The biology of coronavirus COVID-19 - including research and treatments

Paxlovid

Medicines Regulator UK approves Pfizer paxlovid as a treatment for covid. It has a high success rate if taken early in the illness.

https://www.theguardian.com/world/2...roves-pfizers-life-saving-covid-pill-paxlovid

 

Interesting discussion of possible mechanisms by which Omicron is better at evading immune defenses by being less affected by interferons.

https://twitter.com/user/status/1484952570586087430

https://twitter.com/user/status/1484952573878624259

https://twitter.com/user/status/1484952604299960322


The paper this thread discusses:


Omicron variant of SARS-CoV-2 exhibits an increased resilience to the antiviral type I interferon response
https://www.biorxiv.org/content/10.1101/2022.01.20.476754v1

The new variant of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Omicron (B.1.1.529), is genetically very different from other VOCs. We compared Omicron with the preceding VOC Delta (B.1.617.2) and the wildtype strain (B.1) with respect to their interactions with the antiviral type I interferon (IFN-alpha/beta) response in infected cells. Our data indicate that Omicron has gained an elevated capability to suppress IFN induction upon infection and to better withstand the antiviral state imposed by exogenously added IFN-alpha.​

Going to take the opportunity here to plug this book by the creator of Kurzgesagt on the immune system and how so amazing it is at describing the basics of immunology that this mostly makes some sense to me. Mostly. Some.

Immune: A Journey into the Mysterious System That Keeps You Alive

 

They certainly suggest Omicron is slightly better at that trick! The authors don't discuss the specific mechanisms either, but it would be interesting to compare BA.1 to BA.2 and possibly other sub variants too, to narrow down the role of specific mutations in the ORF genes.

I am also not a fan of Kurzgesagt's book at all, particularly the chapter on autoimmunity...

 

I'm wondering: omicron is to become endemic, say most all, but what if and when another powerful variant comes along...will it/could it displace the endemic omicron, do you think?

Probably no one can foretell.

 

None of the variants are going to become endemic for a very long time, if ever. Endemic means a constant transmmissibility close to 1 (meaning a constant level of the virus in the population). That simply isn't going to happen with a highly transmissible respiratory virus. More variants coming along is almost certain, it is just a matter of when.

They don't have to be displaced by more "powerful" variants, just different variants that happen to evade prior immunity. Just like Influenza.

 

Drats! The only flaw in the plan of letting a virus rip was that it could never mutate to another dominant variant. Ooooh, so close. And to think that the only way to have seen this coming was to have basic knowledge of immunology. What a shame that we don't have those anywhere and simply had to try it anyway.

It's not as if this virus was already the 3rd (4th?) major variant, or anything like that. If it wasn't for reality, this plan may have worked. All those beautiful biopsychosocial models of reality, foiled by nature, as is tradition.

https://twitter.com/user/status/1485354857339011080

 

noooooooo

 

Just a note, BA.2 already existed in November (it was designated a unique subvariant on the 6th of December), so it pre-dates the recent policies of many countries to allow circulation of Omicron without lockdowns.

 

A great thread for explaining herd immunity
https://twitter.com/user/status/1486407223215591430

 

No kidding but the herd immunity talk has moved to herd immunity through constant reinfection. You read that right, in those very words. I am not making this up, there are medical doctors currently saying this, in public and behind closed doors. And saying that children are naturally immune from infectious diseases. Who happen to be mostly the same people.

And of course Sweden has decided not to vaccinate children because the risks from vaccines are higher than from infections. Well, they obviously aren't but that's the official policy anyway. But the antivaccine movement will run with it, never have been given that much fuel since Horton-Wakefield debacle.

The pandemic has revealed deep rot within the culture of medicine. I don't think any professional institution has ever faceplanted so hard in the history of our entire civilization. It's really something to watch, feels historical, as in it belongs in the distant past.

 

One (actual, real) secondary benefit of the pandemic may be a way to unblock Alzheimer's research from its rut. Medicine's refusal to deal with the full consequences of the germ theory of disease is truly fascinating, especially given that the roots of this denial literally predate it. It definitely isn't just intuition that goes to die in immunology.

https://twitter.com/user/status/1488637332689342468

 

Don’t know if this has been posted before?

https://m.dw.com/en/tracking-long-c...sfe8BfPSbzxAZapP51SGAAOvJV9NdpfXCb9-kLS0wXpJY

 

The development of this was discussed on Radio 4 Today programme around 050 today.

It is a RESEARCH criteria, development of which sounds to be true participation approach.

Infectious Disease > COVID-19
U.K. Expert Group Attempts to Define 'Long COVID' in Kids
— Consensus panel comes up with five criteria signifying the condition
by Molly Walker, Deputy Managing Editor, MedPage Today February 7, 2022

email article

A standardized research definition of so-called "long COVID" in children was reached by a panel of clinicians, researchers, and patients to complement the existing World Health Organization (WHO) definition of long COVID for adults.

The panelists started with a survey of 49 statements about long COVID in children and young people, based on existing research. After a consensus meeting, these were whittled down to 10 statements. A final vote settled on the five most important statements to define long COVID in this age group, reported Sir Terence Stephenson, PhD, of UCL Great Ormond Street Institute of Child Health in London, and colleagues.

Their definition of long COVID for patients ages 2 to 24 years, published in the Archives of Disease in Childhood, includes continuing or developing symptoms (at least one of which is physical) after testing positive for COVID that:

• Affects their physical, mental, or social well-being
• Interferes with some aspect of daily living, such as school, work, or relationships
• Persists for a minimum duration of 12 weeks after initial testing for COVID

"To the best of our knowledge this is the first research definition for Long COVID" among children and young people, Stephenson's group wrote, noting that it is "comparable to the clinical case definition [of long COVID] in adults proposed by WHO."

They added that the definition of long COVID has been nebulous for children and young people, since they tend to present with milder illness than adults. Stephenson conducted prior research on long COVID among U.K. children and found that two-thirds reported symptoms 3 months after their COVID diagnosis, with 30% reporting three or more symptoms. Both of these rates were higher than among a group of children who had tested negative for COVID (53.3% and 16.2%, respectively).

His team put together three panels of people with different sets of expertise: "Service Delivery" (such as clinicians), "Researcher," and "Lived Experience," or patients. Of the 120 participants, 23 were in the Lived Experience panel, 50 were in the Researcher panel and 47 were in the Service Delivery panel.

The 49 initial statements were derived from existing research, systematic reviews, U.K. health guidance on COVID, and empirical data from Stephenson's prior study. Participants first scored the statements based on their own opinion, then were given a chance to change them twice after that: after seeing their group's median score and after seeing all three groups' median score.

The consensus meeting where the 10 statements were whittled down to five consisted of 17 people, four from the Service Delivery panel, 11 from the Researcher panel, and two from the Lived Experience panel.

Limitations to the data include that only two members of the Lived Experience panel were present during the consensus voting, that the study was primarily performed in the U.K., and concerns about the distinctions between the research definition of long COVID and the threshold where a patient could access healthcare.

"In our view, the decision whether a child or young person can see a healthcare professional, access any support needed, or be referred, investigated or treated for long COVID should be a shared decision involving the young person, their carers and clinicians," they wrote.

 

Not sure where to put it, technically this is more about disinformation, but the disinformation is about biology so... Anyway we have reached the phase of the pandemic in which blatant lies are published in national newspapers and get amplified for political and ideological aims. Well we've always been in that phase but now it's the dominant force.

For reference, Francois Balloux (the guy in the bushes), a pandemic contrarian and LC denier, said he has been infected 3 or 4 times and pretty sick at least once. And here he is saying that reinfections are impossible, more or less. Anyway 20-30 years, wherever he got this. Anyway this claim is a blatant lie, and it's said by someone who should know better and yet here we are. A professor of genetics who is director of a lab at UCL.

I think it may be worth doing a thread on pandemic disinformation. It's clearly the new phase we are in right now, especially with most countries having dropped all basic measures, even not reporting deaths anymore. Even though someone falling cases and deaths are celebrated. Also clearly an open eugenics phase, but then one comes with the other.

We're literally doing no better than during the 1918 pandemic, when they didn't even know about viruses and mass communication was impossible. Amazing. The biggest self-ass-kicking in human history.

https://twitter.com/user/status/1493920907592716292

 

"Stratification of hospitalized COVID-19 patients into clinical severity progression groups by immuno-phenotyping and machine learning"
Deep immune profiling suggesting three immune-type groups that predict clinical course from acute infection.
Thread

 

Association between pharmaceutical modulation of oestrogen in postmenopausal women in Sweden and death due to COVID-19: a cohort study (2022) Sund et al
https://bmjopen.bmj.com/content/12/2/e053032

Conclusions Oestrogen supplementation in postmenopausal women is associated with a decreased risk of dying from COVID-19 in this nationwide cohort study. These findings are limited by the retrospective and non-randomised design. Further randomised intervention trials are warranted.

("Sund" means healthy in Swedish. Good name for a medical professor )

 

Re issues with menstruation post vaccination.
It's definitely an issue .
https://twitter.com/user/status/1507823993776005127

 

> I think it may be worth doing a thread on pandemic disinformation. It's clearly the new phase we are in right now, especially with most countries having dropped all basic measures, even not reporting deaths anymore.

whose case and death numbers can be trusted? can i trust jhu numbers in particular?

the numbers seem relatively low ehere i am. this is urgent needed knowledge for me bcause i am going to dentist /unvaccinated/ tomorrow or next day [copltely unprotected unless i cdn get the vaccine-like evusheld].

full vaccination means going even more months on doxycycline to barely keeep dental abscesses down. [eta: means taking the time to get fully v means having to keep teeth from emergency. which means taking doxycyline for even more months.]

[why am i unvaccinatged? bacause doctor had said during delta that getting vaccinated would be tempting fate. then omicron came. now that is gone and next omicron soon. now doctor says get fully vaccinated before dentist. getting v takes time.]

so idk what to do at all but knowing numbers are accurate would at least be a partial tiny bit of knowledge.

aso there are /no/ emergency dentists or weekend dentists to my knowlede an next dental appt poss is in about 2m. u s a.

 

?
I do similarly. So odd. I can only assume you only assume as to why.

Sorry to diverge from thread topic. When your teeth fracture and crumble you are more inclined to flaunt protocol.

 

Since those of us in England are about to lose (probably have already lost, in effect, because I get the impression that there's probably not an LFT to be had - and the other nations are only weeks behind us) access to free lateral flow tests, this article suggesting when might be the best time to use your dwindling supply of them might be of help:

When should lateral flow tests be used in England now they must be paid for?