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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 Immunity to Covid-19 may wane just 2-3 months after infection, study suggests
The fact is that immunological memory does not equate to having antibodies in the bloodstream all the time. The title of the article is pure clickbait, at the very least.
lbeltrame··on Immunity to Covid-19 may wane just 2-3 months after infection, study suggests
See the comments at https://news.ycombinator.com/item?id=23578910. tl;dr: the press doesn't understand how immunity works.
lbeltrame··on New studies suggest no long-term immunity from Covid-19
There's another study in Nature that shows that there are barely-detectable antibodies which have a very potent neutralizing activity (https://www.nature.com/articles/s41586-020-2456-9). Key passage from the abstract:

> Thus, most convalescent plasmas obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.

lbeltrame··on The Coronavirus Will Win
> Anything short of a successful human trial is ... nothing.

RECOVERY just posted their preliminary results on dexamethasone. The NIAID trials showed efficacy of remedisivir. But getting a trial right can take some time. RECOVERY started in March, and had to enroll 10,000 patients or so.

A lot of trials are running at this point, it is a matter of collecting data and drawing conclusions. Antibody based therapies are probably the ones going to be the most effective, but I worry about the cost (they aren't cheap).

> The false hope of a vaccine or cure has caused some US governors to announce waiting for a vaccine before ending lockdown.

That is misguided as much as saying that there is no cure (yet). In fact, I'd say that most governments focused too much on vaccines and too little on pharmacological interventions.

FTR, for SARS, a lot of programs were halted because it fizzled out, and so it was impossible to actually test them. For MERS though, there were vaccines in development (and still are), and that's why most of the stakeholders were this fast in getting candidates ready.

lbeltrame··on The Coronavirus Will Win
The article writer totally underestimates the effort it takes to get a drug or a vaccine to the patient.

"Months of intense research" have yielded at least 200+ compounds being tested for various activities. Large consortia have formed. A lot of things are being done in parallel to speed up testing (see vaccine research).

It takes time to prove efficacy: remedisivir only showed its efficacy in a 800+ people cohort. At first the time to administration was not correct: lopinavir-ritonavir were thought to be not working, but perhaps they do if given earlier in treatment, and what not.

I don't know what the author's expectations are, but we're witnessing a very fast pace of drug development and testing (not without warts, of course). What did the author expect, a miracle cure in 6 months? Most of the drugs being tested at this point are repurposed: the new ones will be tested through the summer and early autumn.

And there are wins like with dexamethasone, which is effective and cuts down mortality.

I recommend (to the author) a thorough reading of what's going on before launching in such a pessimistic piece. Yes, we might still be in hot waters. No, it's not that we will be destroyed by this coronavirus.

By the way, indications from early data from vaccine development tells us that it immunity is generated. The open questions are the duration, and the efficacy in a diverse population. But that's what trials are for. The fastest vaccine ever made took 4 years, IIRC. We're close to having results in 8 months (positive or not, the data will tell).

P.S.: The cold is mainly caused by rhinoviruses. Coronaviruses only account for a small percentage of that.

lbeltrame··on Coronavirus: Dexamethasone proves first life-saving drug?
That statement is not correct because it does not take into account the pharmacokinetics of the drug.

See the discussion here[1] (from the person who wrote the open letter to Lancet on the now-retracted HCQ study).

[1] https://twitter.com/jwato_watson/status/1272734274823663616

lbeltrame··on Coronavirus: Dexamethasone proves first life-saving drug?
To be even more precise, ineffective in hospitalized patients. UMN has done another study for "outpatient" (that is, not hospitalized) treatment and sent the results for review.

I'm not expecting any different results than from this one, but we'll know soon enough.

The RECOVERY study is also studying azithromycin, a drug commonly administered with HCQ when used against this disease. It would be ironic if that one proves to be effective (study is still ongoing).

lbeltrame··on Coronavirus: Dexamethasone proves first life-saving drug?
"Standard of care" basically means "whatever the current protocol to treat the disease is" (normally it means "the accepted treatment", but there isn't one yet), which can mean just trying to keep the fever down, supplementation of fluids, but also administration of drugs (with the exception of the one tested, of course).

As you can imagine, it is quite variable in what it means, because it varies across countries and occasionally even hospitals (I'm sure the RECOVERY people have taken this into account, though).

It is different from a placebo study because in that case your control is something you know is inert and "does nothing".

lbeltrame··on Coronavirus: Dexamethasone proves first life-saving drug?
This is quite big as a result, although it was done against standard of care (so it can mean a lot of things), because it improves survival.

This brings the list of currently effective pharmacological treatments to two:

- remedisivir (reduces hospital stay, might improve survival)

- dexamethasone (improves survival if requiring oxygen)

lbeltrame··on An exploratory statistical analysis of Akira and Ghost in the Shell
Not sure if "iconic", but I recommend Millennium Actress for an interesting way to weave a story which goes through the evolution of the Japanese film industry.

The screenplay was written by Sadayuki Murai, who put a unique touch on whatever he worked in (he also worked with Satoshi Kon in Perfect Blue).

Also not a film, but I found "Mōryō no Hako" (a short series adapted from a 1995 book) worth watching: at the heart it's basically a crime story, but the execution, with some "hallucinated" scenes, and also the characters are interesting.

lbeltrame··on American Indian tribes thwarted in efforts to get coronavirus data
> their leaders said that “asymptotic transmission is rare” which is a deadly lie

How it is a lie? People talk a lot about the presence of asymptomatic transmission, but:

1. No one knows for sure if completely asymptomatic people are contagious, and the extent of such contagiousness;

2. People equate asymptomatic with presymptomatic, which is a totally different story;

3. The evidence is at best, inconsistent. There is one case report of a non-contagious "asymptomatic" (reading the paper, the symptoms were there, just not the usual ones), and Singapore contact tracing of a number of completely asymptomatic people did not seem to find infected people in contact with them.

Presymptomatic state is a different matter, and it looks more contagious, but again, a lot of it is speculation, because it's really hard to measure.

This transmission is there. The extent of it is not known.

lbeltrame··on Airborne transmission as the dominant route for the spread of Covid-19
I'm not too convinced, because yet again this is a correlation, not a direct experimental measurement. In this pandemic, there are a lot of models and approximation, and very few studies with hard experimental evidence.

What the paper says may be true, but I'd love to see more experimental data.

lbeltrame··on [dead]
Likely detection of viral RNA, which does not mean anything by itself (it does not equate to infectious virus).

There haven't been many studies (to my knowledge) that actually try to see if surface transmission is a thing. The most sophisticated ones try to culture virus in cells from sampling on surfaces, but that's not sufficient anymore: cells in culture don't have an immune system, nor physical barriers like the nose and mouth. It is likely that animal testing is required at this point.

lbeltrame··on Wuhan hospital traffic, search engine data indicate virus activity in Fall 2019
It looks like another preprint found antibodies in the airways mucosa instead of blood. That would perhaps explain why some were undetectable.
lbeltrame··on Welcome to the 21st Century: How to Plan for the Post-Covid Future
> I could imagine the country that discovers it giving priority to their citizens when there is, at first, limited supply but withholding it indefinitely for advantage seems like it would not happen because of the incredible profit motive.

Turns out that those doing vaccine trials have actually thought of that, and most of them are making partnerships in different countries to prevent "bad side effects" from this (such as forced seizure).

lbeltrame··on Widespread mask-wearing could prevent Covid-19 second waves, study shows
> And btw. the "second wave" will come for certain in the fall

Are there any hard data on this, or just predictions? Or are you talking about influenza, as you mention later?

lbeltrame··on Wuhan hospital traffic, search engine data indicate virus activity in Fall 2019
There's a recent paper that analyzed about 7,000 sequences of known isolates and tried to give an estimate, whose lower limit is close to that date, IIRC.
lbeltrame··on Wuhan hospital traffic, search engine data indicate virus activity in Fall 2019
Are you sure about this claim? I live there and I didn't hear such region wide figures, only local city data.

In Bergamo it's closer to that from early data, but for example in Milano it might be from 4 to 10 (but in this case the sample was blood donors, so skewed towards younger and healthy).

lbeltrame··on Wuhan hospital traffic, search engine data indicate virus activity in Fall 2019
At least the abstract says something different:

> Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.

Very low levels, but still produced. (Note that I still have to dig through the paper.)

lbeltrame··on Wuhan hospital traffic, search engine data indicate virus activity in Fall 2019
> because 80% of people exposed to covid don't produce antibodies

Are there any data available to support this claim? That would mean that the virus is cleared by the innate immune system and not the adaptive, but it is still a pretty bold statement.

The last I read (a Nature Genetics study, if I recall) was that the antibody quantity was lower in milder cases (but with a large inter-person variability).

lbeltrame··on Wuhan hospital traffic, search engine data indicate virus activity in Fall 2019
The current phylogenetic data go as far as October as the farthest estimate, as far as I can see.
lbeltrame··on New Zealand is officially Covid-19 free, final case has recovered
If the disease can be treated with drugs, it may become no longer dangerous to the population. This could be another solution.

Note that I don't mind a vaccine, but it's not the only solution.

lbeltrame··on [dead]
I've read the article and the linked papers, and IMO this stems from a huge misunderstanding on what "insert" is, given inserts in DNA and RNA sequences can occur with replication errors and then can be kept due to selective pressure. So, that can't prove or disprove what this person is saying.

The part with the "previous version" of the paper is also fishy, given that it is not shown.

lbeltrame··on Fear, Groupthink Drove Unnecessary Global Lockdowns – RealClearPolitics
What exactly about it? As an Italian, I saw most of the measures as excessive and panic-driven. Most of the country did not need a lockdown at all. Perhaps the model made by the Italian expert panel wasn't that good (it predicted, upon reopening, 150,000 Italians needing ICU care in a worst case scenario by June 4th - obviously that did not happen). And the "plan", if there was one, was simply to wait it out - until some people realized it was going to cause quite a lot of harm.

Of course, the media kept on fueling panic, and also some non-government experts (one in particular saying until recently that masks and physical distancing were useless to reduce spread).

Yesterday even one of the people who handled the lockdown in one of the regions said that perhaps it was too heavy-handed.

Italy is not a good example of things done right. Not at all.

lbeltrame··on Switzerland's lockdown has sharply reduced the cases of Covid-19
I think it's quite important, because it may drive local public policy depending on the results: especially if one considers the models of "shield immunity" (discussed at length in one Nature publication a few weeks ago) in reducing transmission (no government has taken interest in them, AFAICS).
lbeltrame··on Switzerland's lockdown has sharply reduced the cases of Covid-19
Most studies I've seen did their own validation because of this. Of course this doesn't mean the tests were accurate (or not).
lbeltrame··on Switzerland's lockdown has sharply reduced the cases of Covid-19
> - A serology study is conducted at the moment in Geneva, it seems that our estimates of seroprevalence (Fig. 5: only 3% country wide by April 24) are consistent with the study (Appendix Fig. 7). We were very happy of that.

What about individual regions? I ask because most of the dynamics I've seen originate around hotspots, and thus it may be interesting to see how individual regions were affected (because it may drive different responses).

E.g., the Spain seroprevalence study said 5% country wide. But the estimates per regions can be as up to 3 times that (Madrid itself is ~11%).

lbeltrame··on Noisy Cicadas Are Widely Misunderstood
Speaking of noisy cicadas, in Japan they're extremely noisy. Often when I check old videos of my trips there the sound is so high that it makes my voice hard to hear...
lbeltrame··on Widely disseminated hydroxychlroquine study retracted by authors
There were also glaring issues with the statistics, as outlined in Andrew Gelman's blog[1].

[1] https://statmodeling.stat.columbia.edu/2020/05/25/this-contr... (one of the many posts there)

lbeltrame··on Widely disseminated hydroxychlroquine study retracted by authors
The Raoult paper wasn't that great, to be honest. But it did ask some questions in the discussion section which are still (partly) unanswered today.
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