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Cont: 2019-nCoV / Corona virus Pt 3

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It seems to say that they are looking at 2 to 5 of the 142 studies they are aware of.

I don't really see any good evidence so far for chloroquine, but it seems like people are rubbing their hands together with glee to crap on this drug whether it worked or not just to score political points

That's scary

Just monday we saw piles of headlines that dishonestly said something to the effect of "Chloroquine study ended because of heart problems" Technicallty I guess you could say thats true, maybe

But really it was: Part of a study using higher doses ended because of heart issues. The rest of the study is ongoing. The doctors participating in it say they want to keep researching it.
 
Given that the inspections took place around 2 years before the outbreak, I think that it's fair to say that the probability that the inspections were related to the outbreak is fairly low. The article doesn't state why the US was allowed to inspect the lab; perhaps it was a requirement for maintaining an international certification?

At the time, they were running a joint research project with a US university. Hence, inspections.
 
Many maybe, but I doubt most. Every doctor I've been to in China has been pro TCM.

And rightly so! I don't think anyone who has experienced a draconian lockdown first hand knows just how necessary and vital TCM is to one's daily routines. And perhaps I shouldn't say this, but I don't think I want to live in a world that doesn't have Turner Classic Movies.
 
I was hoping that the number would go to zero very quickly. But this is not to be the case. Not sure where the new cases are coming from since over 64% of cases originated overseas.

When you have asymptomatic spreaders it's going to be extreme;y difficult to get it to zero.

I suspect the best we (NZ & Oz) can hope for is to keep the new infections low enough to test, isolate and stomp on new outbreaks.

We're going to be faced with the choice of accepting South Korea-level tracking or prolonged shutdowns.

If it was so easy, why has the WHO been underfunded for years?

Because the countries that can afford it, but have failed to increase its budget are short-sighted, selfish dicks.

I also think the H1N1 swine 'flu pandemic did nobody any favours. It gave everyone a false sense of security.

Review of hydroxychloroquine in covid-19
(Spoiler it probably doesn't work.)
https://www.cebm.net/covid-19/hydroxychloroquine-for-covid-19-what-do-the-clinical-trials-tell-us/

Still too little, but the results to date show for sure it isn't going to be the magic bullet we're looking for.

The fact we're halfway through April and have no idea what other drug trials are showing tends to indicate nothing is going to work well enough to matter.
 
Some interesting statistics coming through.

Russia showing the world how to treat Covid-19: over 20,000 cases but a mere 198 deaths and only 8 critical cases.

All hail Russia!

Surely, they wouldn't be lying?
_______________________

And it looks very much like the disease is on the loose in Africa, with disturbing rises in case loads in Tanzania & Congo. We're about to see some dangerous growth in numbers in that region.
 
It seems to say that they are looking at 2 to 5 of the 142 studies they are aware of.

... because those are the only ones with published results.

The facts on the ground right now are that the available research shows it's harmful and ineffective.

Prescribing it off label - outside of a clinical trial - is malpractice.
 
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No particular reason for chosing today, other than I have been updating my data.

From a somewhat arbitrary 21 March, 2020, I calculated the daily increase in deaths from COVID-19, as a fraction of the previous day's total; per the WHO daily situation reports*. Up to 4 April.

The minimum is ~0.12; the maximum ~0.43.

Starting with 5854 COVID-19 deaths (cumulative) on 4 April, I estimate the soonest "85k US deaths attributed to Covid-19" will be 18 April, and the latest 28 April, with a mid (geometric mean) by 26 April. Allow ±1 day for all manner of variables.

One way to look at these numbers is this: if 85k is reached in May (or later!), it could be considered evidence that the massive/draconican measures put in place in March and April succeeded in "flattening the curve".

Sadly, I think the numbers tell us that 240k deaths is too optimistic (it is more likely than not that there will be more than 240k). :(

*there is no realistic number for 22 March, so I interpolated between 21 and 23 March.
It wasn't until 12 April that the daily fractional increase in total US covid-19 deaths (per the daily WHO situation reports) was below 0.12, when the total number of such deaths was given as 18,516.

The "latest" estimate in the post of mine I've quoting ("and the latest 28 April") refers to assuming that the fraction is 0.12 every day, starting on 4 April. Of course, if the fraction was >0.12 every day until the 12th, the estimate for every day will also be less than the actual. No surprise then that the estimate for the 12th is 14,602.

The actual value of the fraction for the last three days is:
13th: 0.104
14th: 0.075
15th: 0.068

Is the curve being flattened?
 
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And rightly so! I don't think anyone who has experienced a draconian lockdown first hand knows just how necessary and vital TCM is to one's daily routines. And perhaps I shouldn't say this, but I don't think I want to live in a world that doesn't have Turner Classic Movies.

I was pissed when I found my new cable package, which btw includes higher levels like HBO, does not include TCM. I'm much more interested in watching older, classic movies during the lockdown than the latest ones.
 
Some interesting statistics coming through.

Russia showing the world how to treat Covid-19: over 20,000 cases but a mere 198 deaths and only 8 critical cases.

All hail Russia!

Well, there is at least one country that trumps Russia, North Korea.
No cases
No death
Total immunity

Ok, now seriously, I remember talking about NK when this all started in China. Seems like there has not been any mention of NK since then.
 
Well, there is at least one country that trumps Russia, North Korea.
No cases
No death
Total immunity

Ok, now seriously, I remember talking about NK when this all started in China. Seems like there has not been any mention of NK since then.

Oh I've seen some news like week back. They have zero cases, zero deaths, the big leader said. Soldier behind him had a face mask though.
 
Here are the recent numbers for Massachusetts.

The columns are: date, total confirmed cases to that date, increase factor of total confirmed cases for the day, and new confirmed cases for the day.

"S" indicates Saturdays and Sundays, which might affect the timing of reporting and thus shift the numbers of cases between days.

"*" and "+" indicate a new all-time high for new confirmed cases on that day.

Code:
3/21     525   1.27    112   S
3/22     646   1.23    121   S
3/23     777   1.20    131
3/24    1159   1.49    382 +  <--- business closures / lockdown
3/25    1838   1.59    679 +
[COLOR="SeaGreen"]3/26    2417   1.32    579
3/27    3240   1.34    823 +
3/28    4257   1.31   1017 * S[/COLOR]
[COLOR="RoyalBlue"]3/29    4955   1.16    698   S
3/30    5752   1.16    797
3/31    6620   1.15    868
4/01    7738   1.17   1118 +
4/02    8966   1.16   1228 +
4/03   10402   1.16   1436 *[/COLOR]
4/04   11736   1.13   1334   S
4/05   12500   1.07    764   S
[COLOR="DarkRed"]4/06   13837   1.11   1337
4/07   15202   1.10   1365
4/08   16790   1.10   1588 +
4/09   18941   1.13   2151 *
4/10   20974   1.11   2033	
4/11   22860   1.09   1886   S
4/12   25475   1.11   2615 * S[/COLOR]
[COLOR="SeaGreen"]4/13   26867   1.05   1392 <--- 1.5 hr. change in data closeout time
4/14   28163   1.04   1296
4/15   29918   1.06   1755[/COLOR]

The interesting and unexpected behavior in this data is pointed out by the coloration, showing stable periods where the rate of increase of cases is roughly constant (which causes an exponential rise of new confirmed cases per day at that rate, so as to eventually exceed any previous maxima) separated by rapid "step-downs" after which the rate of increase drops to a new lower range and the new cases per day, at least at first, decrease sharply.

I'll consider the overall "leveling off" to have occurred when the overall trend in the cases per day is no longer increasing, taking the rough day to day variations into account. Or equivalently, when "step-downs" occur before rather than after new highs are set within a current regime.

The step-down pattern occurs consistently in each of the largest and medium sized individual MA counties, as well and nearly as clearly as in the state aggregate. The main differences between counties are that less populous counties and also wealthier counties have consistently shown slightly smaller growth rates during a given stable period. The differences are a matter of plus or minus one percentage point from the aggregate state figure, which made little difference early on when the growth rates everywhere were above 10% (1.10), but in recent days that same spread in percentages results in the least populous counties having likely leveled off a few days ago (their data is of course relatively noisier), and medium-density counties might be leveling off now, while the most populous counties are still rising noticeably day to day (but not yet exceeding previous highs) during the current "green" period.

I'm not really sure how to understand these phenomena. The measures being taken haven't really changed since March 24th, with the exception of increased usage of (mostly homemade) face masks during the most recent week. It's understandable that cases contracted before the lockdown would take a week or more (average 5-6 days) to become confirmed, so at first the increase rate would continue to be high. Which the data shows, for the early black and green periods. But why the later step-downs weeks afterward? That is to say, why do they happen at all, but not happen sooner?

One way to model it would be to assume a large number of asymptomatic carriers with a long statistical tail of durations before they either become symptomatic or recover completely, and that pool has to dwindle away before the new cases can level off. But in that case, why wouldn't the greater number of new cases occurring during those weeks make the asymptomatic pool even larger? (It's been true all along, and still true, that only people with symptoms have been getting tested. We're not really doing contact tracing yet either.) And, research so far doesn't suggest that the number of asymptomatic cases is a very high ratio.

Another possible model is that herd immunity is taking over, within a small sub-population of "behaviorally vulnerable" people -- which would have two main components: careless people, and people still working in public-facing "essential" jobs.

The epidemiologists who make forecasts must have some other hidden variable in mind, because even though their predictions haven't been very accurate (e.g. about specific dates when peaks will occur), they've been consistent with the general pattern we're seeing everywhere -- that is, that cases will level off at a peak relatively soon, rather than increasing at some percentage per day until herd immunity kicks in.
 
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Another possible model is that herd immunity is taking over, within a small sub-population of "behaviorally vulnerable" people -- which would have two main components: careless people, and people still working in public-facing "essential" jobs.

It's bugging the hell out of me, I tell ya.

I think there's merit in the idea that herd immunity is being achieved, and part of that is the certain knowledge that Covid-19 had been spreading for weeks prior to busting out in the old folks' home in Seattle.

What evidence is there that a significant percentage of people hadn't been infected by that stage?

We desperately need immunological tests, because it might well the peak is over and measures can be released, but without evidence that would be bloody dangerous.
 
Here are the recent numbers for Massachusetts.

The columns are: date, total confirmed cases to that date, increase factor of total confirmed cases for the day, and new confirmed cases for the day.

"S" indicates Saturdays and Sundays, which might affect the timing of reporting and thus shift the numbers of cases between days.

"*" and "+" indicate a new all-time high for new confirmed cases on that day.

Code:
3/21     525   1.27    112   S
3/22     646   1.23    121   S
3/23     777   1.20    131
3/24    1159   1.49    382 +  <--- business closures / lockdown
3/25    1838   1.59    679 +
[COLOR="SeaGreen"]3/26    2417   1.32    579
3/27    3240   1.34    823 +
3/28    4257   1.31   1017 * S[/COLOR]
[COLOR="RoyalBlue"]3/29    4955   1.16    698   S
3/30    5752   1.16    797
3/31    6620   1.15    868
4/01    7738   1.17   1118 +
4/02    8966   1.16   1228 +
4/03   10402   1.16   1436 *[/COLOR]
4/04   11736   1.13   1334   S
4/05   12500   1.07    764   S
[COLOR="DarkRed"]4/06   13837   1.11   1337
4/07   15202   1.10   1365
4/08   16790   1.10   1588 +
4/09   18941   1.13   2151 *
4/10   20974   1.11   2033	
4/11   22860   1.09   1886   S
4/12   25475   1.11   2615 * S[/COLOR]
[COLOR="SeaGreen"]4/13   26867   1.05   1392 <--- 1.5 hr. change in data closeout time
4/14   28163   1.04   1296
4/15   29918   1.06   1755[/COLOR]

The interesting and unexpected behavior in this data is pointed out by the coloration, showing stable periods where the rate of increase of cases is roughly constant (which causes an exponential rise of new confirmed cases per day at that rate, so as to eventually exceed any previous maxima) separated by rapid "step-downs" after which the rate of increase drops to a new lower range and the new cases per day, at least at first, decrease sharply.

I'll consider the overall "leveling off" to have occurred when the overall trend in the cases per day is no longer increasing, taking the rough day to day variations into account. Or equivalently, when "step-downs" occur before rather than after new highs are set within a current regime.

The step-down pattern occurs consistently in each of the largest and medium sized individual MA counties, as well and nearly as clearly as in the state aggregate. The main differences between counties are that less populous counties and also wealthier counties have consistently shown slightly smaller growth rates during a given stable period. The differences are a matter of plus or minus one percentage point from the aggregate state figure, which made little difference early on when the growth rates everywhere were above 10% (1.10), but in recent days that same spread in percentages results in the least populous counties having likely leveled off a few days ago (their data is of course relatively noisier), and medium-density counties might be leveling off now, while the most populous counties are still rising noticeably day to day (but not yet exceeding previous highs) during the current "green" period.

I'm not really sure how to understand these phenomena. The measures being taken haven't really changed since March 24th, with the exception of increased usage of (mostly homemade) face masks during the most recent week. It's understandable that cases contracted before the lockdown would take a week or more (average 5-6 days) to become confirmed, so at first the increase rate would continue to be high. Which the data shows, for the early black and green periods. But why the later step-downs weeks afterward? That is to say, why do they happen at all, but not happen sooner?

One way to model it would be to assume a large number of asymptomatic carriers with a long statistical tail of durations before they either become symptomatic or recover completely, and that pool has to dwindle away before the new cases can level off. But in that case, why wouldn't the greater number of new cases occurring during those weeks make the asymptomatic pool even larger? (It's been true all along, and still true, that only people with symptoms have been getting tested. We're not really doing contact tracing yet either.) And, research so far doesn't suggest that the number of asymptomatic cases is a very high ratio.

Another possible model is that herd immunity is taking over, within a small sub-population of "behaviorally vulnerable" people -- which would have two main components: careless people, and people still working in public-facing "essential" jobs.

The epidemiologists who make forecasts must have some other hidden variable in mind, because even though their predictions haven't been very accurate (e.g. about specific dates when peaks will occur), they've been consistent with the general pattern we're seeing everywhere -- that is, that cases will level off at a peak relatively soon, rather than increasing at some percentage per day until herd immunity kicks in.

An important metric is missing here: the number of tests having been carried out per day. As the state's capacity to test increases over time we should expect an increase in confirmed cases just from that. The capacity could also increase in jumps if it is the result of another testing lab coming on line. A second metric I would like to see is the percentage of negative vs positive tests. If that percentage increases over time it should indicate a growing problem, or the opposite if it decreases.
 
An important metric is missing here: the number of tests having been carried out per day. As the state's capacity to test increases over time we should expect an increase in confirmed cases just from that. The capacity could also increase in jumps if it is the result of another testing lab coming on line. A second metric I would like to see is the percentage of negative vs positive tests. If that percentage increases over time it should indicate a growing problem, or the opposite if it decreases.


That data is available. I'll get to work collecting those numbers, and report later (not tonight).
 
Why would they want to make a lot of political capital?
Countries do. That’s why they’re sending ventilators and masks around the world (even if it is substandard, in some cases), so they look like the good guys. Down the line, it’ll be easy to say ‘who helped you when the virus got bad? The US or us’?

They would still get painted with the " mean, capitalistic, I'm better than you " brush..
Eh? I think I have missed something.

Besides, they're a little short right now, having plowed a couple of trillion back into their own economy.
Oh, you thought I meant the US. Why would I suggest the US, having withdrawn funding, would put funding into the WHO to make political capital? That would make the US look like it didn’t know what it was doing.
 
I'm not really sure how to understand these phenomena. The measures being taken haven't really changed since March 24th, with the exception of increased usage of (mostly homemade) face masks during the most recent week. It's understandable that cases contracted before the lockdown would take a week or more (average 5-6 days) to become confirmed, so at first the increase rate would continue to be high. Which the data shows, for the early black and green periods. But why the later step-downs weeks afterward? That is to say, why do they happen at all, but not happen sooner?

Case numbers would be very valuable but only if there was consistency about who gets tested and when and the test results had the same delays.

This doesn't yet exist. Hopefully it will at some point and rapid result tests will also become the standard. A 6 to 10 day wait for a test result is not real useful.

So right now I mostly used daily death counts. They tend to be pretty definitive. Well, aside from NY City apparently having about 200 deaths per day from COVID-19 that were never reported because they died at home and didn't have enough resources to test them.

Death counts have an average of about 3 weeks from infection. But they also have a long tail since some are in ICU weeks before expiring.

Availability of more expansive, and rapid, PCR testing as well as serological surveillance will be critical to selective re-opening of counties and/or regions. This will allow tightening when required w/o runaway cluster growth.
 
Interesting! :)

Here are the recent numbers for Massachusetts.

The columns are: date, total confirmed cases to that date, increase factor of total confirmed cases for the day, and new confirmed cases for the day.

"S" indicates Saturdays and Sundays, which might affect the timing of reporting and thus shift the numbers of cases between days.

"*" and "+" indicate a new all-time high for new confirmed cases on that day.

Code:
3/21     525   1.27    112   S
3/22     646   1.23    121   S
3/23     777   1.20    131
3/24    1159   1.49    382 +  <--- business closures / lockdown
3/25    1838   1.59    679 +
[COLOR="SeaGreen"]3/26    2417   1.32    579
3/27    3240   1.34    823 +
3/28    4257   1.31   1017 * S[/COLOR]
[COLOR="RoyalBlue"]3/29    4955   1.16    698   S
3/30    5752   1.16    797
3/31    6620   1.15    868
4/01    7738   1.17   1118 +
4/02    8966   1.16   1228 +
4/03   10402   1.16   1436 *[/COLOR]
4/04   11736   1.13   1334   S
4/05   12500   1.07    764   S
[COLOR="DarkRed"]4/06   13837   1.11   1337
4/07   15202   1.10   1365
4/08   16790   1.10   1588 +
4/09   18941   1.13   2151 *
4/10   20974   1.11   2033	
4/11   22860   1.09   1886   S
4/12   25475   1.11   2615 * S[/COLOR]
[COLOR="SeaGreen"]4/13   26867   1.05   1392 <--- 1.5 hr. change in data closeout time
4/14   28163   1.04   1296
4/15   29918   1.06   1755[/COLOR]

The interesting and unexpected behavior in this data is pointed out by the coloration, showing stable periods where the rate of increase of cases is roughly constant (which causes an exponential rise of new confirmed cases per day at that rate, so as to eventually exceed any previous maxima) separated by rapid "step-downs" after which the rate of increase drops to a new lower range and the new cases per day, at least at first, decrease sharply.

I'll consider the overall "leveling off" to have occurred when the overall trend in the cases per day is no longer increasing, taking the rough day to day variations into account. Or equivalently, when "step-downs" occur before rather than after new highs are set within a current regime.

The step-down pattern occurs consistently in each of the largest and medium sized individual MA counties, as well and nearly as clearly as in the state aggregate. The main differences between counties are that less populous counties and also wealthier counties have consistently shown slightly smaller growth rates during a given stable period. The differences are a matter of plus or minus one percentage point from the aggregate state figure, which made little difference early on when the growth rates everywhere were above 10% (1.10), but in recent days that same spread in percentages results in the least populous counties having likely leveled off a few days ago (their data is of course relatively noisier), and medium-density counties might be leveling off now, while the most populous counties are still rising noticeably day to day (but not yet exceeding previous highs) during the current "green" period.

I'm not really sure how to understand these phenomena. The measures being taken haven't really changed since March 24th, with the exception of increased usage of (mostly homemade) face masks during the most recent week. It's understandable that cases contracted before the lockdown would take a week or more (average 5-6 days) to become confirmed, so at first the increase rate would continue to be high. Which the data shows, for the early black and green periods. But why the later step-downs weeks afterward? That is to say, why do they happen at all, but not happen sooner?

One way to model it would be to assume a large number of asymptomatic carriers with a long statistical tail of durations before they either become symptomatic or recover completely, and that pool has to dwindle away before the new cases can level off. But in that case, why wouldn't the greater number of new cases occurring during those weeks make the asymptomatic pool even larger? (It's been true all along, and still true, that only people with symptoms have been getting tested. We're not really doing contact tracing yet either.) And, research so far doesn't suggest that the number of asymptomatic cases is a very high ratio.

Another possible model is that herd immunity is taking over, within a small sub-population of "behaviorally vulnerable" people -- which would have two main components: careless people, and people still working in public-facing "essential" jobs.

The epidemiologists who make forecasts must have some other hidden variable in mind, because even though their predictions haven't been very accurate (e.g. about specific dates when peaks will occur), they've been consistent with the general pattern we're seeing everywhere -- that is, that cases will level off at a peak relatively soon, rather than increasing at some percentage per day until herd immunity kicks in.
A case means a person who was tested, and the test result is positive for Covid-19, right?

Those doing the tests report results to some central point, the state Department of Public Health? Where they are collated and rolled up into some numbers released to the public, right?

Is the distribution of test/result delay (the time between when a test is given and when the result is available/reported) known? Has that distribution changed over ~the past month?

How about the distribution of testers (Quest, hospital or university labs, etc)? The distribution of the test type/kits?

There may also be differences in the rates of false positives and false negatives, by weird variables such as air temperature and/or humidity. Or general health of the “patient”. Or ...

In short, to what extent are the numbers in your table free of any number of systematic effects which are ~independent of actual Covid-19 infection?

ETA: d’oh! Multi-ninja’d :(
 
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