Miscalculation at every level left U.S. unequipped to fight coronavirus | Hacker News Reader

Miscalculation at every level left U.S. unequipped to fight coronavirus

wsj.com

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I still remember how when the pandemic was breaking out, I and my colleagues in the lab were not taking this seriously because we were so confident we'd be able to get it under control. All we had to do was test rigorously, and, like c'mon. It's just qPCR. I remember overconfidently asserting that, like, the USA invented PCR - we know how to do it. laugh out loud. Hell, I had a plate in the machine as I was speaking! Colleagues agreed. After all, it only got so bad in china because they were covering it up, right? We just gotta run more tests, trace, and isolate. The stuff we were working on the lab was hard fundamental questions - the science needed to stop the pandemic was some PCR and quarantining people. And, the CDC was developing our own diagnostic instead of using the WHO's, but that makes sense, they're the CDC. What were the odds that they'd screw up so badly that the FDA would describe conditions as so bad they'd be reason enough to shut down the lab if they weren't the CDC? What were the odds that our friends in testing labs would find themselves describing the CDC as having "simply failed at molecular biology" [0]?

Of course, I use the past tense when describing our feelings about our research since we're certainly not working on it now. It's all nonessential. We're not allowed to go to the lab now unless you really need to water the plants or feed the mice. Just to keep a sustaining gene pool of our model organisms alive, so we can breed back what we need when we get back.

We really learned a lesson in humility. Part of miscalculating is having the wrong set of assumptions to derive calculations from. I don't think we were the only people who should have known better that were arrogant and overconfident.

We're hearing from some local labs that they have enough reagents to run tests, they have the right primers, they have what they need. But they can't get the cotton swabs they shove all the way up your nose and the little plastic collection things they need to administer the test. Cotton swabs. And little plastic vials.

We're talking about developing a vaccine, a cure, privacy-respecting contact tracing, fighting a once in a generation pandemic, keeping the hospital system from being overwhelmed. And we don't have the cheap disposable plastic and cotton things we need to run a test.

Truly a lesson in humility.

[0]https://www.nature.com/articles/d41586-020-01068-3

Adding to the list of CDC failures was their utter failure to procure masks. You know, those things that would be absolutely vital for just about any epidemic or pandemic (never mind the respiratory variety that we knew would be the most likely). It’s not like preparing for an epidemic is the raisin d’etre for the CDC or anything. I’m normally not this snarky, but I too thought the CDC was the one functioning agency but it turns out that it’s closer to the opposite. And not only that, but their utter incompetence killed tens of thousands.

The agency was also gutted, and the group set up to respond to threats like this let go with the idea that they could be hired back whenever.

I really hope that the sterility issues the fda found in the cdc labs that held up testing[0] aren't indicative of the standards of the BSL 4 facilities handling smallpox, anthrax, etc ...

[0] https://www.nytimes.com/2020/04/18/health/cdc-coronavirus-la...

That isn’t entirely true.

https://www.reuters.com/article/uk-factcheck-trump-fired-pan...

Even so, it sounds like the US pandemic response was put in a worse place by that change, and that’s the real point. I’m not saying it was excellent before; they never had a chance to prove themselves.

> It is true that the Trump administration has seen fit to shrink the NSC staff. But the bloat that occurred under the previous administration clearly needed a correction

This seems like a poor call. Shrinking staff and joining divisions together sounds like a easy way to get parts of your product that are unowned and unmaintained. When it comes to protecting against pandemics, I’m not sure the primary goal ought to be saving money.

I would be fascinated to learn more about what the officials in the organization did about COVID.

Credible source?

"The angry Left just can't stop attacking, even in a crisis."

That's a John Bolton tweet quoted in the piece. Full context:

> On March 14, 2020, John Bolton described the changes made to the team as streamlining. He tweeted: “Claims that streamlining NSC structures impaired our nation's bio defense are false. Global health remained a top NSC priority, and its expert team was critical to effectively handling the 2018-19 Africa Ebola crisis. The angry Left just can't stop attacking, even in a crisis.”

It seems true to me. There was a team dedicated to pandemic response and now there isn’t. The fact that some of the members of the team were reassigned to a broader focus area that included pandemic response doesn’t make that false.

The CDC, US Surgeon General, and WHO have all claimed with a straight face that masks don't protect you from getting the virus. I guess that's why they didn't see any value in stockpiling them. /s

I too assume that surgeons wear those masks for funsies.

Of course the “masks don’t work” was pure, transparent, bullshit from the very beginning. It didn’t even pass the smell test. Now if the argument was “please save masks for healthcare workers first, they’re higher risk” that would be fine. But “they don’t work”? Fuck off.

Edit: I’m referring to the CDC here, not you personally, dear HN commenter.

If you tell people to save masks for healthcare workers... then the hoarding would have been worse.

At least by telling people masks don't work... peer pressure would keep them from buying them?

It doesn’t look like anyone bought it, masks still sold out quickly and health care providers are still reusing N95 masks. And in exchange the CDC spent a large amount of their credibility; a real lose lose.

That's because the lies were so transparent. In the US we were told (by our wonderful Surgeon General) that citizens who wore masks were actually more apt to get covid than persons without masks.

I'm curious, was the official word always that even N95 masks didn't protect the wearer? Or just that "masks" in general (i.e., lesser masks) would not protect wearers?

https://twitter.com/Surgeon_General/status/12337257852839321...

Here he claims masks (general) do not protect you. But they do protect healthcare workers. It amazes me that he was willing to put two such contradictory claims in the same tweet. It was just such a transparent lie. Given the context and implication, I think it is referring to "medical" grade masks including N95, surgical masks, etc.

I’m genuinely not sure what makes me angrier: the lie, or how fucking lazy it was. The least he could do is come up with something that’s at least plausible.

Look at how effective it is. Even still in this thread.

You have a depressingly good point.

N95 masks protect healthcare workers because HC workers know how to properly fit them; the general public does not have this training and thus N95 masks are wasted on the GP.

Another part of the confusion is that early on (six weeks ago) the assumption was that the virus spread like the flu, i.e. via droplets from coughing and sneezing. Masks alone (without face shields) are of little benefit for droplet-spread disease because they don't protect your eyes. Now we know the virus spreads via aerosols which are generated by talking or even breathing. Cloth masks do indeed help for aerosols by trapping virus particles electrostatically and by increasing humidity, both of which keep the virus out of your respiratory tract. Or so the latest thinking goes.

Hanlon's Razor applies, but this virus is also an insidious bastard that behaves very differently from what public health experts had expected.

I don’t buy it.

First of all, there are very different rationales for healthcare workers and the general public to wear masks. Healthcare workers know they will be exposed, so the protocols must be damn near perfect. The general population does not know if they’ll be exposed, they’re trying to work in aggregate to put a drag on the viruses’ spread; even partially effective mask wearing slows that down. The general population can also practice social distancing, while healthcare workers must spend hours in close personal contact with positive patients by the nature of their jobs, vastly increasing their risk.

Second, this ignores the fact that mass mask usage prevents you from getting someone else sick. This is in fact exactly why surgeons wear surgical masks. Since we’ve known for months that this disease has asymptomatic transmission, the public health rationale for even cloth mask usage was obvious from the very beginning.

I used to think like what OP said. But after seeing the response in Asian countries with their much larger families and denser cities working against them and yet slowing the spread, masks might be playing an important role there. It also reminds everyone constantly. It does stop me from touching my face as well. So yeah, even if it's not perfect it's going to help quite a bit.

N95 masks are used as part of a package of PPE. That includes eye shields, gloves, and gowns. There's a complex protocol to put them on, and to take them off.

Without the rest of the kit, and without careful adherence to correct donning and doffing, there are at best marginal benefits to mask wearing.

There's some concern that those marginal benefits are eliminated if people wearing masks go on to engage in risky behaviours. These behaviours include increased touching of their face (often without immediate handwashing afterwards), reductions in distance between people, increase in frequency of leaving the home, etc etc.

Nonsense.

PPE is designed to mitigate a completely different level and type of risk. PPE is designed for medical professionals who by the very nature of their job must spend hours in physical contact with known sick patients. The protocols must be strict because failure means guaranteed infection.

I on the other hand have no obligation to physically touch random strangers, thank god, and don’t have to go interact with known sick people. Instead I’m trying to provide some protection for myself, and trying to work in aggregate to reduce the risk that asymptomatic carriers spread the disease while doing essential activities. “Marginal benefits” in this context is also known as “reducing R0”, which is absolutely a public health goal.

Now all of that is a good argument for saving N95 masks for medical workers and relying on surgical or cloth masks for the general public, especially in the light of PPE shortages. But that is an entirely different argument from “masks don’t work”.

> I on the other hand have no obligation to physically touch random strangers, thank god, and don’t have to go interact with known sick people.

What's the point of wearing the mask then?

Gotta go get groceries at some point, and that means breathing in the air someone else exhaled.

Where's your evidence that the virus is present in the air that people exhale?

We know it’s a highly infectious respiratory disease with asymptomatic transmission, this isn’t rocket science.

You've just destroyed your own argument.

If you're wearing a mask to protect against droplets then maybe you'd get marginal benefits. But if your concern is virus carried in the water vapour that people exhale, then an N95 isn't nearly enough to protect you.

Even if the mask is 10% effective that's still better than nothing.

Not if it's causing people to decrease social distancing or to touch their face.

The 'marginal benefits' have been studied and are around 90% effective. Quit spreading negativity please. Its pointless, and gains you only imaginary internet points.

> and are around 90%

90% what?

It makes no sense to claim "90% effective".

90% reduction in numbers of people infected? Of droplets inhaled? Of droplets exhaled?

Something like 90% of people with a mask, any mask, not infected after sharing space for an hour or two with sick people. In an airplane. Pretty solid protection.

The problem is no one likes to look stupid, and this is one of the cases where anyone who can spell words together was able to see through the BS. Whether they are going to hoard it or not, the solution is not for an expert to lie to the public.

I don’t know if that’s true or not, but I’m certain that lying to the public about what they can do to stop the virus was a bad call and will have lasting harm.

We hear the same over the pond. The argument is that the masks may not be fit for purpose or be used incorrectly, thus might actually be more contagious as people will tend to touch their faces more often etc. The official stances are still that people need training in order to use masks correctly, and the masks must meet standards to protect the user. All masks may protect others to some degree though.

"Masks work, don't work" are not cogent arguments.

It's the same with plastic gloves. Their usage in ie. grocery stores etc. may not help as much as incorrect usage may work against the intention. Again the argument is that if you get your hands dirty, you know you need to wash your hands and might think twice before touching face. Even washing hands properly require some training.

We've since learned that less extreme measures may be good enough once you have control, testing and tracking.

No one knows why the CDC issued the guidelines that they did. There's also fairly little doubt that the CDC in previous decades would've been smarter and better organized.

A lot of the commentary about the matter is disingenuous. Of course they won't filter out all the infectious agents for all healthcare workers forever. It was a matter of risk mitigation, just as much as shelter-in-place is. Getting infected is a numbers game, as is the live-locking of available hospital capacity.

Surgeons wear masks to protect the patient from droplets from the surgeon's nose and mouth, which otherwise could easily fall right into the patient's open wound.

which is still relevant for slowing down the spread of a respiratory virus.

> Of course the “masks don’t work” was pure, transparent, bullshit from the very beginning. It didn’t even pass the smell test.

No, that's not true. Maybe the advice was wrong, but it wasn't "pure, transparent, bullshit." It was always clearly stated that N95s worked if worn properly, but there was a lot of debate if surgical masks would offer much protection or not (they're known to be inadequate for certain viruses). Especially early on, people didn't understand much about this virus, such as the particle sizes involved or if asymptomatic transmission was real or not. There were a lot of factors to weigh in the recommendation in an environment of uncertainty.

> Now if the argument was “please save masks for healthcare workers first, they’re higher risk” that would be fine.

They did make that argument:

https://www.marketwatch.com/story/the-cdc-says-americans-don...

> Most people don’t know how to use face masks correctly, and a rush to buy masks could prevent the people who need them most — health care providers — from getting them, said Dr. Amesh Adalja, a scholar at the Center for Health Security at the Johns Hopkins Bloomberg School of Public Health.

> In fact the U.S. surgeon general recently urged the public to “STOP BUYING MASKS!” “They are NOT effective in preventing general public from catching #Coronavirus, but if healthcare providers can’t get them to care for sick patients, it puts them and our communities at risk!,” wrote Surgeon General Jerome Adams on Twitter US:TWTR

> But “they don’t work”? Fuck off.

It's also pretty clear that they were right that tons of people in the general public don't know how to wear masks correctly. I don't go out much, but when I do there's always a bunch of fools wearing N95s improperly (not using both straps, bunching both straps together behind the head, not shaping the noise area to fit the face). I even see people wearing surgical masks improperly (e.g. not covering the nose, not shaping the nose area, not folding out the material to stretch from the nose to under the chin, etc.).

There's also the issue that the general public is unlikely to follow the kinds of rigorous protocols that make N95s effective in a healthcare setting.

There are two core problems with your argument:

1) Wearing masks is a trainable skill. None of us know how to use condoms initially either, yet literally millions of Americans use them effectively yearly.

2) Masks don’t have to be worn with perfect correctness to produce an effect in aggregate. If mask usage was even 30% effective, this would drop R0 by roughly as much, which is a big freaking deal.

The N95 vs surgical mask is a tricky balance to strike; of course N95 should be saved for those at the highest risk, and if you know your mask will be sprayed with virus droplets, extra precautions must be taken. But that’s much more relevant to medical workers, not those of us who want to reduce risk going to the grocery store.

> Wearing masks is a trainable skill. None of us know how to use condoms initially either, yet literally millions of Americans use them effectively yearly.

Not really. Do you have a qualitative fit test handy? Because you need to do a fit test with one to figure out if an N95 you chose actually works properly, even if you're wearing it properly. Healthcare workers are tested, and the kits cost $200 or more.

https://www.medline.com/jump/product/x/Z05-PF07344

https://www.3m.com/3M/en_US/company-us/all-3m-products/~/3M-...

> [Surgical] Masks don’t have to be worn with perfect correctness to produce an effect in aggregate. If mask usage was even 30% effective, this would drop R0 by roughly as much, which is a big freaking deal.

I think that's why they ended up changing the recommendation.

And that’s a really good argument for surgical masks and not N95s; N95s could be used by the public, but given the shortages and the lack of fit tests any gains of N95 over surgical masks, if they exist, are not worth the increased cost and shortage of N95 masks for health care professionals.

The problem is that this isn’t the nuance that the Surgeon General or the CDC originally went with. His argument was literally “You can increase your risk of getting it by wearing a mask if you are not a health care provider”, and “STOP BUYING MASKS”, neither of which distinguishes between N95s, surgical masks, and cloth masks.

This is utter, complete nonsense.

Most people don't wash their hands properly either, but we tell people to do it because even washing hands poorly is better than not. Even "fools" wearing masks wrong would help more than not having them at all.

The parent is right: was pure, transparent, bullshit. If they were intending to preserve masks for healthcare workers, then just say that. Telling people they don't work was not just stupid, it was dangerous and almost certainly made the situation worse. Don't lie to people about their health.

Actually surgeons wear the masks to protect the patient not themselves. That's very similar to what likely is the biggest benefit of widespread mask use, reducing the infectiosness of people.

It’s amazing how many people blindly repeat this as if it’s a good argument. It’s not a good counter argument at all.

Stopping other people from catching something you might have is a fantastic reason to ask everyone to wear a mask during a pandemic. It’s actually probably the main reason you’d want to do so, from a public health perspective, because it helps you prevent asymptomatic thread. The idea that the surgeon general would beg everyone to not wear a mask is utter madness.

I completely agree with you, they make perfect sense from a public health perspective and it was a major fck up by most of the health organisations World wide to say they wouldn't (if intentional or not doesn't really matter).

However I was replying to a comment that was implying surgeons are using them to protect themselves. That is just wrong. There are enough good arguments for masks, one does not need to make incorrect statements.

So was it a straight out lie or incompetence? I remember reading here in HN that a lot of the masks do not actually protect you from the infection. But rather what a mask does is that it stops YOU from spreading the infection if you are infected.

I know it's hard to believe that the CDC et. al. would just blatantly lie to you. But consider that they were simultaneously saying that masks WOULD protect healthcare workers. Here's an example tweet where the surgeon general claims that masks do not protect regular people, but they do protect healthcare workers. This is obviously nonsensical, those two things can't both be true.

https://twitter.com/Surgeon_General/status/12337257852839321...

Additionally, the surgeon general has repeated this claim on live television as recently as a week ago. There is no way he's that incompetent.

Healthcare workers are in all-day contact with COVID patients that have late stage symptoms (fluid in lungs) and they perform operations where fluids spray around.

Of course do not / do protect are simplifications as the effects are not binary. This is needed for communicating with the public, the meaning was "don't help much" vs "make a significant difference".

If the health authorities always used the precise and caveat-ridden language of medical journal papers in order to ensure each sentence is logically correct when interpreted literally, they wouldn't get any messages through.

The guidance about public usage of masks has changed in a lot of countries because the guidance changed from "no evidence that it protects the public from infection enough to make difference in epidemic spread" to "let's take even the small benefit of reducing spray from the potentially infected mask wearers". It's a sensible change when the mask shortages let up.

No need to fan the flames of lightly assuming malice from health authorities, it's a bad time for that.

Except he repeated the claims in long format many times. Here's an example. https://www.youtube.com/watch?v=WvKSy1bwT70

I agree with you that right now it's absolutely crucial that organizations like the CDC maintain credibility, which is what makes this such a huge problem. Me calling out the lie is not the problem. The lie is the problem.

I still don't see lies or malice. The guy correctly recounts that like other national health orgs, they changed their recommendation, and tells why they did so.

Don't be fooled by the way he dances around the key point we're all talking about. He is still claiming the mask does not protect the wearer. He claims masks only help stop you from spreading it if you are infected.

Isn't this still technically almost correct? The surgeon's masks don't entirely filter the virus out of the air. However, they work for a society because they prevent the virus from spreading into the air from those who are already infected.

The surgeon general disagrees with this claim. He claims that the masks do protect the healthcare workers. You can see the claim in this tweet, where he also claims that the masks don't protect you.

https://twitter.com/Surgeon_General/status/12337257852839321...

  the masks do protect the healthcare workers

Because properly equipped healthcare workers are also wearing eye protection. SARS-CoV-2 will quite happily enter at the eyes; in fact, eyes are a bigger attack surface than nostrils.

With respect to protection from SARS coronaviruses, wearing just a mask and no eye protection is like a hockey goalie wearing a helmet but no mask.

> like a hockey goalie wearing a helmet but no mask.

An apt comparison -- a damage reduction by 66% using only a fabric mask is massively worse than a damage reduction by 95% using proper PPE and procedures. In fact, it leaves you 7 times more likely to get infected (get hurt by a puck). But if anyone tried to sell the NHL-watching public the line that "helmets don't help", they would be rightfully humiliated in public.

For a helmet to help, it needs to be fit for purpose, otherwise they're dangerous as people assume they provide safety.

When found, copy-cat masks are destroyed at border control, as they also don't provide the benefits to contain contagion.

I initially started following the WHO, CDC, and a few other health related agency Facebook pages when this pandemic actually started to take off in North America (mid-March).

I had to stop following the WHO and CDC Facebook pages because the value of information they were posting was so poor, I was IMHO better of not having access to it.

> Adding to the list of CDC failures was their utter failure to procure masks.

The CDC and prior administrations recognized the problem, but they weren't given the budget to solve it:

https://www.propublica.org/article/us-emergency-medical-stoc...:

> How Tea Party Budget Battles Left the National Emergency Medical Stockpile Unprepared for Coronavirus

> Dire shortages of vital medical equipment in the Strategic National Stockpile that are now hampering the coronavirus response trace back to the budget wars of the Obama years, when congressional Republicans elected on the Tea Party wave forced the White House to accept sweeping cuts to federal spending....

> The stockpile’s mission has steadily expanded as it confronts new public health emergencies. With limited resources, officials in charge of the stockpile tend to focus on buying lifesaving drugs from small biotechnology firms that would, in the absence of a government buyer, have no other market for their products, experts said. Masks and other protective equipment are in normal times widely available and thus may not have been prioritized for purchase, they said.

> “It just was never funded at the level that was needed to purchase new products, to replace expiring products and to invest in what we now know are the really necessary ancillary products,” said Dara Lieberman, director of government relations at the Trust for America’s Health, a nonpartisan public health advocacy and research group.

Similarly, the ventilator problem was recognized in the mid-2000s and a solution was nearly ready by 2013. However a corporate acquisition derailed the project because the new owners thought a low-cost ventilator wouldn't be profitable enough and would compete with their other product lines:

https://www.nytimes.com/2020/03/29/business/coronavirus-us-v...:

> The U.S. Tried to Build a New Fleet of Ventilators. The Mission Failed.

> Thirteen years ago, a group of U.S. public health officials came up with a plan to address what they regarded as one of the medical system’s crucial vulnerabilities: a shortage of ventilators....

> Money was budgeted. A federal contract was signed. Work got underway.

> And then things suddenly veered off course. A multibillion-dollar maker of medical devices bought the small California company that had been hired to design the new machines. The project ultimately produced zero ventilators.

> That failure delayed the development of an affordable ventilator by at least half a decade, depriving hospitals, states and the federal government of the ability to stock up. The federal government started over with another company in 2014, whose ventilator was approved only last year and whose products have not yet been delivered...

> Government officials and executives at rival ventilator companies said they suspected that Covidien had acquired Newport to prevent it from building a cheaper product that would undermine Covidien’s profits from its existing ventilator business....

> In 2014, with no ventilators having been delivered to the government, Covidien executives told officials at the biomedical research agency that they wanted to get out of the contract, according to three former federal officials. The executives complained that it was not sufficiently profitable for the company.

  they weren't given the budget to solve it

When the Obama administration was consuming the GOP-created PPE stockpile in 2009 and not replacing any of it, his party controlled both houses of Congress... including a filibuster-proof majority of 60 in their Senate caucus for much of the 111th Congress. It's disingenuous to blame this on any "tea party" effect.

I wouldn't call the undersuply of masks a failure. There is only so much supply and creating new production lines takes month. Without fighting wars, how should it be possible to procure enough masks when the entire world needs masks?

The mistake lies in not demanding that each and everybody covers their faces with whatever they have. There is no need to filter the air if the virus is not released.

You might find this article interesting.

https://www.google.com/amp/s/www.forbes.com/sites/daviddisal...

The idea is that they should have been stockpiling them for decades. We’ve seen 3 major respiratory epidemics in the last few decades and we had a high degree of confidence that we were due for another. Masks were cheap for a very, very long time before the outbreak.

  The idea is that they should have been stockpiling them for decades

Their shelf life is generally 5 years at most. Stockpiling "for decades" is worse than useless.

Each hospital having a year rotating supply of the basics shouldnt be an issue though. Anyone know if there are national guidelines?

Then make provisions to ramp up supply. Partner with private industry to secure the supply chain.

I have a couple of questions that I hope you would have insight in to.

* Why did the CDC decide to develop their own diagnostic? Was there some issue with the WHO test that they were trying to avoid? Or just internal politics

* What was the core issue with the CDC's tests? (It's possible that I'm not equipped to understand this, but an ELI5 would be great)

(Edit - I have tried to research this, but for #1 it seemed kind of murky and #2 looks like either poor quality control or poor design - https://www.vice.com/en_us/article/y3mkpx/how-the-cdc-botche.... I'm hoping for some clarity on these)

From my understanding the US policy is to always use kits developed in domestically. The problem with the test was one of the reagents for negative control was contaminated so it could not distinguish between positive and negative tests. This component of the test was suppose to be an extremely basic process, so much so that none of the epidemiological response plans ever accounted for this possible failure mode.

Not only is it standard procedure in recent pandemics for the US to make their own kits as the pother poster noted, but other developed countries do the same thing. China, Japan, Korea, and the UK all made their own kits too. These are just the countries I checked into. The WHO kit by the way is the one made by Germany, not some grand international super-kit. Imagine if it had been the faulty one.

And developed countries wouldn't actually use WHO kits, just the protocol to manufacture their own tests. The WHO distributes kits only to poor countries. Everyone still runs into the same issues ramping up production.

This makes it even stranger that of all developped nations only the US didn't manage to get this right.

Ah yes I had missed that. Thanks

1) No idea

2) You found the article I was about to link actually. Basically, for a PCR test, what you're doing is making a lot of a particular sequence of DNA if it's present. You set up the reaction conditions so that if a particular sequence of DNA is present in your test tube (actually a plate but same difference), that sequence of DNA will make a lot more of itself. If there isn't that sequence of DNA, nothing will happen. You don't get to pick the entire sequence youa re looking for. You basically hae to pick a start region and and end region for the piece of DNA you want to amplify. So if the nucleotide sequence for a coronavirus gene was atcgctatagc, and you are using 3 letter long end regions (in reality you use longer length sequences and regions), you might pick your targets as atc and agc from each end. Therefore, any sequence of dna in your sample with atg and agc will get amplified and you will get a signal telling you that a dna sequence that starts with that first target sequence and ends with that second target sequence is there. If you don't get a signal, that means no coronavirus.

When picking that sequence (known as a primer sequences since it primes the replication reaction), you have to be careful. Lets say that in your body you have a gene that goes gtcatcagctga or something. Inside of that sequence, your primer sequences are present. If you run a test for your desired sequence, you're going to get signal from non-coronavirus DNA.

In order to make sure there are no overlaps in your primers, you, well, this is the part that's hard to believe. You type in your sequences in to a website and hit a button. Hence the following excerpt from the article you found:

“I just put the primers as input into this program and within seconds it tells you there’s problems with it,” Altman said. “It’s freely available. It’s not hard to use at all. It’s one of those things you’d do as a basic quality control check. It seems like they hand-designed these primers and it seems like they didn’t use computer tools to check it.”

So, yeah. Everyone's still having a hard time wrapping their head around it. All it boils down to is that you want to find sequences of dna that are present in coronavirus but not in humans (and also maybe the reverse for some types of controls). It's, I mean. I don't have words for it. Designing primers is like the first thing an undergrad who joins a lab for a research project or internship is taught.

And I had it rough when I was designing primers like 3 years ago. In those ancient times, I had to design the primer by opening a whole new tab and going to a whole new website! (The site is https://www.ncbi.nlm.nih.gov/tools/primer-blast/). So much work. Thankfully the lab I was working in implemented an electronic lab notebook (I think it was benchling?) that had the feature built in. Now i don't have to open another tab.

I'm being flippant but also, common, this is the CDC. The WHO had no problem doing it. Private labs had no problem doing it. It's not something weird about this virus. It's just, i don't know. There must have been deeper issues.

Great reply, thank you. I feel like this filled the gap I was missing. Sounds like we're in regular expression territory, and the rest falls in to place in my mind.

I think I was expecting the error to be somehow more technical or down in the weeds somehow.

For want of a nail the shoe was lost...

>Truly a lesson in humility.

Not at all. You are making a fundamental, erroneous assumption: that the actions taken were made in good faith.

This is a political failure. Trump and his administration chose again and again to put politics above public health. Over and over, given a choice, he chose to pander to his base and attack his perceived enemies rather than helping the country. These weren't miscalculations. The miscalculations happened at the state and local levels, but at the federal level there was very much a knowing purpose.

Try demo-trading for more lessons.

I live in Canada and our response between January - mid March was in line with the U.S. where the government said things like "the risk to Canadians was low" and "asymptomatic people are not main drivers of epidemics." That laissez-faire attitude perpetuated the belief that we didn't need to screen people at airports, or force people coming in from hot zones to self-isolate for 14 days.

Meanwhile, a country like Vietnam which doesn't have the same technological or financial resources as North America managed to quell the spread through mass quarantines and aggressive contact tracing done as early as February. They literally fenced off a village that had one known infection.

Taiwan acted quickly and decisively throughout the key time periods of the crisis. Things like stockpiling and producing more PPE in January, making quarantine taxi's ferry potential infected to their homes instead of allowing them to take public transit, using technology to aid with contact tracing, mandatory use of masks in public spaces, thermal screenings at airports and stations...

Looking back, I think we both woefully under-estimated the potential for asymptomatic/pre-symptomatic individuals to spread the virus. As a society we looked at the low numbers and scoffed at the idea of doing proactive preventative measures... until it all hit the fan and we had to hard stop.

i think there is a lot of superiority feeling in Western countries over Asia and then in Western countries against each other. For example when things started happening in Italy the Germans thought that it's an Italian problem.

As far as the US goes it was pretty clear that the administration didn't want to deal with this at all at home. So they were constantly behind the curve and did things only when basically forced.

> For example when things started happening in Italy

As someone who lived in Italy and now lives in the US, this was driving me absolutely crazy. They have a great health care system, and are a transparent democracy. When things started to happen rapidly there, it was very, very clear that the same situation would play out in the US, and yet there were still a lot of "just a flu" people.

> When things started to happen rapidly there, it was very, very clear that the same situation would play out in the US...

When it was still restricted to China, I was able to reassure myself into complacency with memories of the original SARS. China contained that, so maybe they will contain this one, too?

As soon as it hit Italy hard, that story didn't work anymore, and it was clear it was only a matter of time before it spread everywhere.

I went back to my home-town in mid-Feb and we had thermal screening at the Airport. All the staff working there wore mask and gloves. We were asked lots of questions, noted our contacts, backup contact just in case mine fails. The north-eastern region of India, including my home-town, have zero to low positive cases right now. We also border with Myanmar.

That same week, I flew in and out of Delhi, UP, Rajasthan, and Bangalore without seeing any screening.

A few days back (mid-APR), we (me, my father-in-law, and my wife) got calls asking how my Japanese friend is doing as he was there in my home-town too (in Feb).

> They literally fenced off a village that had one known infection.

Some countries frankly have a different arsenal of tools available to them in how they can respond.

It’s sad but true that the more authoritarian regimes are able to lockdown harder and faster.

When Trumped raised the notion of fencing off hotspots, Cuomo called the idea of a physical cordon 'totally bizarre, counter-productive, anti-American, anti-social' Added that such an order would be tantamount to a 'federal declaration of war' and a 'civil war discussion'.

I do wonder if the intent is to lockdown and contact trace their way all the way to the point until a vaccine is developed, tested, and can be administered widely, and if that is the intent if they will ultimately be successful and at what cost?

Depending on the overall timescale, this could amount to judging the race after the first few miles of a marathon.

There's pretty strong evidence that a light, mostly voluntary, shelter in order, with restrictions on crowds and certain crowded-y places like bars, (AKA the SF bay area policy) is largely sufficient. If the whole US had the bay area's mortality and infection rate we wouldn't be having the same conversation. In terms of "freedom", I haven't felt like if I needed to go into work it would be a problem, and I've gone in twice to take care of critical on-prem infrastructure.

> There's pretty strong evidence that a light, mostly voluntary, shelter in order, with restrictions on crowds and certain crowded-y places like bars, (AKA the SF bay area policy) is largely sufficient

Maybe that’s dependant on location. AFAIK Italy and Spain tried the voluntary model before having to be more authoritarian.

I don't know what italy and spain did, but when i say mostly voluntary, I really don't mean completely voluntary. the bay area has shut down bars and entertainment venues, and food service has no sit down service. Everything else has basically voluntary compliance - notwithstanding possible bad behaviors in neighborhoods I don't pass through anymore, there aren't cops going around arresting people for not obeying personal space distancing (though you could probably get in trouble, at least post facto via lawsuit, if someone found out your open air office was filled to the brim with employees).

I’m not 100% up to speed on San Fran stats, but looking here [1] it seems like up until last week they were running about 400 tests per day with about 20% coming back positive. Hospitals were basically empty.

I’m not sure what “mostly voluntary” means when businesses are forced to close.

Testing rate is much lower in CA than in NY and MA. So is case count and fatalities per million.

MA has been locked down pretty hard for about two months now. We are still seeing thousands of new cases a day. It certainly hasn’t had the same effect here as it did in the Bay Area.

I strongly suspect there is something distinctly different is happening in MA vs. CA and it’s not due to varying degree of lockdowns.

[1] - https://missionlocal.org/2020/04/29-daily-figures-on-sf-coro...

The article you linked to shows that the positive rate mostly hovers in single digits.

The article I linked embeds a Google Data Studio page:

https://datastudio.google.com/u/0/reporting/1Hl_OTbyKWVYUaEA...

In April the average percentage positive was 10.4%. Over the last 56 days since the first positive test, the average positivity rate was 12.4%, and it was greater than ten percent 62% of the time.

Even granting what you just said it is still far from your 20% claim. And your way of averaging does not make sense. For example in March there was a day when 3 tests were reported with 1 test positive for a whopping positive rate of 33%, which would contribute half a point to the number you just calculated. How is that reflective of anything meaningful? To get meaningful average, you need to total the positives and divide that by the total tests over the period of concern. You can't simply average ratios.

You're right. Neither "with about 20% coming back positive" nor "mostly hovers in single digits" precisely describes the positivitiy rate for that area over time.

Rather than debate who was more wrong about the precise positivity rate in SF, I think the more fundamental discussion is around GP's comment that there's pretty strong evidence that a "light, mostly voluntary, shelter in order" is largely sufficient to achieve the low case count and mortality seen in the Bay Area.

I think that's not only far from proven, but there are many counterpoints of areas which have been locked down hard for many weeks and yet still saw pervasive community spread, and high case and fatality rates.

CA had it's first known case on Jan 25th, and a week later Day 7 the 3rd case in CA was discovered in Santa Clara, bring the US total to 7. Day 40 / March 4th CA reports its first death. Day 43 / March 7 San Francisco bans large gatherings in city-owned facilities. By March 13th (Day 49) Santa Clara bans gatherings of 100+ people and schools close as of March 16th. March 16th, Day 52, marks the first shelter-in-place orders.

MA had it's first known case on Feb 1, the second known case was not reported until March 2. (Do we call March 2nd as Day 1 or Day 30? Lets go with 30.) By March 6 (Day 36) total cases in the State were up to 8. By March 12 (Day 42) total cases were up to 108. On March 13 (Day 43) the Boston Marathon was postponed and gatherings of 250+ were banned. On March 15th (Day 45) Baker ordered all restaurants closed, and banned gatherings over 25 people, and announced public schools would be closed starting March 17th (Day 47). On March 20th (Day 50) MA had its first reported COVID death. By March 23rd (Day 53) the governor announced a "stay-at-home advisory", closed all non-essential businesses, recommended social distancing protocols, etc.

By CA's Day 40 they had 50 cases and a reported death, while MA at their Day 40 also had about 50 positive cases (most of which contact traced to a Biogen conference) but no reported deaths. By Day 50 MA had tested 5,000 and had over 300 cases and saw their first death. CA by their Day 50 also had about 300-400 cases. Both states closed on Day 52 or Day 53 of their respective outbreak.

At the beginning both states responded approximately the same. As of today, the outbreaks are entirely distinct.

I think a better analysis would compare e.g. Boston to one specific major metro area of CA, not a whole state-by-state level comparison.

I think what is clear is that China, the initial epicenter, exported far fewer cases than Europe. This can be seen by examining countries around China and far more integrated with China and overseas Chinese communities. Really this is a disease mainly spread by close contact. So the dominant spreaders are those with high community contact. I remember the feeling of OMG when seeing the announcement of all the high flying jetsetting group getting hit in March. I am on the west coast, yet our cases didn't start going exponential until after Europe exploded. Yes Seattle and Bay Area were likely seeded from China. But it started with low count, and coupled with our sprawl and high percentage of Asians who were attuned to the seriousness of the outbreak in China, it was a simmering outbreak. The east coast otoh got a major frontal assault from Europe.

I'd take the Vietnam numbers with a grain of salt. 0 Deaths seems suspect.

It is unfortunate that this is getting downvoted, but I feel that it is true to at least have an open mind on the number. So, I'd like to give a bit of my own personal context here. I moved to Saigon 4 years ago and I follow the VN news very closely. I've traveled 15k+ km through the whole country (along with Laos and Cambodia), by motorbike. I have been in the largest cities and explored some of the most remote areas.

The thing you need you realize here is that this is the first time the govt, north to south, has really truly cared for its citizens. It sounds harsh, but think about it. No expense spared. 60,000+ people put up in quarantine. Borders locked. Full public reporting of the contact tracing. Locking down entire towns (some I've even been to myself in the not too distant past). The response has been swift and very very nationalizing.

Unlike watching US people split down the middle and fighting about everything, Vietnamese people are quite proud of their country. There is a lot of 'saving or displaying face' type news and actions. At one point, the country went two weeks without a new case... daily proud updates in all the news about this... until some girl flew in from out of town with it and super spread it to a whole bunch more people. After that, things got even more serious.

The point is... the govt is very proud of their track record of zero deaths. Reuters went in and tried to get the govt. to talk about their claims and nobody would speak [0]. If you are so proud of your number, why not tell the world all about how you got there?

This is a govt that hasn't been exactly known for being the most umm, how do I say it nicely ... clean? By the way, one of the heads of their cdc got caught profiteering off test kits.

So, while I'd love to believe that all the sudden the vn govt cares about its citizens more than anything else and that their numbers are magically amazing because of so much hard work. I just find it really hard to believe that a country that borders China and has a litany of social issues, could be so perfect.

I mean, how many millions of pigs did they cull from swine flu? It wasn't like they were able to do nearly as well controlling that one and it wasn't even human!

Oh and one more thing... this won't last. Social distancing is easing in the country. People are going out in masses over the weekend because it is Liberation day. The timing couldn't have been worse. Just look at some of the images in this FB group [1]. Da Lat is a very small mountain town, that is tens of thousands of people. Mostly kids... which means they will go home to their parents... =( This is Vietnam's Florida beaches event...

[0] https://www.reuters.com/article/us-health-coronavirus-vietna...

[1] https://www.facebook.com/groups/ghiendalat

I am not great at markets, startups, business ventures, etc. But I feel like these things are broken:

* Governments and only governments can and should prepare for national emergencies, because saying Hospitals don't have enough PPE for pandemics is like saying your local farm doesn't have enough stockpile of rice to server the public during a famine/war. Private institutions have no incentives to serve the greater good of the country.

* Manufacturing is an industry every nation should invest in. If labor is expensive, the government should subsidize it so that the essential skills to manufacture and the infrastructure to do so remains functional even though market forces tells consumers otherwise. "Made in Switzerland" marketing can only do so much when the T-shirt costs CHF 120 vs. CHF 11.99 on Amazon which is probably made in Bangladesh. I am not saying govt should subsidize T-shirt manf, just trying to make a point.

* Dismantle short-term capitalism that exists in the stock market. Public companies should disclose their financials on a yearly basis or even every other year. Capitalism needs to be refactored to orient itself for long-term gains. Also making it illegal to not act in the interest of share holders is an insane law - CEOs should have the ability to put moral, environmental and other concerns in front of their priority list and not just creating value for the shareholders. This whole system is messed up.

* Executives sold off their country's soul to China, made a bank, cut corners, fucked consumers and went to the bank laughing. They paid off senators and govt officials, created a greater divide in the income distribution around the world. Limit executive pay for public and private firms.

* Reliance on China needs to change, diversify manufacturing supply chain. Just making sanitizer in US doesn't help if 90% of the ingredients are shipped from China.

> Private institutions have no incentives to serve the greater good of the country.

What are the incentives for government to serve the greater good of the country, specifically, why should government be uniquely qualified to decide what is good for everyone. As the old joke goes, "democracy is the belief that the people know what they want, and they deserve to get it, good and hard". But nobody in the world really lives in a democracy, it's even worse! There's indirection. To believe that governments are qualified to serve the "greater good" is to believe that people are qualified to select people who are good at judging the greater good. And that's not even counting the next layer of indirection. You're really hoping people are qualified to select people (politicians) that select people (unelected bureaucrats) that know what the greater good is.

There are many, many cases, when private enterprise (often, but not exclusively, for-profits operating in a nonprofit/goodwill capacity) has been the most effective responder in national emergencies, for example Walmart immediately providing tons of supplies in the wake of Hurricane Katrina.

There is a wide window of human activity between a selfish money grubbing capitalist firm, and the government.

> What are the incentives for government to serve the greater good of the country

"We the People of the United States, in Order to form a more perfect Union, establish Justice, insure domestic Tranquility, provide for the common defence, >promote the general Welfare<, and secure the Blessings of Liberty to ourselves and our Posterity, do ordain and establish this Constitution for the United States of America."

> why should government be uniquely qualified to decide what is good for everyone

The government is uniquely qualified to be the actor of last or only resort in a number of situations.

> There are many, many cases, when private enterprise (often, but not exclusively, for-profits operating in a nonprofit/goodwill capacity) has been the most effective responder in national emergencies, for example Walmart immediately providing tons of supplies in the wake of Hurricane Katrina.

Indeed we all remember when Walmart's convoy of soldiers arrived at the Superdome to finally open a supply line to the thousands that sheltered there. Or when Walmart's sailors airlifted or floated out 33,000 citizens stranded in floodwaters.

"We the People of the United States, in Order to form a more perfect Union, establish Justice, insure domestic Tranquility, provide for the common defence, promote the general Welfare, and secure the Blessings of Liberty to ourselves and our Posterity, do ordain and establish this Constitution for the United States of America."

Man! If every organization held true to its founding ideals. do no evil, or heck, March of Dimes. You know, that document you cite also has a list of ten amendments, of which I know zero have been held to over 200 years. That's right, even the US has violated the 3rd amendment by quartering soldiers in warzones, for example Afghanistan, and even WWII (the amendment does not specify homes of citizens).

Do you think the US follows this clause of the constitution? Did you even know it was there? "In Suits at common law, where the value in controversy shall exceed twenty dollars, the right of trial by jury shall be preserved, and no fact tried by a jury, shall be otherwise re-examined in any Court of the United States, than according to the rules of the common law."

Forgive me if your assertion that the least binding part of a legal document that has brooked all sorts of breaches to its principles holds very little confidence.

> why should government be uniquely qualified to decide what is good for everyone. > The government is uniquely qualified to be the actor of last or only resort in a number of situations.

You're begging the question.

You asked “What are the incentives for government to serve the greater good of the country“ and I gave you an answer: it’s the reason why governments were created. Are they perfect? No. Can they be entirely replaced by the private sector? No.

If you really believe that governments were created "for the greater good of their people", I strongly suggest you review the entirety of human history.

I'm not religious, but the hebrew bible has a really fascinating parable (1 samuel 16) about the israelites wanting "a king" (and importantly, describing there motivations for such) and god begrudgingly granting their wish with a warning for what was to come.

Governments serving their people is a very modern and very imperfect concept. I would argue we're not there yet.

The US produces lot of corn which is used to make ethanol, a key ingredient in sanitizer. Ethanol is already produced in large quantities in the US because it's used as a biofuel. So sanitizer is a pretty bad example. PPE is quite a different story. The US has got the resources (gas, cellulose), it only needs long term gov't contracts with manufacturers for strategic stockpiles. It's not black and white and you don't need to become a socialist society.

Bit of a tangent:

> The US produces lot of corn which is used to make ethanol > Ethanol is already produced in large quantities in the US because it's used as a biofuel

Isn't it kind of the other way round? Ethanol is produced from corn in large quantities because of government support requiring that more ethanol be used than the market would independently want, because of the political power of the subset of the US that grows a lot of corn.

I.e. oversupply of corn -> regulation to create artificially large market demand for corn+derived biofuel.

The EU also mandates use of ethanol in gasoline so no, it's not the other way around. Ethanol production in the US is not necessarily aligned with states mandating its use as fuel.

https://en.m.wikipedia.org/wiki/Ethanol_fuel_in_the_United_S...

I don't think limiting executive pay is the answer, that would punish people who did nothing wrong. It's treason to sell out your country under foreign influence and it should be tried as such. China figured out our weakness is decision makers can be bought or coerced and we don't have the backbone to do anything about it.

A good place to start would be enforcing the FARA https://en.m.wikipedia.org/wiki/Foreign_Agents_Registration_...

I think calling it a miscalculation is beyond extremely generous.

It's the wall street journal. They want to blame government...not a lack of leadership by the party they best align with.

The pervasive use of passive voice is a dead giveaway.

This is unfair. The WSJ editorial page is bananas but the reporters are top notch.

the reporters have great access and great information. The tone and perspective though are what they are.

https://archive.md/qrkt3

Everyone should read: The ‘Red Dawn’ Emails: 8 Key Exchanges on the Faltering Response to the Coronavirus

https://www.nytimes.com/2020/04/11/us/politics/coronavirus-r...

Full emails here: https://int.nyt.com/data/documenthelper/6879-2020-covid-19-r...

It seems like experts at least at an exceedingly clear grasp of the situation, with fair accurate predictions based on available data on the time. It doesn't seem like there was much "miscalculation" by subject matter experts, but bureaucratic incompetence on many levels that still persist.

Why is this downvoted? I'm about a quarter through and have found this totally intriguing. Their concerns in late January seem spot on. I'm glad it got shared.

What are the disaster vectors that the government should plan and equip for? What scale should be prepared for each?

https://www.washingtonexaminer.com/washington-secrets/new-wa...

It amazes me that the entire strategy of the U.S. government is "Everybody stay inside and wait until this goes away". Two months into this, that still seems to be all there is.

"And what if it doesn't go away by itself?" "Then we stay inside for another month!"

We're not waiting for it to go away by itself. We're keeping the rate of spread below the threshold where we overwhelm our hospital capacity. This buys us time to scale testing and develop things like contact tracing, drugs, and vaccines that will be our weapons in the next stage of this fight.

How is this getting downvoted?

This is the strategy. We're not gonna wait out the vaccine but we certainly won't have overwhelmed hospitals like Italy.

Not sure. My other comment in the thread got hit with a downvote at basically the same time. If there's a constructive discussion to be had, I'd like to have it. If I got something wrong, I'd like to be corrected. But I'm getting the sense that I somehow hit a nerve with the comment above about the strategy not being to just sit and wait, which is interesting. If theres a way to improve the tone of my communication to not generate some reflexive downvotes I'd also like to know that.

On busy HN topics, you can assume downvotes are just part of the noise and not worry about it. The arrows in the UI are so close together, it’s easy to hit the wrong one by mistake.

(Less charitably, for a busy topic the odds are there’s someone around for whom it happens to be their conspiratorial hobby horse and this manifests as downvotes on anything “mainstream”.)

I think to some of us "flatten the curve" is starting to feel like a March strategy to a May problem. A month ago everyone was concerned about ventilators and hospital beds and as far as I know the USA never hit capacity outside of, possibly, New York City. It's fantastic that we never got there, but now we need to focus on the new problems, which are vastly more complicated. We flattened the curve, but now we're staring down the barrel double digit unemployment, food shortages, businesses and jobs which will never come back, and probably many things we can't even imagine at this point.

The problem with preventative measures is that if they work, people always thing we overreacted. The curve is staying flat because we are staying in lockdown. If we opened the curve, the infection rate would start going up again on its S curve to herd immunity. It'll be worse if we open up and then have to go right back and shut down again. That'll probably hurt the credibility of future efforts to open up if anything, since if someone you know in your community was one of the fatalities after the governemnt said it was safe to open up and the pandemic roared back, why would you trust the government when they say that this time you can actually open up for real?

It seems to be the strategy in the sense smashing a window with a hammer is a strategy to kill a fly. Hospitals are so empty that workers are being furloughed, say nothing about the unused field hospitals and naval ships. The Lombardy scenario does not appear to be on the table.

Edit: I should add that I didn’t downvote.

Many positions at a hospital aren't related to treating someone with coronavirus. For example, elective and non-time-sensitive surgical departments should have nothing to do right now.

The ICUs aren’t even close to full, and indefinite delays of non-emergency care also has real consequences.

There are only about 7,300 ICU beds in California [1]. If we're at 20%, that's only about two doublings before people start being rejected for care. In March, we were seeing a doubling every few days, with ICU requirements following [2].

I'm not disagreeing that we need to let people be infected if we want to achieve herd immunity, but I think it's a tough choice in deciding which portion of the population you put out to partially die, since letting everyone out at once will result in some high R0 value again, and a vaccine may be on the way. These politicians are in a lose-lose situation here. Anything they do will result in someone being harmed.

[1] https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-guida...

[2] https://www.mercurynews.com/2020/03/28/coronavirus-gov-newso...

And people are dying from other causes while we sit and wait.

> Lombardy scenario does not appear to be on the table.

It already happened in New York. Maybe not quite at exactly the the same scale, but it looked like it was pretty awful just the same.

The scale is kind of the entire point. The logic behind Flatten The Curve is preventing excess deaths that result from a collapsed health care system. Even NY, which was literally sending covid-positive patients back into nursing homes, didn’t get there.

They were doing similar kinds of triage, from what I can tell: https://nypost.com/2020/03/31/were-bringing-covid-19-patient...

NYC has had 12,774 deaths to date, out of 9 million people or so.

Lombardy has had 13,679 deaths with a total population of around 10 million.

So broadly, they're fairly similar, although Lombardy as a region is much larger than NYC.

I was wondering the same thing...

The problem is the public patience is running out and we have not really used the time well.

We didnt overwhelm hospitals, we have contact teaching apps developed, we have a drug that's likely to be approved tonight or tommorow, and we have multiple vaccines in trials. We should have done a far better job early on, especially with testing, but the biopharma sector has risen to the challenge to move faster than basically every before.

So, you are right that the "correct" and reasonable thing to do would be to use the social distancing to buy time to set up things to control the virus when you relax social distancing.

Not so much a vaccine -- "18 months" is actually already very optimistic for a vaccine, it could be years.

BUT. To increase your medical capacity, so that when cases go up you can handle them. From making sure there's enough PPE to making sure there's enough staff-- to setting up things like daily checks on people isolating at home to see if their risk level has gone up and they should be hospitalized (people can go from okay to dead very quickly with this disease).

And then also -- setting up an enormous testing regime. If you don't know what the infection rate is, you are "flying blind" -- you need to know when you relax 'lockdown' in some ways, how much of an effect this has on infection, so you can adjust accordingly, figure out the ways you can optimize for maximizing social and economic activity while minimizing infection. You have to know the infection rate to do this!

And then, based on testing, you need contact tracing (and more testing) to try to catch infected people before they infect others, to keep slowing down the infection rate even while relaxing "lockdown". And you need comfortable (voluntary) isolation facilities so people can be isolated away from their households so their households don't get infected -- and can be closer to medical care should they need it.

And you need all kinds of education and social support to make people comfortable and secure enough to increase compliance with all of this.

So okay, yes, that is the point of the waiting. Or... it's supposed to be.

The problem is we're doing really bad at setting this stuff up. So that's the point... but it's not clear that's what we're doing. This stuff should have been ramped up, with a seriously "apollo moon shot" level of focus and investment -- starting in january. But at the end of April, we haven't made too much progress at much of it.

So it can appear that all we're doing is waiting... for, like, some kind of miracle, or for it to go away. Which will not work.

So the arguments over the "lockdown" in terms of "have we waited long enough or should we wait longer" are totally missing the point. The "lockdown" sucks, it is TERRIBLE. But to end it, we have to as a society be doing things that we are somehow really failing at doing. It is somewhat baffling, and highly alarming -- how is one of the richest countries on the planet, a huge locus of medical and public health expertise -- doing so poorly at this. And instead of expressing alarm about this and collective resolve to make it better... people are fighting about "the lockdown" as if it is an independent "wait it out", have we waited it out long enough? As if it is unrelated to the things we gotta be doing to make 'long enough' happen. It is a mess. It's gonna get worse before it gets better, at this point.

I think there are serious issues which we need to start addressing in this lockdown discussion;

1) Hospitalization rates have been shown to be about an order of magnitude lower than estimates.

2) The most effective treatment is no longer limited by availability of invasive ventilation but rather widely available non-invasive ventilation and frequent repositioning.

3) Hospitals across the country are mostly empty and furloughing workers because their “elective” (e.g. chemo and surgical) wards were all shut down and now everyone is afraid to go to the hospital even when they’re having a cardiac event or a stoke

4) A steady drumbeat of serological studies are showing IFR is lower than estimated, and asymptomatic or mild spread much more prevalent. NYC hospitalization rate is < 2% based on serology.

5) Now that the scale of the economic devastation is becoming clearer and the scale of non-COVID deaths caused by lockdown are coming into focus, a clearer headed calculation can be made about the true immediate trade-offs of a lockdown, to say nothing of long term effects.

I’m personally concerned that we’re going to blow our chance to gain significant widespread immunity during summer months where IFI prevalence is low and vitamin D levels are high. A surge next winter concurrent with a flu spike is the worst case scenario.

We’re also starting to see stress on the food supply chain, or if it wasn’t going to be an issue it probably is now with the latest media coverage enough to provoke some major hoarding of meats / protein in the coming weeks. It’s almost comedic when you can’t buy toilet paper, it’s a different kind of problem when major grocery staples go missing.

These are all important points which weigh on the side of lightening up on restrictions. It’s a spectrum, and right now we are pressing full tilt to lockdown when the actual purported and scientific purpose of lockdown is no longer being served.

I'm from Australia where our government is slowly easing restrictions because our daily case count has been in the single digits for multiple consecutive days now, and even then it is very gradual. Reopening resturants and bars is still very far on the horizon.

In the US, even with full lockdown restrictions for several weeks now, the daily death count has hovered at 2,000 for almost two infection cycles (first >2k death day was Apr 7th).

If 'full' lockdown only achieves stabilisation of the death rate, how is easing restrictions, which as far as I can see only rationally relies on the still-shaky evidence from serology studies, what exactly is the plan?

I genuinely ask this in a state of disbelief at the current "end lockdown" narrative circulating in the US. Here in AUS/NZ the Gov didn't fuck around; we locked down, had brutally strict measures for 6 weeks now, and at this point nobody is rushing to re-open (except for a few regional cities that haven't even had cases), while the US has been at 2,000 deaths a day.

As long as you can keep your borders effectively shut for the next year or so I think you’ll be in great shape. That ship has sailed in the case of the US.

As I understand it, there is a bimodal approach to managing an epidemic. You’re on a totally different pathway of successful suppression, where you’ve never actually seen exponential community spread. Your endpoint is not herd immunity.

The US probably was seeing uncontrolled exponential community spread in ~January. There are major metro areas which have 20%+ prevalence. The only endpoint left for the US is herd immunity.

So you would not expect the same measures to be taken, as long as AU is striving to maintain suppression I think that means your local measures will have to remain quite a bit stricter than a country trying to obtain herd immunity as quickly as possible.

EDIT: (Since HN won’t let me reply) You’ve had a total of 6,700 detected cases and 63% of those were imported.

Your total community spread over this entire time was what we see in two days in Massachusetts.

You’ve done 500k tests total, the US is presently running 160k tests a day. Harvard just came out with a study saying they thought we would need to get to 5 million tests a day. This is what I mean by bimodal.

Show me evidence that there is 20% prevalence please. What I have seen so far has been very limited study with very shaky evidence (the RKI in Germany back pedalled pretty quickly on the results of the antibody test for example)

NYC's initial antibody study tested 3,000 people and came back with 21.2% positive.

NYC expanded their antibody testing to 7,500 people last week and as of Monday it had come back with a 24.7% positive rate.

> Building on an initial testing run of 3,000, another 4,500 random New Yorkers have been screened since last week for antibodies, which would indicate that their immune system battled the bug, the governor said in his daily Albany press briefing.... Some 24.7-percent of those tested in the city were found to have antibodies, up from 21.2-percent in the first round.

https://nypost.com/2020/04/27/cuomo-says-nearly-25-of-nyc-re...

We had an R0 greater than 1 for a long enough period that if the response wasn't on point, we'd be in a similar position to the US.

One aspect that's missed is our testing rate - 500,000+ tests performed so far with a 1.2% positive rate. That's half of South Korea's.

None of this is to blow my Aussie horn. Whilst I'm proud to live in a country that handled this crisis well, I can't help but feel frustration at many of the remarks that Trump has said, particulary comments such as "can you really believe the numbers coming out of these countries?" it's just baffling considering that the AU-US alliance is unshakeable and there is no reason to mistrust our figures.

All stats sourced here: https://www.health.gov.au/news/health-alerts/novel-coronavir...

It's difficult for us to believe any country's officially reported test numbers because ours (and most European ones) are known to be at least order of magnitude below the actual number of infections.

That was the strategy. If that was still the strategy we'd be opening up much faster, as was observed in sibling comments, hospitals are laying people off now and other such things.

Since we are not opening up, that does not seem to be the strategy any more, regardless of what is stated. What is done matters a lot more than what is said.

What is the strategy now? That's a good question. Based on the actions I see, I find it hard to construct an answer to that question. But there sure does seem to be an unhealthy large dollop of deciding that Lockdowns are Rightthink and Opening Up is Wrongthink. I've noticed how few people advocating for continuing the lockdowns for months more provide concrete metrics for when we should stop.

Because most of the sensible concrete metrics you would have based on the whole "flattening the curve" plan have been met.... yet... here we are.

The nicest and happiest interpretation is just lag time, since of course you can't turn on a dime and change policy on a metaphorical Tuesday at 3:14:34 pm just because you finally hit a milestone. I'd put more stock in that interpretation if there wasn't such substantial attacks being put forth on what seems to be the very idea that some places may be able to open up now. But if in the next couple of weeks we do start substantially opening up (NY may not be able to, maybe a couple of other areas) then perhaps it was just latency in the end.

Hospital layoffs aren't necessarily because they have overcapacity. Elective procedures were canceled, and all non-covid departments were basically shut down in NYC at the peak. In NY, the plan is to start reopening on May 15, with frequent testing, with the metric being the replication rate (trying to keep R0 below 1.1). There are plans. The US did not approach this crisis in a centralized way which we probably should have, so opening up is going to be a collection of 50 plans as well, but that's not no plan.

"Hospital layoffs aren't necessarily because they have overcapacity. Elective procedures were canceled, and all non-covid departments were basically shut down in NYC at the peak."

There is this peculiar internet pattern I've seen many times now, where people seem to believe if they can explain why X happened, they can therefore prove X didn't happen. It is one of those things I just can't wrap my head around. You say in one sentence that hospitals don't have overcapacity right now, then explain exactly why they do.

That's overcapacity. They shut down everything to make capacity for the incoming crush of Covid cases, and those have almost entirely not materialized. So we are grossly overcapacity for Covid cases, in the vast majority of the country.

"In NY"

New York is the outlier. It is not what the entire country should be basing its plans on. It isn't even what the entire State of New York should be basing its plans on.

"so opening up is going to be a collection of 50 plans as well, but that's not no plan."

I didn't say there was no plan. I'm observing that the stated plan is deviating from the actions. Almost everywhere, we have nominally hit the benchmarks that were the initial trigger for re-opening things, but for the most part, anyone reopening things is doing it against massive political pressure and criticism, while people, yea verily even people in power like governors, are pushing for it to continue for more weeks or months with no end criterion given.

I'll reiterate that one possibility is just lag, but if in another month there's still a lot of lockdowns going on in non-outlier areas, that's clearly not going to be what's going on.

(I know there's a lot of grumbling online, but my personal position is, my job is nearly unaffected, our schools are already closed for the rest of the year regardless and I'm planning on staying home no matter what the state does, and I live close enough to one of the outlier areas that I would be perfectly fine with me personally still being in significant lockdown in another month. But what's good for me isn't what's good for everybody in the country.)

Testing and tracing is still very much the strategy, just that we still don't have the capacity for it.

The head of the federal government has utilized the defense production act to force people to work in meat processing plants where the virus is rampant - but has done much less to get testing, tracing, and PPE unblocked. States appear to be struggling as well. Hard to tell about a lot of the details; there's definitely a 'fog of war'.

Dictators ride to and fro upon tigers from which they dare not dismount. And the tigers are getting hungry.

Yeah, at this point how likely is COVID-19 going to be eradicated? Even with a vaccine?

As far as I know we have vaccines for many viruses which aren't eradicated, but maybe that's just because we haven't vaccinated enough? Then again, if herd immunity works then why isn't chicken pox eradicated?

At this point it just seems like it's here to stay like the seasonal flu and we're mostly just doing economic harm to ourselves...

Chicken pox goes dormant in nerve cells then it reactivates after immunity fades (shingles). That's how new generations keep getting it. Now there's a vaccine given to children but the world is still full of us carriers for a long time.

There is a huge number of flu strains out there so that's a different kind of problem. Along with the fact that the immunity provided by a vaccine is not 100% anyway, and often much lower for influenza viruses.

Of course coronaviruses have been around a long time too (many as common colds) without much (any?) success in combating them.

> Now there's a vaccine given to children but the world is still full of us carriers for a long time.

Strictly speaking, the chickenpox vaccine is a live (attenuated) virus, so even the vaccinated will continue carrying it. I was born in the mid 90s, so I am part of the first generation who got the chickenpox vaccine. About 10 years ago I had a small outbreak of shingles, just on part of one hand.

It’s weird to think about all the viruses that live inside us without us realizing 99% of the time, until we do.

Even if we can't eradicate it, an effective vaccine should be able to get it to the same state as tuberculosis, where the average person in a country with a good health system doesn't have to worry about it.

The day that my work group decided to start working from home, there were roughly a couple thousand reported C19 cases in the US. The conventional wisdom among the people around me was that we stay inside until the game changes, which could happen for a variety of reasons:

* We gain a definitive understanding of how the virus works: Its prevalance, severity, etc., and can adapt our plan based on that information.

* Effective vaccine, treatment, etc.

* Massively scale up testing, tracking, etc., so the spread can be controlled effectively.

Sure. What bugs me is that testing is still minimal, and there doesn't seem to be any attempt at setting up a tracking system. Vaccine/treatment is still at least a year away, and a year of lockdown doesn't seem feasible

Of the sources I read for coronavirus news is a daily chart posted on RealClearPolitics.

Per today's chart, the US has the most confirmed cases, the most tests taken, and one of the lowest deaths per million.

It's tough to judge which countries are doing well and which aren't, even given stark contrasts in policy. I don't think it's possible to harshly condemn (or praise) anyone at this point.

The US beat every single expert pre-peak total deaths prediction; by a lot. There are supply chain issues to fix, and the few spots that could not deal with the case load need to be fixed, but by any scientific measure against the predictions, we did excellent.

https://www.imperial.ac.uk/media/imperial-college/medicine/s...

p16: "In the most effective mitigation strategy examined, which leads to a single, relatively short epidemic (case isolation, household quarantine and social distancing of the elderly), the surge limits for both general ward and ICU beds would be exceeded by at least 8-fold under the more optimistic scenario for critical care requirements that we examined. In addition, even if all patients were able to be treated, we predict there would still be in the order of 250,000 deaths in GB, and 1.1-1.2 million in the US."

EDIT to rrss's comment:

First, note that ~60k is how many people died and tested positive AND were coded as COVID-19. It's not necessairly how many people died because of a COVID-19 infection. We will not know the real #'s until all-cause death is examined. There appears to be a significant drop in "normal" pneumonia deaths for example. It also ignores the error bars on the testing false/positive/negative rates.

Second, I'll restate: The US beat every single explicitly enumerated via a integer expert pre-peak total deaths prediction; by a lot.

If the authors had given a table for the US, we could see what their model predicted, but they did not, and _you_ assuming that the US is a linear relation to GB may or may not be accurate.

You are misrepresenting the conclusions of that report. The report clearing distinguishes between "mitigation" and "suppression" in the second paragraph.

> However, the resulting mitigated epidemic would still likely result in hundreds of thousands of deaths and health systems (most notably intensive care units) being overwhelmed many times over. For countries able to achieve it, this leaves suppression as the preferred policy option.

The aggressive social distancing implemented in the U.S. falls under "suppression," and therefore is not considered in the predictions you quoted:

> suppression will minimally require a combination of social distancing of the entire population

Two paragraphs after the bit you quoted:

> We therefore conclude that epidemic suppression is the only viable strategy at the current time. The social and economic effects of the measures which are needed to achieve this policy goal will be profound. Many countries have adopted such measures already, but even those countries at an earlier stage of their epidemic (such as the UK) will need to do so imminently.

The report predicted 5,600-48,000 deaths in Great Britain if all four interventions discussed were put in place. The UK has had ~26,000 deaths.

This prediction for GB (suppression) is 80-98% lower than the prediction you quoted (mitigation). A naive application of these ratios to the US suggests that the predicted number of deaths with all interventions would be something like 24,000 - 220,200. The U.S. is currently at ~60,000 deaths.

So, erm, no - the United States has not "beat every single expert pre-peak total deaths prediction; by a lot."

No, GB's excess mortality compared to last year is already greater than 35 thousand death, and that's not taking into account the 4-day lag between the actual death and the report (unlike "covid19" hospital death. GB is not testing home sudden death (that are often caused by cardiac arythmia that might be induced even in very mild covid19 cases), so only excess mortality data is reliable:

https://www.euromomo.eu/graphs-and-maps/#z-scores-by-country

[edit] That said, your argument still stand and in fact is even better with this data

Uk exess mortality is already at 35 000, quite close to the "successfull suppression" plan that put the death toll at 40 000.

"First, note that ~60k is how many people died and tested positive AND were coded as COVID-19. It's not necessairly how many people died because of a COVID-19 infection. We will not know the real #'s until all-cause death is examined. There appears to be a significant drop in "normal" pneumonia deaths for example. It also ignores the error bars on the testing false/positive/negative rates."

Do you have a website like euromomo for excess mortality in the US? Covid19 causes arrhythmia in 7% of cases, even very mild ones [0] and arrhythmia is the main cause of sudden death for people over 40 years old (i have ectopic heartbeat so i'm a bit concerned with this)

[0] https://www.uptodate.com/contents/coronavirus-disease-2019-c...

> If the authors had given a table for the US, we could see what their model predicted, but they did not, and _you_ assuming that the US is a linear relation to GB may or may not be accurate.

The Imperial College team actually did model country-by-country numbers in a follow up report on March 24th:

https://www.imperial.ac.uk/mrc-global-infectious-disease-ana...

The United States estimates for several different scenarios are:

Unmitigated: 2,654,410 deaths

Mitigation strategy (social distancing whole population): 1,358,164 deaths

Mitigation strategy (enhanced social distancing of elderly): 1,090,267 deaths

Suppression strategy (triggered at 1.6 deaths per 100,000): 474,227 deaths

Suppression strategy (triggered at 0.2 deaths per 100,000): 84,124 deaths

The differences between mitigation and suppression are explained in the paper.

Thank you. Any estimate on when we crossed the supression strategy death/100k threshold?

The triggers considered were 0.2 deaths / 100k population / week and 1.6 deaths / 100k population / week. For the U.S. that corresponds to ~700 deaths / week and ~5,200 deaths / week.

The United States as a whole hit the first trigger (according to reported deaths from https://github.com/nytimes/covid-19-data/blob/master/us.csv) sometime around 3/19, and second trigger sometime around 3/27.

replying to your reply via edit:

> _you_ assuming that the US is a linear relation to GB may or may not be accurate.

Right, this is why I called it 'naive.'

My main point stands: your comment misuses the prediction that does not assume full suppression as if it applied to the current situation of aggressive social distancing.

> The US beat every single explicitly enumerated via a integer expert pre-peak total deaths prediction; by a lot.

From 'nodamage's comment pointing to the ICL's "Report 12," they predicted 84,000 deaths for the U.S. in a situation where suppression measures were put in place around 3/19.

Given that the U.S. reported number of deaths is at ~61,000 and still seeing 1,500+ deaths per day, this doesn't exactly make me want to claim victory against the estimate - more like 'thanks for the predictions, ICL team, for helping convince people and governments to shut down.'

The ~60k could be an overestimate, yeah. Maybe it's counting people that have coronavirus and are then hit by a truck, or people who would have died of pneumonia regardless of covid19.

But it could be the other way around, too: https://www.nytimes.com/interactive/2020/04/28/us/coronaviru....

https://www.cdc.gov/nchs/nvss/vsrr/covid19/index.htm

> COVID-19 death counts shown here may differ from other published sources, as data currently are lagged by an average of 1–2 weeks.

> *Data during this period are incomplete because of the lag in time between when the death occurred and when the death certificate is completed, submitted to NCHS and processed for reporting purposes. This delay can range from 1 week to 8 weeks or more, depending on the jurisdiction, age, and cause of death.

Indeed. As this tails off, it's going to be the official spot to check the prediction[1] linked here against.

https://news.ycombinator.com/item?id=23028036

Also: https://mobile.twitter.com/johncardillo/status/1256577527662...

Neat, so come back in a few months.

Also, I haven't got a clue who John Cardillo is, but that tweet doesn't really say much other than he thinks something is a scam. The 37k currently reported at the CDC link corresponds to the deaths reported for ~12 days ago at https://github.com/nytimes/covid-19-data/blob/master/us.csv, so it isn't clear that the discrepancy is not largely explained by the lag to process death certificates.

EDIT:

I looked at some of his other tweets, and it seems like he is upset that the count here from the National Vital Statistics System https://www.cdc.gov/nchs/nvss/vsrr/covid19/index.htm doesn't match the count here https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/case..., and interprets that to mean that the CDC is lying to the U.S. population. I disagree with that assessment, and the CDC explains the NVSS data here: https://www.cdc.gov/nchs/nvss/vsrr/covid19/tech_notes.htm:

> Provisional death counts in this report will not match counts in other sources, such as media reports or numbers from county health departments.

John Cardillo says that "You’ve been misled while lunatics try to destroy your county and steal your way of life" (presumably he means "country"?), the CDC explains the discrepancy. I'll go with the CDC.

I agree. Per capita we are doing exceptionally better than most European countries. My European friends think it’s like a warzone over here but outside of pockets in NYC and smaller pockets around the country the hospitals aren’t full. Whether or not that is due to our response or certain characteristics of our nation (e.g. very spread out, lots of space) is up for debate, sure. But we are doing very well.

Exceptionally? The US is better than some European countries, but significantly worse than others https://ourworldindata.org/grapher/total-covid-deaths-per-mi...

Also if it is true that there had been significant community spread early on, thenthe US number is strongly underestimated. If not the US is on a different part of the curve and behind the deaths in Spain or Italy.

>> The US beat every single expert pre-peak total deaths prediction; by a lot.

This is mostly because the UW IHME model was brutally terrible as was the Imperial College modeling. They predicted insane amounts of death that had no chance of happening while baking in social distancing orders.

We massively overreacted and the convenient out is "well, we beat the models, that's a good thing!"

Not if the dose was more poison than antidote. I could have predicted 5 million deaths pulling it out of my ass and I shouldn't get credit for the US coming in under that estimate.

"We massively overreacted"

I agree, but that was not an accident. Cui bono?

Seems worth repeating: "We can't let the cure be worse than the problem itself"

https://twitter.com/GPIngersoll/status/1255564315891032064

I don't think it was malice in this case, though I get your point. I think the people that did the models were just incompetent and also shaded them to be overconservative because they felt it would be better (so slightly fraudulent, perhaps).

But all evidence points to the IHME to just be terrible at their jobs and influenced a country to massively over-react.

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