Outside Topic Covid-19 considerations

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RE: Covid-19 considerations - OutsiderFan - 02-29-2020

One of my online sources did some digging into what the CDC means when it warns of "significant disruption" as it did this week. The CDC published guidelines for dealing with influenza pandemics in 2017: https://stacks.cdc.gov/view/cdc/11425

I'll let y'all draw your own conclusions. The reason I'm sharing is because this provides some insight into what may happen, so y'all can prepare and not be caught off guard.

My greatest takeaway is these guidelines - IMO, smartly - put local and state public health officials in charge of implementing these CDC guidelines as they see fit. So Santa Clara County's Health Department (Dr. Sara Cody) is going to be deciding how to handle, for example. The fact the county can do its own testing and widen surveillance, more than likely will expedite things like school closings.

Dr. Cody is a Stanford grad, if it makes y'all feel any better: https://www.sccgov.org/sites/opa/nr/Pages/saracody.aspx

RE: Covid-19 considerations - oldalum - 02-29-2020

Dr. Cody has been a personal friend of mine for decades, we are fortunate she is the Public Health Officer for Santa Clara County because she is terrific. As you would imagine, she has been working extremely hard; as proof, she declined my recent offer of free tickets to Stanford MBB vs. Colorado. Now that's dedication to the job! --even if her priorities could be viewed on this board as misplaced :)

RE: Covid-19 considerations - M T - 02-29-2020

(02-28-2020, 01:12 PM)oldalum Wrote: ... And the "more robust" analysis you cite says that "All CFR estimates should be viewed cautiously at the current time as the sensitivity of surveillance of both deaths and cases in mainland China is unclear." And their point estimates for CFR based on all infections are under 1%, albeit with wide confidence intervals.

That quote is from a British report published on or before Feb. 10 (based on data up to 8 Feb, reported in news on 10 Feb). The WHO-China joint mission ended Feb. 24 and would seemingly supersede this, with on-site investigation.

As I read this report, ALL the numbers in this report were based on assumptions on top of a small data sample. Wuhan (pop. 11M city; 18M metro) as of Feb 25, had 2000+ deaths, 7000+ in hospital currently, and 10,000+discharges. This report's data for Hubei province (pop 59M, including Wuhan) is based on 29 deaths and 36 recoveries. That's fine for a back-of-the-envelope, first rough estimate, but not for something one should quote when data is available on a much larger scale. I wouldn't call it robust.

"assuming exponential growth at rate 0.14/day
assume 5-day period from onset to report and 1-day period from death to report
assuming infected individuals test positive for 14 days
assuming infected individuals test positive for 7 days
This estimate relies on information from just 2 deaths reported outside mainland China thus far and therefore has wide uncertainty.

"Given that the estimates of CFR across all infections rely on a single point estimate of infection prevalence, they should be treated cautiously. In particular,the sensitivity of the diagnostics used to test repatriated passengers is not known, and it is unclear when infected people might test positive, or how representative those passengers were of the general population of Wuhan (their infection risk might have been higher or lower than the general population)."

Because I consider this report to be untrustworthy, I won't quote their CFR for within Hubei, but it was much, much higher than has been mentioned here (for instance, from the WHO). I consider those numbers to be evidence this report to be worthless. The numbers they reported under 1% seemingly are even more dependent on assumptions than their numbers for Hubei.

RE: Covid-19 considerations - BostonCard - 02-29-2020

First death in the US was reported today. Sadly won’t be the last.

BC

RE: Covid-19 considerations - Langdude - 02-29-2020

In the town right next to mine - Kirkland...

-m.

RE: Covid-19 considerations - Erika - 02-29-2020

(02-29-2020, 04:27 PM)Langdude Wrote: In the town right next to mine - Kirkland...

-m.

Just up the road from me as well. The grocery stores have been crazy all week, everyone is stocking up. So glad I just retired (from UW).

RE: Covid-19 considerations - oldalum - 02-29-2020

I am just not that concerned about the details about CFRs and methods and reports and statistical adjustments and whatnot: my only point is that the published CFRs are uncertain and are likely to change as better evidence becomes available. My apparent mistake has been to say anything else in support of that point, which then becomes fodder to be picked at. To me it is incontrovertible that IF there is a significant number of mild and asymptomatic cases, then the current CFRs are likely too high. My best guess--and it's just a guess--is that due to such case ascertainment bias, the CFRs will likely end up lower than currently published. That's an opinion and can be proven wrong. If conclusive evidence proves me wrong, then like any good scientist I will cling even more tightly to my opinion, kicking and screaming all the way down. And that's my last word on the subject (until my next one)

RE: Covid-19 considerations - M T - 02-29-2020

(02-28-2020, 04:47 PM)Goose Wrote:
(02-28-2020, 03:00 PM)M T Wrote: A news article of Feb 15 says:
Quote:Zhang Hongxing, head of Wuhan's health commission, said last week the city tested about 6,000 to 8,000 people daily

Do you know, or does anyone hear know, are the tests being done in Wuhan the same test as the CDC is using, and if not, what the test they are using actually is? I have no idea myself. Not to say one is "better" than another at this point, but if they are different, it may be an issue.

If you click on that link, the article contains information about which test Wuhan uses (Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) technique) and in what situations is a test done, and the physical collection of a sample. Apparently (only) Hubei Province is also using lung imaging to classify patients as "clinically diagnosed" (detecting "advanced symptoms" which I presume means pneumonia), when the lab tests can't be done. The different testing would seem to make the data messier to analyze.

I haven't looked at the CDC testing protocol.

RE: Covid-19 considerations - Langdude - 02-29-2020

(02-29-2020, 06:03 PM)Erika Wrote:
(02-29-2020, 04:27 PM)Langdude Wrote: In the town right next to mine - Kirkland...

-m.

Just up the road from me as well. The grocery stores have been crazy all week, everyone is stocking up. So glad I just retired (from UW).

My wife went to CostCo today. No parking. Long lines. Totally sold out of some staples.

-m.

RE: Covid-19 considerations - cardcrimson - 02-29-2020

(02-29-2020, 09:38 PM)Langdude Wrote:
(02-29-2020, 06:03 PM)Erika Wrote:
(02-29-2020, 04:27 PM)Langdude Wrote: In the town right next to mine - Kirkland...

-m.

Just up the road from me as well. The grocery stores have been crazy all week, everyone is stocking up. So glad I just retired (from UW).

My wife went to CostCo today. No parking. Long lines. Totally sold out of some staples.

-m.

Swingline and Bostitch?!? Crisis indeed!

RE: Covid-19 considerations - winflop - 02-29-2020

When calculating lethality, be careful of what you put in the denominator. The correct denominator is (people who have died + people who are no longer infected). It is not total number of cases, because many of those cases have not yet been resolved.

I don't know what those numbers are currently, but I know that the lethality is higher than what is being reported

RE: Covid-19 considerations - M T - 02-29-2020

(02-28-2020, 11:07 AM)oldalum Wrote: the latest from the CDC and NIH on the case fatality rate, articles published today in the New England J of Medicine: free NEJM article

On the basis of a case definition requiring a diagnosis of pneumonia, the currently reported case fatality rate is approximately 2%. In another article in the Journal, Guan et al. report mortality of 1.4% among 1099 patients with laboratory-confirmed Covid-19; these patients had a wide spectrum of disease severity. If one assumes that the number of asymptomatic or minimally symptomatic cases is several times as high as the number of reported cases, the case fatality rate may be considerably less than 1%. This suggests that the overall clinical consequences of Covid-19 may ultimately be more akin to those of a severe seasonal influenza (which has a case fatality rate of approximately 0.1%) or a pandemic influenza (similar to those in 1957 and 1968) rather than a disease similar to SARS or MERS, which have had case fatality rates of 9 to 10% and 36%, respectively.

Am I missing something? I see no suggestion of any basis for that assumption mentioned in this editorial. The assumption could be that there are 1000x or 0.001x asymptomatic cases as confirmed cases, as far as I can tell. So I don't understand how they can then say "This suggests...".

Had the authors said, "Based on experience with .... viruses, one might suspect <assumption>", then that at least is based on something.

Btw, another bit of evidence, in my opinion, that mildly symptomatic cases were being found in China is described in this Feb. 28 article about a Feb 28 NEJM article (reference 5 in the above NEJM editorial)

Quote:Most of an 1,100-patient cohort (with laboratory-confirmed COVID-19 in 552 hospitals in 30 Chinese provinces through Jan. 29) hospitalized in China for COVID-19 did not initially have fever, and many had no radiologic abnormalities....
Cough was the most common symptom, with over two-thirds presenting with cough upon admission.
Interestingly, only about 40% presented with fever, though nearly all developed fever while hospitalized....
Researchers reported a median incubation period of 4 days.
While ground-glass opacity was the most common finding on chest CT imaging, they added that in 18% of non-severe cases, no radiographic or CT abnormality was found.
Patients stayed in the hospital for a median of 12 days, during which time most received a diagnosis of pneumonia.
Incubation period could only be estimated in 291 patients with documented information.
Also, it was restricted to patients admitted to hospitals and therefore shed no light on characteristics or prevalence of less severe disease for which patients received outpatient care or none at all.

One third admitted to the hospital did not have a cough.
60% admitted to the hospital did not have a fever.
This cohort, however they were chosen, only included hospital patients with confirmed COVID-19.
I'm curious what was necessary for them to be admitted.
Had they already tested positive? If so, what was necessary or sufficient for them to be tested?

Apparently, many of these patients got into the hospitals very early in the disease, before their symptoms fully developed. Presumably that gave them a better chance for a favorable outcome.

RE: Covid-19 considerations - BostonCard - 02-29-2020

Also worth mentioning that in addition to the fact that the CFR are estimates, it depends on both demographic factors (it is now known that the fatality rate for Covid-19 is higher in older people than younger people, so a country with a lot of older people might be expected to have a higher case fatality rate than one with a lot of younger people), and healthcare system factors (the availability of ventilators, for example, would be crucial).

BC

(02-28-2020, 11:33 AM)cardcrimson Wrote: As pneumonia seems to be a big risk with Covid-19, a dumb question from someone who's had pneumonia twice. Will the pneumonia vaccine help the severity of Covid-19, not necessarily with the disease itself? In other words, since I've had the pneumonia vaccine, will it lessen the severity of Covid-19 should I catch it? My guess is that's it's a completely different bug. . . .

Yes, the vaccine you had (pneumovax) protects against pneumonia caused by Pneumococcus, a bacterium. It will not protect you from a Covid-19 pneumonia.

Note that in addition to the pneumonia caused by the virus, at least for influenza, the viral infection makes you prone to a secondary bacterial super-infection (often times with Staph aureus). I would guess that the coronavirus does too, but I haven't seen enough case reports to know for sure.

BC

RE: Covid-19 considerations - Goose - 03-01-2020

(02-29-2020, 09:30 PM)M T Wrote: If you click on that link, the article contains information about which test Wuhan uses (Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) technique) and in what situations is a test done, and the physical collection of a sample. Apparently (only) Hubei Province is also using lung imaging to classify patients as "clinically diagnosed" (detecting "advanced symptoms" which I presume means pneumonia), when the lab tests can't be done. The different testing would seem to make the data messier to analyze.

I haven't looked at the CDC testing protocol.

Unfortunately saying the test uses Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) technique is a bit like saying wine is made by fermentation of grapes. To really compare the tests, one would have to know what the target fragments are and what primers are used. The odds that two different groups tasked with developing a test for the virus would choose the same target fragments and the same primers without coordination in that task are essentially zero. There are lots of different possibilities that will "work", but with different specificity, different false positives, and different sensitivities, as well as different difficulties of manufacturing. Some primer choices even for the same fragment are "better" than others. While there is software that can help with this choice, it is far from an exact science to obtain an "optimal" one. It is also necessary to ensure the primer that is manufactured for general use is really the "same" as the one used to develop the test (not degraded or contaminated in some way). This isn't real hard to do, but with all the time pressure to get the test out there that step may have been skipped, which can add to the confusion.

Normally, validating a test like this is a long process with many testing steps to determine exactly how the test performs. The one test the CDC dropped out (of the original three) was probably present to increase the specificity of the test from say 95% to 99.9%. It wasn't just window dressing. Unfortunately they had trouble with it. Not a big surprise with the time pressure to get this done and in the field. The good news is that PCR testing is pretty common in medicine these days, and many hospitals have the machines that do it. Once you have a "kit" it is a mostly automated process and with validated test works very well. The current tests are being validated "on the fly", which isn't optimal, but is unfortunately necessary.

Note that I am not by any means an expert in this field and the above is derived from conversation with others.

RE: Covid-19 considerations - 82lsju - 03-01-2020

Quote:"Based on that data, the fatality rate in Hubei, the province in which Wuhan sits, was 2.9%. Outside Hubei it was 0.4%.

There are various reasons why the rate in Hubei would be expected to be genuinely higher than elsewhere. Its hospitals had no warning of the sudden influx of covid-19 patients and were thus overwhelmed, whereas hospitals in other cities had more time to prepare, laying in respirators and oxygen. Hubei’s doctors had to work out how to treat a brand-new disease, whereas those elsewhere have been able to learn from both their successes and failures.

But many experts think that a lot of the difference stems from the early-stage small-denominator problem. In other places there has been time and an incentive for less severe cases to be diagnosed, and so the fraction that has proved fatal is lower. At the moment, epidemiologists reckon the true rate for covid-19 is in the range of 0.5-1%. For SARS, a disease caused by another coronavirus which broke out in 2003, the rate in China was never fully ascertained; but worldwide, the WHO put it at about 10%. The rate for seasonal flu in America is typically around 0.1%.

The fatality rate is not an inherent property of the virus; it also depends on the care received. This puts poorer countries at particular risk. They tend to have weaker public-health systems in the first place, and thus can expect higher levels of serious disease and death—including, sometimes, among overstretched and inappropriately protected front-line health-care workers. "

https://www.economist.com/briefing/2020/02/29/covid-19-is-now-in-50-countries-and-things-will-get-worse?fsrc=scn/fb/te/bl/ed/theworldgetsreadycovid19isnowin50countriesandthingswillgetworsebriefing

RE: Covid-19 considerations - OutsiderFan - 03-01-2020

OK, given I totally understand the balance that must be walked between protecting the public, social disruption, and keeping the economy going, I'm not going to come down too hard on public health officials in the U.S. or other countries for how this whole SARS-CoV-2 thing has been managed. It's something kind of unprecedented, and certainly never been seen in the age of corporate and social media insta-sharing. Instead, I will say this is why the CDC screwing up the testing so early in the game is so catastrophic, and why any skepticism I had that this thing is going to ravage the U.S. as much or more as other countries, was removed last week.

(I have no clue why these tweets aren't posting correctly, sorry)

On the topic of testing in South Korea (which is arguably the best source of data so far)
https://twitter.com/BBCLBicker/status/1233701679586922498

Complication rates in South Korea
[tweet]https://twitter.com/BBCLBicker/status/1233721824489267205[/tweet]

This tweet thread is quite sobering, especially for those in the Seattle area.
https://twitter.com/trvrb/status/1233970271318503426

The gist is this thing has been spreading among the population for weeks, all around the world, totally undetected. Governments have assumed that because there weren't many cases confirmed, that meant the spread was minimal. The Washington and South Korean data included here, along with the exploding cases in Iran, Italy, Germany, France, really everywhere, proves the point.

No, it's not THAT deadly. The issue is that with 20% of infected requiring hospitalization, and a R0 so outrageously high, this has the ability to totally overwhelm our health care system. I read the other day the U.S. only has 1,000,000 hospital beds. If just 10% of the population gets it (which is much lower than most epidemiologist projections), that would be 30,000,000 Americans. If 20% require hospitalization, that's 6,000,000 for 1,000,000 beds. And this doesn't even begin to address the cost of everyone needing to pay for that medical care. If there ever was a time for a ounce of prevention being worth a pound of cure, this would seem to be it.

The only way China slowed this was by effectively locking people in their homes. No other country has done this, and even Italy's efforts to contain have seemingly failed, ostensibly because there was too much spread by the time cases were detected, for containment to work. Amazingly, France put out a statement yesterday saying it's not even going to bother with quarantines because they don't work. They have banned gatherings of more than 5,000 people, but I kind of think France is right that quarantines won't work because to have this many cases means it's already spread too much to be contained by quarantines.

RE: Covid-19 considerations - Spiny_Norman - 03-01-2020

(02-29-2020, 09:38 PM)Langdude Wrote:
(02-29-2020, 06:03 PM)Erika Wrote:
(02-29-2020, 04:27 PM)Langdude Wrote: In the town right next to mine - Kirkland...

-m.

Just up the road from me as well. The grocery stores have been crazy all week, everyone is stocking up. So glad I just retired (from UW).

My wife went to CostCo today. No parking. Long lines. Totally sold out of some staples.

-m.

And yet, people still helped themselves to the food samples.

RE: Covid-19 considerations - oldalum - 03-01-2020

(03-01-2020, 10:55 AM)OutsiderFan Wrote: If 20% require hospitalization, that's 6,000,000 for 1,000,000 beds.

keep in mind the spread of infection over time: the 6,000,000 won't need hospital beds all at the same time. I feel reassured that we have enough beds to accommodate 1,000,000 hospitalized coronavirus patients at one time, as long as everyone else agrees not to get sick with anything else. :)

RE: Covid-19 considerations - JustAnotherFan - 03-01-2020

(03-01-2020, 01:59 PM)oldalum Wrote:
(03-01-2020, 10:55 AM)OutsiderFan Wrote: If 20% require hospitalization, that's 6,000,000 for 1,000,000 beds.
keep in mind the spread of infection over time: the 6,000,000 won't need hospital beds all at the same time. I feel reassured that we have enough beds to accommodate 1,000,000 hospitalized coronavirus patients at one time, as long as everyone else agrees not to get sick with anything else. :)

Ha ha .. ha ... ha ...

RE: Covid-19 considerations - M T - 03-01-2020

(03-01-2020, 01:59 PM)oldalum Wrote:
(03-01-2020, 10:55 AM)OutsiderFan Wrote: If 20% require hospitalization, that's 6,000,000 for 1,000,000 beds.
keep in mind the spread of infection over time: the 6,000,000 won't need hospital beds all at the same time. I feel reassured that we have enough beds to accommodate 1,000,000 hospitalized coronavirus patients at one time, as long as everyone else agrees not to get sick with anything else. :)

There are 750,000 staffed beds in acute-care hospitals in the US; about 74,000 in California.

Wuhan (and the world) had patient 0 get sick on 1 December. They're 3 months into this. Wuhan got locked down 7 weeks later (23 Jan) and have been locked down for 36 days at this point. Wuhan (pop 11M) still has 6400 serious patients. (If you want to compare, Santa Clara County is 2M, 9-county SF Bay Area is 7.75M, Calif is 39.5M).

I made a spread sheet of the daily data published by China for Wuhan and Hubei for 13 Feb to 29 Feb in case anyone wants a copy. deaths/(deaths + hospital discharges of confirmed cases) over the last 7 days is a rough CFR of 3%, but that number continues to fall (whether detection, treatment, care, less overload, I don't have evidence). Daily new cases are roughly 600. They are discharging roughly 1700/day. Their high water mark for hospitalized was about 38,000, with a peak of serious cases about 9700.

As I said in another post, it appears they are hospitalizing a significant percentage of patients before a fever and/or cough appears, with a median incubation of 4 days (for that one study's cohort). My guess is they are testing exposed people and putting positive tests in the hospital.

It appears the US has chosen, from the first few patients, to have positive-test patients stay at home, presumably unless/until they become serious.
As I understand it, a fever is required before the CDC will do a test.