%CI: 11-36%) of previously acquired immunity. Fairly likely the reality lies somewhere between these (somewhat increased transmission and somewhat increased immune escape) and it represents an additional public health problem. There is some evidence for increased severity but the uncertainty in that is substantial.
cmmid.github.io
Estimates of severity and transmissibility of novel SARS-CoV-2 variant 501Y.V2 in South Africa
Using globally available data sources with mathematical models, we analysed the transmissibility and severity of a novel SARS-CoV-2 variant, 501Y.V2, in South Africa.
cmmid.github.io
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2hats
Dust.
A new variant identified in Brazil (Manaus) which has turned up in 46% of samples collected over two weeks in December. With biologically significant mutations E484K, K417T, and N501Y it has been declared as a new lineage P.1 (descendent of B.1.1.28). Extensive local transmission points to an independent evolution, but some key commonalities in spike mutations with B.1.1.7 and B.1.351 "raises concern about convergent evolution to a new phenotype, potentially associated with an increased propensity for re-infection of individuals".
virological.org
Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings
Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings Nuno R. Faria1,2,3, Ingra Morales Claro3,4, Darlan Candido2,3, Lucas A. Moyses Franco3,4, Pamela S. Andrade3,4, Thais M. Coletti3,4, Camila A. M. Silva3,4, Flavia C. Sales3,4, Erika R. Manuli3,4, Renato...
virological.org
Supine
Newt Member
Looks like naming strategies are evolving to improve communication in how mutations are evolving:
virological.org
Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings
Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings Nuno R. Faria1,2,3, Ingra Morales Claro3,4, Darlan Candido2,3, Lucas A. Moyses Franco3,4, Pamela S. Andrade3,4, Thais M. Coletti3,4, Camila A. M. Silva3,4, Flavia C. Sales3,4, Erika R. Manuli3,4, Renato...
virological.org
2hats
Dust.
A new preprint investigates the effect of recently seen mutations on ACE2 affinity.
501Y seen in the B.1.1.7 (UK) variant exhibits 2.5x affinity compared to previous variants. The 501Y plus E484K mutations seen in B.1.351 and B.1.1.248, P.1 (SA and new Brazilian variants) exhibit 13x affinity.
But it is not yet clear as to the implications of this for transmissibility/pathogenesis, as a tighter binding and other mutations in those variants, in tandem with E484K, might even inhibit transmission (this has been seen in some other combinations of mutations).
www.biorxiv.org
DOI: 10.1101/2021.01.06.425392
B.1.1.248, P.1 are clearly variants to keep an eye on and require further analysis.
501Y seen in the B.1.1.7 (UK) variant exhibits 2.5x affinity compared to previous variants. The 501Y plus E484K mutations seen in B.1.351 and B.1.1.248, P.1 (SA and new Brazilian variants) exhibit 13x affinity.
But it is not yet clear as to the implications of this for transmissibility/pathogenesis, as a tighter binding and other mutations in those variants, in tandem with E484K, might even inhibit transmission (this has been seen in some other combinations of mutations).
SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor
SARS-CoV-2 is constantly evolving, with more contagious mutations spreading rapidly. Using in vitro evolution to affinity maturate the receptor-binding domain (RBD) of the spike protein towards ACE2, resulted in the more contagious mutations, S477N, E484K, and N501Y to be among the first...
B.1.1.248, P.1 are clearly variants to keep an eye on and require further analysis.
Indeliblelink
\......👁&👁......./
... potentially associated with an increased propensity for re-infection of individuals".
Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings
Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings Nuno R. Faria1,2,3, Ingra Morales Claro3,4, Darlan Candido2,3, Lucas A. Moyses Franco3,4, Pamela S. Andrade3,4, Thais M. Coletti3,4, Camila A. M. Silva3,4, Flavia C. Sales3,4, Erika R. Manuli3,4, Renato...
Some evidence of that in this paper.
Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020
Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil Authors Paola Cristina Resende1*, João Felipe Bezerra2, Romero Henrique Teixeira de Vasconcelos2, Ighor Arantes3, Luciana Appolinario1, Ana Carolina Mendonça1, Anna Carolina Paixao1, Ana Carolina Duarte...
virological.org
I'm guessing this is the same case/patient and someone's got the age wrong. ?
Genomic Evidence of a Sars-Cov-2 Reinfection Case With E484K Spike Mutation in Brazil
To date, uncertainty remains about how long the protective immune responses against SARS-CoV-2 persists and the first reports of suspected reinfection began to be described in recovered patients months after the first episode. Viral evolution may favor reinfections, and the recently described...
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2hats
Dust.
See previously second reference in post #159. E484K has demonstrated degrees of immune escape in this and the "SA" variant and in the lab.Some evidence of that in this paper.
Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020
Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil Authors Paola Cristina Resende1*, João Felipe Bezerra2, Romero Henrique Teixeira de Vasconcelos2, Ighor Arantes3, Luciana Appolinario1, Ana Carolina Mendonça1, Anna Carolina Paixao1, Ana Carolina Duarte...
2hats
Dust.
A 'predecessor' to the B.1.1.7 "UK" variant (N501 mutation, here specifically N501T) was seen in Italy in August in a 59-year-old man with persistent COVID infection. DOI: 10.1016/S1473-3099(21)00007-4
weltweit
Well-Known Member
Doesn't look good that you can be infected by one strain and then later by another.Some evidence of that in this paper.
Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020
Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil Authors Paola Cristina Resende1*, João Felipe Bezerra2, Romero Henrique Teixeira de Vasconcelos2, Ighor Arantes3, Luciana Appolinario1, Ana Carolina Mendonça1, Anna Carolina Paixao1, Ana Carolina Duarte...
elbows
Well-Known Member
Its pretty consistent with pre-pandemic knowledge. Whats different this time is that we will get much more research into the underlying factors that contribute to waning coronavirus immunity. ie will will learn more about how much mutations contribute to that picture, and how much waning immunity within an individuals body contributes.
2hats
Dust.
Two new US variants reported, identified in Columbus, Ohio. One, COH.20G/501Y, includes the N501Y mutation seen in 20B/501Y.V1 aka VOC 202012/01 (B.1.1.7, the "UK" variant) and 20C/501Y.V2 (B.1.351, the "SA" variant). The other is reported as having three mutations in the spike. No details yet.
wexnermedical.osu.edu
e2a: One of these variants looks like it has mutations Q677H (spike), A85S (matrix), D377Y (nucleocapsid).
Researchers Discover New Variant of COVID-19 Virus in Columbus, Ohio
Here is some information from The Ohio State University Wexner Medical Center I wanted to share with you.
wexnermedical.osu.edu
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2hats
Dust.
One of the "Brazilian" variants already circulating in the UK.A new preprint investigates the effect of recently seen mutations on ACE2 affinity.
501Y seen in the B.1.1.7 (UK) variant exhibits 2.5x affinity compared to previous variants. The 501Y plus E484K mutations seen in B.1.351 and B.1.1.248, P.1 (SA and new Brazilian variants) exhibit 13x affinity.
But it is not yet clear as to the implications of this for transmissibility/pathogenesis, as a tighter binding and other mutations in those variants, in tandem with E484K, might even inhibit transmission (this has been seen in some other combinations of mutations).
DOI: 10.1101/2021.01.06.425392SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor
SARS-CoV-2 is constantly evolving, with more contagious mutations spreading rapidly. Using in vitro evolution to affinity maturate the receptor-binding domain (RBD) of the spike protein towards ACE2, resulted in the more contagious mutations, S477N, E484K, and N501Y to be among the first...
B.1.1.248, P.1 are clearly variants to keep an eye on and require further analysis.
e2a: analysis of the phylogenetic tree indicates the variant now found in the UK is not the B.1.1.248 lineage.
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Indeliblelink
\......👁&👁......./
The preprint is now upTwo new US variants reported, identified in Columbus, Ohio. One, COH.20G/501Y, includes the N501Y mutation seen in 20B/501Y.V1 aka VOC 202012/01 (B.1.1.7, the "UK" variant) and 20C/501Y.V2 (B.1.351, the "SA" variant). The other is reported as having three mutations in the spike. No details yet.
e2a: One of these variants looks like it has mutations Q677H (spike), A85S (matrix), D377Y (nucleocapsid).Researchers Discover New Variant of COVID-19 Virus in Columbus, Ohio
Here is some information from The Ohio State University Wexner Medical Center I wanted to share with you.
Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio
Following the worldwide emergence of the p.Asp614Gly shift in the Spike (S) gene of SARS-CoV-2, there have been few recurring pathogenic shifts occurring during 2020, as assessed by genomic sequencing. This situation has evolved in the last several months with the emergence of several distinct...
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2hats
Dust.
Quite possible it will happen sooner or later, though likely in degrees of reduction of efficacy rather than all out failure. More likely to happen the longer the virus is left to circulate in large populations unchecked.
Similar timeframe - synthesise new DNA, just like RNA for Pfizer, Moderna. But then they all need to convince the regulatory bodies that they work and are safe. Maybe some will eventually produce polyvalent vaccines to better target a number of variants of concern as determined by sequencing. Likely manufacturing and distribution of new versions and demands for such in preference to previous are going to throw up issues.
2hats
Dust.
This article is a good summary of where we are up to with recent, key variants. In particular the P.1 variant which appears to be spreading rapidly around Manaus, Brazil, where a high level of seropositives have previously been recorded. Whether this is happening because it escapes previously acquired immunity or that immunity is now on the wane is very much an active area of investigation.
www.sciencemag.org
Science | AAAS
www.sciencemag.org
Daniel Griffin who does a weekly clinical report talked about a similar suspected reinfection a while ago (about June) where the second infection was a lot more serious (fatal iirc) than the first one. Any idea how frequent this could be? With undetected asymptomatic first infections these could easily sneak under the radar.
This article is a good summary of where we are up to with recent, key variants. In particular the P.1 variant which appears to be spreading rapidly around Manaus, Brazil, where a high level of seropositives have previously been recorded. Whether this is happening because it escapes previously acquired immunity or that immunity is now on the wane is very much an active area of investigation.
Science | AAAS
IMO, that was a really clearly written article -- easy to understand for non-scientists, and covering a lot of ground
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