One of the super-interesting things here, is that apparently everyone was in the specific window where they test positive for the virus. This implies the population was recently infected, had not been previously infected, and it spread almost completely within a tight window.
This implies a shocking high R(effective) for that population. In 2 weeks we'll have super interesting data one way of the other on the CFR.
A prison is very much like a cruise ship from a viral perspective. We know from the cruise ship data like the Diamond Princess that most people had no symptoms initially, but overtime most people became symptomatic [1].
Of course if we are really lucky and the prison was infected with a naturally attenuated strain we should make use of it [2].
SARS, MERS, and now SARS-2 are all known for super-spreader events where occasionally one person just infects a ton of other people. And we know from testing that the amount of live virus in a person's phlegm can vary by many orders of magnitude so I guess that isn't surprising. There are a lot of people who infect just one other person but the overall R(effective) is substantially driven by the long tail.
Exactly! What are the chances of that, compared to a gross error in the testing, like someone processing the samples was infected and not very careful?
>> .. that apparently everyone was in the specific window where they test positive for the virus.
The data comes from 4 prisons. It is theoretically possible that all 4 of them happened to be in the same window after an initial infection, but it doesn't seem very likely.
I guess the only way to be sure is to do follow up tests every week or so, hopefully that will happen.
I repeatedly point this out. There was the church choir practice where 45 out of 60 people were infected within what two hours? There is also a Korean call center where about 2/3 of the people in an open office were infected.
I've repeatedly linked to CDC study that estimates r0 in Wuhan before lockdown at between 3.8 and 8.7. Median 5.8.
Take away: Completely avoid being indoors with large groups of people.
The CFR will be an interesting (though tragic) data point, but I wouldn't generalize too much from it. The demographics of the inmates are probably not representative, and the health care that prisoners receive is absolutely not of the same quality that civilians may receive.
The Princess cruise was a good indicator of CFR for a specific demographic range when they tested early, often, and had access to quality care. If the CFR of this prison will tell us anything, it will be a counterpoint to such information showing what happens when quality of care is greatly diminished.
Are these tests covid-19 specific or are they based on IgM/IgG?
> The results of the tests for IgG, IgA, and IgM levels are usually evaluated together. Abnormal test results typically indicate that there is something affecting the immune system and suggest the need for further testing. Immunoglobulins testing is not diagnostic but can be a strong indicator of a disease or condition. There are a number of conditions that are associated with increased and decreased immunoglobulins.
To add another data point, Singapore has been testing foreign workers living in dormitories extensively, uncovering about 10,000 cases (about 80% of the country's total cases). These are relatively fit individuals between the ages of 20 and 40. However, the number of people in the ICU has remained remarkably consistent at about ~20 people in the past 10 days (Fingers crossed it remains that way).
I've read that asymptomatic carriers are though to be less infectious than those with symptoms because of the lower concentration of virus in the saliva. Also, many virologists mentioned in recent texts that the initial concentration of the virus you receive can affect how sick you'll get - the more viruses you're exposed to, the faster they can invade the body and the more severe it will get.
Can those two facts be combined into a theory that asymptomatic carriers are more likely to produce more mild and asymptomatic cases?
Don't know if it makes any sense (probably not), but it would certainly explain how in some closed environments there's a prevalence for mild cases, while in others there's a plenty of very sick people, regardless of the age.
I've been tracking the antibody study results in a spreadsheet, and they are suggesting a 10-20x undercount of cases in the official "confirmed" numbers. You can see the data I've collected here: https://docs.google.com/spreadsheets/d/16onEUBWIV5IqN1RCvTla...
I did similar calculations, and found the institutions in charge give us very unreliable data. The term "corona case" is very, very, ambiguous and cannot the understood as such without a detailed explanation on how the counting was done.
Thanks for sharing.
I found the peek in all-case mortality also very interesting, because that way counting is much more unambiguous: dead is dead.
They showed a clear diversion from the "average" in recent weeks, but... they did not show the stdev for the averages. Finally I found a chart that shows that "outliers" are not uncommon.
Your sheet is interesting. Looking at it, the IFR varies from 1.66% down to .11% and the 0.11% is for the Santa Clara, which many considered rather suspect.
The 1.66%, otoh, seems reasonably in line or at least compatible with what's been observed in Korea and elsewhere.
Given age is going to skew things a good deal, it seems like a picture is emerging but not that new a picture. An IFR of even 1% is pretty bad, especially given these statistics show how infectious this virus is.
News articles from around April 10 indicate that mass testing hadn't begun, or was just beginning (1 example here [0])
Reporting on 96% without symptoms is misleading without mentioning this: It gives the impression that the # of coronavirus infections could be up to 24x higher than the known positives cases. But symptoms can take 2-14 days to develop, meaning it is entirely too soon to tell if these are all asymptomatic cases, or merely pre-symptomatic.
There was a nursing home in Massachusetts which had 51 out of 98 residents testing positive but asymptomatic in early April. While this sounded encouraging in the sense no one was critically ill because of coronavirus, a few weeks later 19 had died and about 30 more had tested positive.
Let’s wait a month until there is a clearer picture about the impact of the virus on a particular population of people.
One of the more interesting differences between US prison populations and others is that smoking tobacco is way more prevalent:
> Estimated smoking prevalence among inmates was approximately 50% in 2003–2004, compared to 21% among noninstitutionalized adults. [0]
Which might play a major role in the spread and the actual severity of COVID-19 as French researchers are speculating that nicotine could be responsible for blocking the ACE2 receptors that COVID-19 uses to get into cells, which could explain why there's such a low incidence of tobacco smokers among patients, far below what should be expected [1].
There's nothing really concrete yet, for now they want to experiment with nicotine patches as treatment.
But in that context, prison populations could make for an interesting control group: Maybe the prevalence of smoking is what keeps the virus less severe, due to reduced viral load reaching cells, and thus fewer carriers are symptomatic?
Some possibilities: there is widespread infection from a common source around the same time, and many of those "asymptomatic" inmates aren't going to stay that way; the test has false positives; the population of this prison is comprised mostly of people who tend to be asymptomatic carriers (for example, if most prisoners are in their early 20's); COVID-19 has a lot more asymptomatic carriers than we thought.
Plugging the 96% into New York numbers results in 155,000 / 4 * 100 = 3,875,000 infected people in NYC, or about half the population.
This is assuming that tests in NYC currently include every infected and symptomatic person. Considering the official advice for people with mild symptoms is to stay home (and not seek a test), that assumption is ... optimistic.
It also wouldn't fit with the anti-body tests that have been done in NYC that showed figures closer to 15-20%.
So I'd expect about 1/2 to 2/3 of these 96% to develop symptoms within the next week.
The other possibility is the prison population not being representative of the general population. That's probably true in terms of fatality rates, because they are younger. I'm not entirely sure if that age imbalance is just as strong for any symptoms as it is for risk of hospitalisation and death.
It doesn't appear to mention what type of test was done. Were they checking for current active infection, or for antibodies which would indicate if the person has ever been infected? (if the latter, they may have had symptoms back then)
I am not willing to even consider these results until more details about testing are revealed. There has already been so much misinformation about testing and results that I am incredibly skeptical of any results now.
Before the deluge of "But wait two weeks" comments, I just want to ask at what point we accept that the potentially of totally asymptomatic cases is insanely high, far higher than anyone thought?
Note that until this past week, officially, the symptoms had to be the first three defined by CDC, not the eight or so CDC have expanded now: fever, cough, shortness of breath, chills, repeated shaking, muscle pain, headache, sore throat and new loss of taste or smell, could all appear between two and 14 days after exposure.
In the field it appears many/most of the less severe cases don’t exhibit the initial set they had defined, so patients experienced illness written off as not COVID-19.
From what I’ve heard from the field, a careful patient history finds there was typically a bout of unusual “but it can’t be COVID” illness with a set of the expanded set of symptoms in almost every “asymptomatic” patient.
It’s further speculated these variations may have to do with level of exposure and path of infection, along with the earlier noted lung health and comorbidities.
Like with the death rate, I expect we'll seamlessly transition from "this isn't proof, in 2 weeks you'll see" to "this isn't news, everyone always believed that so it doesn't imply any changes in strategy".
> Before the deluge of "But wait two weeks" comments, I just want to ask at what point we accept that the potentially of totally asymptomatic cases is insanely high, far higher than anyone thought?
Presumably in two weeks, when we know whether more of these thousands of people go on to develop symptoms or not.
Is anybody following up on stories like this? Do we have any from two weeks ago?
I also want to add that this doesn't make the virus less deadly. It just gives it a very population varied IFR. It appears far more deadly for some populations. Near harmless for others. But no clear way to confine it to the harmless crowd.
It’s not like this is the first population that has been nearly exhaustively tested. There was the cruise ship, there was the navy ship, etc. Those have shown between <20% (among the elderly cruise ship demographic) to 60% (among healthy soldiers) asymptomatic.
This certainly adds another data point, but I wouldn’t throw conventional wisdom out the window yet.
I'll venture a guess that by Wednesday the news cycle will be deep in the implications of very high asymptomatic case count... Assuming we don't start seeing contradicting evidence.
When at least one large studied group has an outcome (symptomatic recovered, asymptomatic recovered, or dead). So for this group I guess a few more weeks.
When we know the full extent of the virus? It's an easy question to ask, but an incredibly hard one to answer.
For example, they've been finding that the virus can trigger strokes in otherwise healthy individuals. That's individuals that either exhibit no symptoms or minor symptoms. So while they may otherwise be asymptomatic, we can't know unless we do a full extensive test to see if they're also suffering from unseen clotting issues.
Every article I see about people testing asymptomatic is followed by comments insisting they were asymptomatic when tested, with no idea of whether they stayed asymptomatic or whether virtually all of them had symptoms a few days later, thus basically invalid.
But this doesn't seem like a hard problem to solve, folks. Is nobody bothering to follow up with the asymptomatic people a week later? Just take their mobile phone number, and text them en masse with a quick Y/N question as to whether or not they got sick?
This stuff baffles me. This is literally a matter of life-and-death, and yet the most basic questions seem to be unanswered. (Or are these follow-up surveys being done but the media just refuses to report them because it now feels like week-old news? I'd love to know.)
People can test positive and are most contagious before they show symptoms. As opposed to influenza where people with symptoms are most contagious. The delay in the onset of symptoms is why this is a very difficult virus to contain.
Further, the accuracy of our tests is questionable and hopefully improving.
Finally, viral shedding has been seen up to 35+ days since symptom onset. Meaning if they showed symptoms a month ago, they may still test positive.
As a Canadian, I'm shaking my head at our officials who said "we do know that asymptomatic people are not the key driver of epidemics" as a response to concerns back in January of the potential for the virus to grow in our country via incoming travelers who came from hot spots and were not screened or forced to isolate if they expressed no symptoms.
Now our long term care facilities are being overrun with cases potentially because we waited until deaths piled up before testing asymptomatic caretakers for the virus.
>>> The United States has more people behind bars than any other nation, a total incarcerated population of nearly 2.3 million as of 2017 — nearly half of which is in state prisons. Smaller numbers are locked in federal prisons and local jails, which typically hold people for relatively short periods as they await trial.
That isn't correct. "Local Jails" hold two general populations: people serving less than a year (generally non-felony convictions) and people awaiting legal process. The infamous Rikers Island in NY is technically a "local jail". People regularly stay in these facilities for YEARS. The AVERAGE stay at Rikers is 6+ months. (Total stay, not time between appearances.)
The distinction between "jail" and "prison" in the US is academic. For purposes of disease, and certainly from the perspective of inmates, both are prisons where large populations are locked up in confined quarters for years at a time.
The Reuters article is not useful. It doesn't tell us the type of tests being done, and certainly says nothing about false positives. Like most other articles, this article is what I call "bullshit" but John Ionnidis calls:
I was doing stuff with the Johns Hopkins data and it has all kinds problems with it (not to mention the format is terrible; time series as columns?!). They also tacked on the retroactive New York cases to the end to the time series data. I did a post on it:
No mention of what kind of test was performed. And this article is not alone - most don't bother.
The kind of test matters. A qPCR tests the presence of an active infection. Antibody test determines past exposure.
Each has different expectations for symptoms, communicability, and prognosis.
It's not a lot to ask - just report the kind of test that was done, and do so with in the first two paragraphs. Then let me draw my own conclusions about what the study means.
That's a minimum. Ideally, an article would mention the exact brand of test that was performed. If heterogeneous testing methods were used, report that as well.
I see a lot of people dismissing the shared air space & HVAC systems as possible vectors of infection besides close contact, but you have to remember a very important factor:
Droplets exist in a continuum, not a binary of big == fall to ground, small == stay in the air. There's a range, and as they get smaller they stay in the air longer.
Large droplets (>50 μm in diameter) settle on the ground almost immediately, and intermediate-sized droplets (10–50 μm) settle within several minutes. Small particles (<10 μm), including droplet nuclei from evaporated larger particles, can remain airborne for hours and are easily inhaled deep into the respiratory tract. [0]
As such, while particles that stay aloft longer may not exists in sufficient quantities when it is just one infected, or a few infected inmates, that changes with the # of infected. With each infected inmate the concentrations of those small particles will increase.
Let's say that normally the small particles exist at 3% the necessary quantity to infect another person. Then 33 inmates and staff get sick through close contact, and all of a sudden the concentrations of small droplets is sufficient to infect people. You hit a critical mass, and each additional infection only makes it worse, creating a rapid downward spiral.
[+] [-] jwlake|6 years ago|reply
This implies a shocking high R(effective) for that population. In 2 weeks we'll have super interesting data one way of the other on the CFR.
[+] [-] danieltillett|6 years ago|reply
Of course if we are really lucky and the prison was infected with a naturally attenuated strain we should make use of it [2].
1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7078829/
2. https://www.tillett.info/2020/04/12/how-would-a-search-for-a...
[+] [-] Symmetry|6 years ago|reply
[+] [-] MrPatan|6 years ago|reply
[+] [-] misja111|6 years ago|reply
The data comes from 4 prisons. It is theoretically possible that all 4 of them happened to be in the same window after an initial infection, but it doesn't seem very likely. I guess the only way to be sure is to do follow up tests every week or so, hopefully that will happen.
[+] [-] Gibbon1|6 years ago|reply
I've repeatedly linked to CDC study that estimates r0 in Wuhan before lockdown at between 3.8 and 8.7. Median 5.8.
Take away: Completely avoid being indoors with large groups of people.
[+] [-] Retric|6 years ago|reply
[+] [-] ineedasername|6 years ago|reply
The Princess cruise was a good indicator of CFR for a specific demographic range when they tested early, often, and had access to quality care. If the CFR of this prison will tell us anything, it will be a counterpoint to such information showing what happens when quality of care is greatly diminished.
[+] [-] andrei_says_|6 years ago|reply
> The results of the tests for IgG, IgA, and IgM levels are usually evaluated together. Abnormal test results typically indicate that there is something affecting the immune system and suggest the need for further testing. Immunoglobulins testing is not diagnostic but can be a strong indicator of a disease or condition. There are a number of conditions that are associated with increased and decreased immunoglobulins.
[+] [-] unknown|6 years ago|reply
[deleted]
[+] [-] darkerside|6 years ago|reply
[+] [-] laufj|6 years ago|reply
[+] [-] qznc|6 years ago|reply
[+] [-] finolex1|6 years ago|reply
https://www.moh.gov.sg/news-highlights/details/46-more-cases...
[+] [-] ivanhoe|6 years ago|reply
Can those two facts be combined into a theory that asymptomatic carriers are more likely to produce more mild and asymptomatic cases?
Don't know if it makes any sense (probably not), but it would certainly explain how in some closed environments there's a prevalence for mild cases, while in others there's a plenty of very sick people, regardless of the age.
[+] [-] marcell|6 years ago|reply
[+] [-] cies|6 years ago|reply
Thanks for sharing.
I found the peek in all-case mortality also very interesting, because that way counting is much more unambiguous: dead is dead.
They showed a clear diversion from the "average" in recent weeks, but... they did not show the stdev for the averages. Finally I found a chart that shows that "outliers" are not uncommon.
https://imgur.com/IPNiXRe
[+] [-] joe_the_user|6 years ago|reply
The 1.66%, otoh, seems reasonably in line or at least compatible with what's been observed in Korea and elsewhere.
Given age is going to skew things a good deal, it seems like a picture is emerging but not that new a picture. An IFR of even 1% is pretty bad, especially given these statistics show how infectious this virus is.
[+] [-] ineedasername|6 years ago|reply
Reporting on 96% without symptoms is misleading without mentioning this: It gives the impression that the # of coronavirus infections could be up to 24x higher than the known positives cases. But symptoms can take 2-14 days to develop, meaning it is entirely too soon to tell if these are all asymptomatic cases, or merely pre-symptomatic.
[0] https://www.dispatch.com/news/20200410/coronavirus-in-marion...
[+] [-] ilamont|6 years ago|reply
There was a nursing home in Massachusetts which had 51 out of 98 residents testing positive but asymptomatic in early April. While this sounded encouraging in the sense no one was critically ill because of coronavirus, a few weeks later 19 had died and about 30 more had tested positive.
Let’s wait a month until there is a clearer picture about the impact of the virus on a particular population of people.
https://www.boston.com/news/local-news/2020/04/04/coronaviru...
https://www.wcvb.com/article/85-of-patients-at-wilmington-ma...
[+] [-] freeflight|6 years ago|reply
> Estimated smoking prevalence among inmates was approximately 50% in 2003–2004, compared to 21% among noninstitutionalized adults. [0]
Which might play a major role in the spread and the actual severity of COVID-19 as French researchers are speculating that nicotine could be responsible for blocking the ACE2 receptors that COVID-19 uses to get into cells, which could explain why there's such a low incidence of tobacco smokers among patients, far below what should be expected [1].
There's nothing really concrete yet, for now they want to experiment with nicotine patches as treatment.
But in that context, prison populations could make for an interesting control group: Maybe the prevalence of smoking is what keeps the virus less severe, due to reduced viral load reaching cells, and thus fewer carriers are symptomatic?
[0] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100810/
[1] https://www.qeios.com/read/article/574
[+] [-] elihu|6 years ago|reply
[+] [-] greedo|6 years ago|reply
[+] [-] ooobit2|6 years ago|reply
[deleted]
[+] [-] redis_mlc|6 years ago|reply
[deleted]
[+] [-] IAmEveryone|6 years ago|reply
This is assuming that tests in NYC currently include every infected and symptomatic person. Considering the official advice for people with mild symptoms is to stay home (and not seek a test), that assumption is ... optimistic.
It also wouldn't fit with the anti-body tests that have been done in NYC that showed figures closer to 15-20%.
So I'd expect about 1/2 to 2/3 of these 96% to develop symptoms within the next week.
The other possibility is the prison population not being representative of the general population. That's probably true in terms of fatality rates, because they are younger. I'm not entirely sure if that age imbalance is just as strong for any symptoms as it is for risk of hospitalisation and death.
[+] [-] azakai|6 years ago|reply
[+] [-] ImaCake|6 years ago|reply
[+] [-] alexbanks|6 years ago|reply
[+] [-] Terretta|6 years ago|reply
In the field it appears many/most of the less severe cases don’t exhibit the initial set they had defined, so patients experienced illness written off as not COVID-19.
From what I’ve heard from the field, a careful patient history finds there was typically a bout of unusual “but it can’t be COVID” illness with a set of the expanded set of symptoms in almost every “asymptomatic” patient.
It’s further speculated these variations may have to do with level of exposure and path of infection, along with the earlier noted lung health and comorbidities.
[+] [-] tyingq|6 years ago|reply
[+] [-] SpicyLemonZest|6 years ago|reply
[+] [-] AnthonyMouse|6 years ago|reply
Presumably in two weeks, when we know whether more of these thousands of people go on to develop symptoms or not.
Is anybody following up on stories like this? Do we have any from two weeks ago?
[+] [-] taeric|6 years ago|reply
[+] [-] FabHK|6 years ago|reply
This certainly adds another data point, but I wouldn’t throw conventional wisdom out the window yet.
[+] [-] cjlars|6 years ago|reply
[+] [-] alkonaut|6 years ago|reply
When at least one large studied group has an outcome (symptomatic recovered, asymptomatic recovered, or dead). So for this group I guess a few more weeks.
[+] [-] sroussey|6 years ago|reply
[+] [-] ouid|6 years ago|reply
[+] [-] fzeroracer|6 years ago|reply
For example, they've been finding that the virus can trigger strokes in otherwise healthy individuals. That's individuals that either exhibit no symptoms or minor symptoms. So while they may otherwise be asymptomatic, we can't know unless we do a full extensive test to see if they're also suffering from unseen clotting issues.
[+] [-] crazygringo|6 years ago|reply
But this doesn't seem like a hard problem to solve, folks. Is nobody bothering to follow up with the asymptomatic people a week later? Just take their mobile phone number, and text them en masse with a quick Y/N question as to whether or not they got sick?
This stuff baffles me. This is literally a matter of life-and-death, and yet the most basic questions seem to be unanswered. (Or are these follow-up surveys being done but the media just refuses to report them because it now feels like week-old news? I'd love to know.)
[+] [-] lettergram|6 years ago|reply
Further, the accuracy of our tests is questionable and hopefully improving.
Finally, viral shedding has been seen up to 35+ days since symptom onset. Meaning if they showed symptoms a month ago, they may still test positive.
https://www.aarp.org/health/conditions-treatments/info-2020/...
[+] [-] colmvp|6 years ago|reply
Now our long term care facilities are being overrun with cases potentially because we waited until deaths piled up before testing asymptomatic caretakers for the virus.
[+] [-] sandworm101|6 years ago|reply
>>> The United States has more people behind bars than any other nation, a total incarcerated population of nearly 2.3 million as of 2017 — nearly half of which is in state prisons. Smaller numbers are locked in federal prisons and local jails, which typically hold people for relatively short periods as they await trial.
That isn't correct. "Local Jails" hold two general populations: people serving less than a year (generally non-felony convictions) and people awaiting legal process. The infamous Rikers Island in NY is technically a "local jail". People regularly stay in these facilities for YEARS. The AVERAGE stay at Rikers is 6+ months. (Total stay, not time between appearances.)
The distinction between "jail" and "prison" in the US is academic. For purposes of disease, and certainly from the perspective of inmates, both are prisons where large populations are locked up in confined quarters for years at a time.
[+] [-] giardini|6 years ago|reply
"Lies, Damned Lies, and Medical Science":
https://www.theatlantic.com/magazine/archive/2010/11/lies-da...
Dr. Ioannidis on Why We Don't Have Reliable Data Surrounding COVID-19:
https://www.youtube.com/watch?v=QUvWaxuurzQ&feature=emb_logo
[+] [-] djsumdog|6 years ago|reply
https://battlepenguin.com/tech/fighting-with-the-data/
[+] [-] H8crilA|6 years ago|reply
[+] [-] Jemm|6 years ago|reply
It is like constantly rearranging the furniture while a blind person is in the store.
[+] [-] aazaa|6 years ago|reply
The kind of test matters. A qPCR tests the presence of an active infection. Antibody test determines past exposure.
Each has different expectations for symptoms, communicability, and prognosis.
It's not a lot to ask - just report the kind of test that was done, and do so with in the first two paragraphs. Then let me draw my own conclusions about what the study means.
That's a minimum. Ideally, an article would mention the exact brand of test that was performed. If heterogeneous testing methods were used, report that as well.
[+] [-] ineedasername|6 years ago|reply
Droplets exist in a continuum, not a binary of big == fall to ground, small == stay in the air. There's a range, and as they get smaller they stay in the air longer.
Large droplets (>50 μm in diameter) settle on the ground almost immediately, and intermediate-sized droplets (10–50 μm) settle within several minutes. Small particles (<10 μm), including droplet nuclei from evaporated larger particles, can remain airborne for hours and are easily inhaled deep into the respiratory tract. [0]
As such, while particles that stay aloft longer may not exists in sufficient quantities when it is just one infected, or a few infected inmates, that changes with the # of infected. With each infected inmate the concentrations of those small particles will increase.
Let's say that normally the small particles exist at 3% the necessary quantity to infect another person. Then 33 inmates and staff get sick through close contact, and all of a sudden the concentrations of small droplets is sufficient to infect people. You hit a critical mass, and each additional infection only makes it worse, creating a rapid downward spiral.
[0] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147198/