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lbeltrame

1,168 karma · joined March 24, 2013

[ my public key: https://keybase.io/einar; my proof: https://keybase.io/einar/sigs/zdKAF9cQfDFN6jjK9VMRl3NLESKy4q2GjsXt32UWmSI ]
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lbeltrame··on Covid vaccine: First ‘milestone’ vaccine offers 90% protection
It means that it includes people from different ethnicity, ages (also younger and older people) and some immunocompromised people.
lbeltrame··on Covid vaccine: First ‘milestone’ vaccine offers 90% protection
Neither. It is made of two replication-deficient human adenoviruses, Ad5 and Ad26, IIRC, which carry part or the entire spike protein (I need to check, I don't remember).

One shot is with Ad5, the other with Ad26. This is done because Ad5 is a "known" adenovirus by most population, that means that a sizable fraction has antibodies against it.

lbeltrame··on Covid vaccine: First ‘milestone’ vaccine offers 90% protection
The latest data (preprint, not peer reviewed etc etc) mention memory B and T cells up to 8 months after recovery from the illness. This means that an immunity of one year is probably likely. This would be probably enough to quench the spread, but not to eradicate the virus.
lbeltrame··on Covid vaccine: First ‘milestone’ vaccine offers 90% protection
> All these new technologies, the techniques, the principles were in development since years if not decades.

Yes, I first heard about intramuscular nucleic acid injection around the year 2000. At the time it was naked DNA and not RNA in a lipid nanoparticle suspension, but the principle was the same.

lbeltrame··on Danish Covid-19 mink variant could spark new pandemic
In the thread I linked there should be the exact figures. Vaccines target the whole spike protein (most of them, at least) so it's likely not going to be a problem. It may be for monoclonal antibodies.
lbeltrame··on Danish Covid-19 mink variant could spark new pandemic
It is reason of concern, but the press really likes to blow things out of proportion.

Some better reasoned sanity here: https://www.reddit.com/r/COVID19/comments/jo2muy/mink_and_co...

lbeltrame··on Denmark to Kill Up to 17M Minks After Discovering Mutated Coronavirus
It's not that they don't help, they have a reduced affinity, which is different from no affinity.

For a rational discussion, see the thread in the r/COVID19 subreddit: https://www.reddit.com/r/COVID19/comments/jo2muy/mink_and_co...

lbeltrame··on The West has failed – US and Europe have made a mess of handling the crisis
Let's not forget second or third order effects. A restaurant isn't just a restaurant: it involves a lot of other parts of the economy (for example, maintenance, supplies....).

So, the moment you shut down something "nonessential" you're actually hurting also other, apparently unrelated economic activities.

IOW, it might end up hurting also those providing "essential" services.

lbeltrame··on Coronavirus antibody prevalence falling in England, REACT study shows
On that topic, I found out that using specimen date instead of reporting date (for those health agencies that do that) gives you a far better picture of the trend, since reports can lag a lot due to testing bottlenecks.
lbeltrame··on Coronavirus antibody prevalence falling in England, REACT study shows
Note that this does not mean that immunity is also fading. Antibodies don't exist all the time in the bloodstream: immunological memory (in the case of antibodies, in the form of memory B cells) is what can prompt a quick response in case of reinfection.

In fact, there isn't enough data to even know how long immunity is. And let's not get started with T cell immunity, which seems to play a role with this virus and is not touched by such a study.

lbeltrame··on Vaccine hopes rise as Oxford jab prompts immune response among old and young
There's at least another paper detailing this phenomenon[1] so for sure it warrants further investigation.

[1] https://www.nature.com/articles/s41590-020-00808-x

lbeltrame··on Vaccine hopes rise as Oxford jab prompts immune response among old and young
> None of the vaccines currently on the table are even remotely good enough for 'back to normalish.' The attack rate for this virus is so high that a vaccine good enough (i.e. multiple 9s effectiveness) to allow 'back to normal' almost certainly isn't possible.

Is it? Current studies, AFAIK, give very variable attack rates, from low zeros to around 30%. Only higher if due to close contacts for longer periods of time (carriers, fishing boats, meat packing plants). This preprint on trasmission dynamics and evidence from September[1] has lower figures.

> Everyone who's alive now will almost certainly need to socially distance (and should wear an N95/KN95 mask in public indoor spaces) for the rest of their lives.

I wonder how we're even supposed to build a society that can live without any or very reduced form of contact. I think it's socially unsustainable.

[1] https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3692807

lbeltrame··on Vaccine hopes rise as Oxford jab prompts immune response among old and young
FTR, most side effects appear (according to what Moderna published so far) only after the booster shot. So IMO you can't tell yet if you were given the vaccine or not.
lbeltrame··on Vaccine hopes rise as Oxford jab prompts immune response among old and young
RNA vaccines (Pfizer, Moderna) require storage at -80C, because RNA is a molecule that can degrade easily at higher temperature.

Other vaccines can be stored at -20C, usually.

lbeltrame··on Vaccine hopes rise as Oxford jab prompts immune response among old and young
That's because 70/80% estimates assume that the population is entirely vulnerable, while instead it looks like it's partially vulnerable. Hence the estimates would need adjustment.
lbeltrame··on Vaccine hopes rise as Oxford jab prompts immune response among old and young
Not the "same", but according to a Nature review on vaccines from last month, most vaccines exhibit a very strong immune response (usually, for the two-dose regimen, after the second shot).

The nature of the response varies. Some candidates are more efficient at eliciting the production of antibodies, while others also activate cellular immunity (T cells).

lbeltrame··on Vaccine hopes rise as Oxford jab prompts immune response among old and young
IIRC, the expected price is around $3.50/dose, but I can't find the source for that anymore. AZ and Oxford have pledged not to ask for royalties or whatever, at least until the pandemic is ongoing (that would likely mean all of 2021 at the earliest).
lbeltrame··on Vaccine hopes rise as Oxford jab prompts immune response among old and young
For the FDA to even consider an emergency use authorization, they have put the following requirements:

- Efficacy of at least 60%

- Lower bound of efficacy (confidence interval) >= 30%

- Minimum safety data for at least one or two months post vaccination (I don't remember if it's one or two)

- At least five severe cases in the control arm

- Requirements for the trials to go on even if efficacy is found for an additional year after the trial end (for most of the trials, this means two years in total)

lbeltrame··on Vaccine hopes rise as Oxford jab prompts immune response among old and young
Glass half full: We can measure an immune response also in populations where it's more difficult to get a decent one. An immune response means that the immune system actually is taking action against the viral antigen.

Glass half empty: We don't know how the immune response measured relates to protection from or lessening of the infection. This is what the ongoing trial is trying to find out.

This is, IIRC, the second report of successful immunogenicity in older people. There was a (small) cohort of > 65 year old people tested with Pfizer / BioNTech's vaccine in the Phase 1 trial, and even there immune responses were found and measured.

lbeltrame··on France Sets Record for Most New Coronavirus Cases in One Day
On top of my head, France is one, Spain too, and Italy as well.

> I suspect a big part of the motivation is initial high rates of people claiming they forgot their mask when they get to the shop and insisting they be let in anyway.

As far as I can tell, no shop here (Italy) will let you inside if you don't have a mask. At least in my town shopkeepers enforce this.

lbeltrame··on France Sets Record for Most New Coronavirus Cases in One Day
> Masks do very little in open spaces.

I wonder then why many countries enforce them in open spaces. Note, this meant as a honest question.

> We still don't have the data but I think a large part of infections is happening at home were prophylactic measures are highly impractical and impossible to enforce.

Some research on current evidence was published in Science last month[1]. With the exception of some specific "job related" events (like meat packing plants) or public gatherings, most of the transmission is in fact in the household.

> the assumption being that students are acting as silent spreaders (due to the low morbidity in young people), reaches home and multiplies easily there.

I've seen this a few times, but as far as I can see the current data are absolutely inconsistent. And the largest contact tracing study from India (recently published) was done with closed schools, so no information from there either.

[1] https://science.sciencemag.org/content/early/2020/09/29/scie...

lbeltrame··on France Sets Record for Most New Coronavirus Cases in One Day
No, that's not what I meant. I meant that a positive PCR test without any symptoms can't tell you if:

- you're about to have the disease (presymptomatic)

- you have the disease (asymptomatic)

- you already cleared the virus

You might be infectious, but you don't know. And given the time window of infectiousness, delays in testing can give you a "positive, please isolate" notice when it's too late, and you potentially have spread the virus to others without knowing.

OTOH, antigen tests detect virus proteins (with far lower sensitivity), so it's far more likely that you have an active infection if you are positive.

lbeltrame··on France Sets Record for Most New Coronavirus Cases in One Day
Confirmed PCR cases (can someone from France confirm or disprove this? Is the government only using swabs + PCR?) are a problem, because they keep on piling but you lose track of who's infectious.

You have very large, almost inflated case numbers, but (in the absence of symptoms) you don't know if those people are still spreading the virus or had it and are recovering.

That's because, if you are positive at a PCR test and without any symptom you may:

- Have not yet developed symptoms, and are infectious

- Have no symptoms, and are infectious

- Have cleared the virus, and are no longer infectious

Viral RNA can last in the throat for weeks in some cases (and it's not unique to this virus). That is why you can't detect the virus just with this test in absence of anything else (and the British Medical Journal wrote about this recently: advice to the doctors on how to interpret tests).

The New England Journal of Medicine argued for far more frequent antigen testing as a way to keep track of cases that are important to isolate, that is, the ones that are infectious[1].

My country did the same mistake (also using serological tests to assess positivity and infectiousness, a stupid mistake that just increased the backlog of tests) and of course tracing blew up.

EDIT: You can voice your disagreement instead of downvoting.

[1] https://www.nejm.org/doi/full/10.1056/NEJMp2025631

lbeltrame··on The false promise of herd immunity for Covid-19
You might want to read the discussion section when they mention their modeling of schools. There is an important limitation to be wary of.
lbeltrame··on Effectiveness of Face Masks in Preventing Airborne Transmission of SARS-CoV-2
It is highly important for medical workers to know this (because wards contain far more virus than any other place). For the rest, we have to bear in mind a few limitations outlined there, most importantly:

> To allow quantification, we conducted our studies by using a relatively high dose of virus, and under these conditions, it is possible that the protective capacity of the masks was exceeded.

And this:

> In our experiments, the virus was suspended in culture supernatant without fetal calf serum or was diluted with phosphate-buffered saline. Further detailed analysis will be required to reveal the precise relationship between the protective efficiency of masks and the components of viral droplets/aerosols.

I wonder if they are planning experiments with artificial saliva, like those people which tested the stability of the virus under sunlight did.

lbeltrame··on Effectiveness of Face Masks in Preventing Airborne Transmission of SARS-CoV-2
Very interesting experiment, included the use of quite a bit of engineering to simulate exposure to the virus.

My question after reading it was: the recovered viruses (even those that passed through) were able to infect Vero E6 cells, but would they be able to infect animals, should they get exposed to the recovered virus? Vero E6 cells don't have physical barriers (nose/mouth) or an innate immune system.

EDIT: the reason for the question is: is the virus that "goes through" still enough to infect a person, or would it get stopped by the aforementioned obstacles?

lbeltrame··on Live coronavirus found on frozen food packaging in China
It can infect Vero E6 cells or equivalent, given they said it's "live". But is this enough to infect someone?

The answer is, AFAICS, "unknown". I'm surprised a lot of studies of "virus persistence on surface X" don't (yet) do animal experiments to confirm there's enough to infect something else than cells growing in a monolayer (which don't have physical barriers or other aspecific defense mechanisms).

OTOH, current (scarce) evidence still points at fomite transmission to be not very prevalent at the very least.

lbeltrame··on Covid: Remdesivir 'has little or no effect' on survival, says WHO
FTR, the letter linked in the NY Times article actually advocates the precautionary principle (which implies there isn't enough evidence, only suggestions of such).
lbeltrame··on Covid: Remdesivir 'has little or no effect' on survival, says WHO
I don't read that many studies (I'm envious you can do that ;) as part of my (science) job, but as far as I read on airborne transmission, most of the "evidence" presented is actually modeling, or some IMO questionable studies, like the one - was it Lancet, or NEJM? I don't remember - about potential airborne transmission in a hospital setting. I was left with an "and then?" thought after I finished reading.
lbeltrame··on Covid: Remdesivir 'has little or no effect' on survival, says WHO
Lilly and Regeneron's monoclonal antibodies use exactly that as primary endpoint. Unfortunately, most of them are e.v., with exception of one formulation by Regeneron, which is subcutaneous.
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