Wuhan Coronavirus

[T-Rock]

"I think most people aren’t aware of the risk of systemic healthcare failure due to #COVID19 because they simply haven’t run the numbers yet. Let’s talk math."
"Let’s conservatively assume that there are 2,000 current cases in the US today, March 6th. This is about 8x the number of confirmed (lab-diagnosed) cases. We know there is substantial under-Dx due to lack of test kits; I’ll address implications later of under-/over-estimate."
"We can expect that we’ll continue to see a doubling of cases every 6 days (this is a typical doubling time across several epidemiological studies). Here I mean *actual* cases. Confirmed cases may appear to rise faster in the short term due to new test kit rollouts."
"We’re looking at about 1M US cases by the end of April, 2M by ~May 5, 4M by ~May 11, and so on. Exponentials are hard to grasp, but this is how they go."
"As the healthcare system begins to saturate under this case load, it will become increasingly hard to detect, track, and contain new transmission chains. In absence of extreme interventions, this likely won’t slow significantly until hitting >>1% of susceptible population."
"What does a case load of this size mean for healthcare system? We’ll examine just two factors — hospital beds and masks — among many, many other things that will be impacted."

[Pete]

Originally Posted by grog18b

Saw a good documentary on the Spanish Flu of 1918... Healthy dudes in their 20s were diagnosed at 10am and dead by 4pm... after the first symptoms appeared.

It was a few years back and I don't remember the details but it was an article on how hard it was to find a sample of the Spanish Flu. Something about a National Guard(?) unit stationed in the middle of nowhere above the arctic circle and a number of troops who died from the flue where buried in a small cemetery.

The article was focused on if it would be ethical to dig them up to study the flue.

[T-Rock]

"The US has about 2.8 hospital beds per 1000 people. With a population of 330M, this is ~1M beds. At any given time, 65% of those beds are already occupied. That leaves about 330k beds available nationwide (perhaps a bit fewer this time of year with regular flu season, etc)."
"Let’s trust Italy’s numbers and assume that about 10% of cases are serious enough to require hospitalization. (Keep in mind that for many patients, hospitalization lasts for *weeks* — in other words, turnover will be *very* slow as beds fill with COVID19 patients)."
"By this estimate, by about May 8th, all open hospital beds in the US will be filled. (This says nothing, of course, about whether these beds are suitable for isolation of patients with a highly infectious virus.)"
"If we’re wrong by a factor of two regarding the fraction of severe cases, that only changes the timeline of bed saturation by 6 days in either direction. If 20% of cases require hospitalization, we run out of beds by ~May 2nd."
"If only 5% of cases require it, we can make it until ~May 14th. 2.5% gets us to May 20th. This, of course, assumes that there is no uptick in demand for beds from *other* (non-COVID19) causes, which seems like a dubious assumption."

[T-Rock]

"As healthcare system becomes increasingly burdened, Rx shortages, etc, people w/ chronic conditions that are normally well-managed may find themselves slipping into severe states of medical distress requiring intensive care & hospitalization. But let’s ignore that for now."
"Alright, so that’s beds. Now masks. Feds say we have a national stockpile of 12M N95 masks and 30M surgical masks (which are not ideal, but better than nothing)."
"There are about 18M healthcare workers in the US. Let’s assume only 6M HCW are working on any given day. (This is likely an underestimate as most people work most days of the week, but again, I’m playing conservative at every turn.)"
"As COVID19 cases saturate virtually every state and county, which seems likely to happen any day now, it will soon be irresponsible for all HCWs to not wear a mask. These HCWs would burn through N95 stockpile in 2 days if each HCW only got ONE mask per day."
"One per day would be neither sanitary nor pragmatic, though this is indeed what we saw in Wuhan, with HCWs collapsing on their shift from dehydration because they were trying to avoid changing their PPE suits as they cannot be reused."
"How quickly could we ramp up production of new masks? Not very fast at all. The vast majority are manufactured overseas, almost all in China. Even when manufactured here in US, the raw materials are predominantly from overseas... again, predominantly from China."

[T-Rock]

"Keep in mind that all countries globally will be going through the exact same crises and shortages simultaneously. We can’t force trade in our favor."
"Now consider how these 2 factors – bed and mask shortages – compound each other’s severity. Full hospitals + few masks + HCWs running around between beds without proper PPE = very bad mix."
"HCWs are already getting infected even w/ access to full PPE. In the face of PPE limitations this severe, it’s only a matter of time. HCWs will start dropping from the workforce for weeks at a time, leading to a shortage of HCWs that then further compounds both issues above."
"We could go on and on about thousands of factors – # of ventilators, or even simple things like saline drip bags. You see where this is going."
"Importantly, I cannot stress this enough: even if I’m wrong – even VERY wrong – about core assumptions like % of severe cases or current case #, it only changes the timeline by days or weeks. This is how exponential growth in an immunologically naïve population works."
"Undeserved panic does no one any good. But neither does ill-informed complacency. It’s wrong to assuage the public by saying “only 2% will die.” People aren’t adequately grasping the national and global systemic burden wrought by this swift-moving of a disease."
"I’m an engineer. This is what my mind does all day: I run back-of-the-envelope calculations to try to estimate order-of-magnitude impacts. I’ve been on high alarm about this disease since ~Jan 19 after reading clinical indicators in the first papers emerging from Wuhan."
"Nothing in the last 6 weeks has dampened my alarm in the slightest. To the contrary, we’re seeing abject refusal of many countries to adequately respond or prepare. Of course some of these estimates will be wrong, even substantially wrong."
"But I have no reason to think they’ll be orders-of-magnitude wrong. Even if your personal risk of death is very, very low, don’t mock decisions like canceling events or closing workplaces as undue “panic”."

[T-Rock]

"These measures are the bare minimum we should be doing to try to shift the peak – to slow the rise in cases so that healthcare systems are less overwhelmed. Each day that we can delay an extra case is a big win for the HC system."
"And yes, you really should prepare to buckle down for a bit. All services and supply chains will be impacted. Why risk the stress of being ill-prepared?"
"Worst case, I’m massively wrong and you now have a huge bag of rice and black beans to burn through over the next few months and enough Robitussin to trip out."
"One more thought: you’ve probably seen multiple respected epidemiologists have estimated that 20-70% of world will be infected within the next year. If you use 6-day doubling rate I mentioned above, we land at ~2-6 billion infected by sometime in July of this year."
"Obviously I think the doubling time will start to slow once a sizeable fraction of the population has been infected, simply because of herd immunity and a smaller susceptible population."
"

[T-Rock]

Hopefully they're wrong
But if not, best be prepared. Lol.

Edited to add:
It's a moving target and the true numbers won't come out till next year, but the trend hasn't really changed too much.
3526 Deaths ÷ 104,144 confirmed cases x 100 = CFR.
Unless the reported numbers are wrong (more than likely will be a year from now), we're still looking at a 3.3856967276% mortality rate, roughly 333 times more deadly than the Flu.
https://www.worldometers.info/coronavirus/

[InTheBlack]

Originally Posted by Pete

It was a few years back and I don't remember the details but it was an article on how hard it was to find a sample of the Spanish Flu. Something about a National Guard(?) unit stationed in the middle of nowhere above the arctic circle and a number of troops who died from the flue where buried in a small cemetery.

The article was focused on if it would be ethical to dig them up to study the flue.

They did & it was quite a while ago.

[InTheBlack]

Happy to see the stats on hospital beds, use rate, etc from Liz Specht. Still would like to see her sources though.

Another numbers run:
Seasonal flu so far this season:
https://www.cdc.gov/flu/about/burden...-estimates.htm

34,000,000 – 49,000,000 illnesses
16,000,000 – 23,000,000 medical visits
350,000 – 620,000 medical stays
20,000 – 52,000 deaths

And my browser says "The United States is the third most populous country in the world, with an estimated population of 330,149,796 as of December 16, 2019. "

If COVAN-19 is like seasonal only 10x as deadly (Of course, mostly in the older cohort) then 200,000 to 500,000 deaths. Assuming 80% cases trivial, then maybe not so much load on the overall system for visits & non-fatal hospital stays.

Not sure what to think about infectivity. Less than seasonal or several times? Slower rate is better.

OTOH if 40% get it & the ratio of fatalities is the same as seasonal, then
330M x 40% = cases x (pick % fatal)
say .001 fatal, just like seasonal flu.
then 132,000 fatalities.
But very overloaded system due to admissions.
Which will increase the fatalities by some % (or multiplier) due to lack of medical care.

EDIT:

"As of this story the death rate in South Korea is around .625%"

Say that this is culling the weakest first & true rate is half that:

So 0.003125 x 40% x 330M = 412,500.

[Old Dog New Trick]

China is just having a tough go on this. Must be bad karma for all that intellectual property theft over the years.

Hotel converted to Coronavirus quarantine collapsed.
https://apple.news/AiysF4Ri-Rp6sj7sMw8NKGA

[InTheBlack]

Fascinating article:

https://bedford.io/blog/ncov-cryptic-transmission

Cryptic transmission of novel coronavirus revealed by genomic epidemiology
2 Mar 2020 by Trevor Bedford

...
Knowing that transmission was initiated on Jan 15 allows us to estimate the total number of infections that exist in this cluster today. Our preliminary analysis puts this at 570 with an 90% uncertainty interval of between 80 and 1500 infections.
...
We know that Wuhan went from an index case in ~Nov-Dec 2019 to several thousand cases by mid-Jan 2020, thus going from initial seeding event to widespread local transmission in the span of ~9-10 weeks. We now believe that the Seattle area seeding event was ~Jan 15 and we're now ~7 weeks later.

I expect Seattle now to look like Wuhan around ~1 Jan, when they were reporting the first clusters of patients with unexplained viral pneumonia.

We are currently estimating ~600 infections in Seattle, this matches my phylodynamic estimate of the number of infections in Wuhan on Jan 1. Three weeks later, Wuhan had thousands of infections and was put on large-scale lock-down.

However, these large-scale non-pharmaceutical interventions to create social distancing had a huge impact on the resulting epidemic. China averted many millions of infections through these intervention measures and cases there have declined substantially.

[T-Rock]

You can follow updates that "Trevor Bedford" posts in the link below. He's from Seattle Washington and a no knee jerk reactionary. He's with these folks:
https://bedford.io/team/


And they have done some awesome research genetically mapping SARSCov-2, and he usually posts their teams findings on his Twitter page, although I don't twit, nor have a twit page. He's a scientist, and "hopefully" unbiased:
https://mobile.twitter.com/trvrb . Read his page regularly.

[InTheBlack]

https://www.medrxiv.org/content/10.1....01.20029819v2

Posted March 05, 2020.

COVID-19 Epidemic Outside China: 34 Founders and Exponential Growth
Yi Li, Meng Liang, Xianhong Yin, Xiaoyu Liu, Meng Hao, Zixin Hu, Yi Wang, Li Jin

doi: https://doi.org/10.1101/2020.03.01.20029819
This article is a preprint and has not been peer-reviewed

Abstract

Background: In December 2019, pneumonia infected with a novel coronavirus burst in Wuhan, China. Now the situation is almost controlled in China but is worse outside China. We aimed to build a mathematical model to capture the global trend of epidemics outside China.

Methods: In this retrospective, outside-China diagnosis number reported from Jan 21 to Feb 28, 2020 was downloaded from WHO website. We develop a simple regression model on these numbers: log10 (Nt+34)=0.0515*t+2.075 where Nt is the total diagnosed patient till the ith day, t=1 at Feb 1.

Findings: Based on this model, we estimate that there have been about 34 unobserved founder patients at the beginning of spread outside China. The global trend is approximately exponential, with the rate of 10 folds every 19 days.

[InTheBlack]

https://www.medrxiv.org/content/10.1....20.20025866v2

Posted March 06, 2020.

Estimating the Asymptomatic Proportion of 2019 Novel Coronavirus onboard the Princess Cruises Ship, 2020

Kenji Mizumoto, Katsushi Kagaya, Alexander Zarebski, Gerardo Chowell
doi: https://doi.org/10.1101/2020.02.20.20025866
This article is a preprint and has not been peer-reviewed

Abstract

The potential infectiousness of asymptomatic COVID-19 cases together with a substantial fraction of asymptomatic infections among all infections, have been highlighted in clinical studies.

We conducted statistical modeling analysis to derive the delay-adjusted asymptomatic proportion of the positive COVID-19 infections onboard the Princess Cruises ship along with the timeline of infections.

We estimated the asymptomatic proportion at 17.9% (95% CrI: 15.5%-20.2%), with most of the infections occurring before the start of the 2-week quarantine.

...

the asymptomatic proportion, which is broadly
defined as the proportion of asymptomatic infections among all the infections of the
disease. Indeed, the asymptomatic proportion is a useful quantity to gauge the true
burden of the disease and better interpret estimates of the transmission potential. This
proportion varies widely across infectious diseases, ranging from 8% for measles and
32% for norovirus up to 90-95% for polio [4-6]. Most importantly, it is well established
that asymptomatic individuals are frequently able to transmit the virus to others [7-8].
...

Out of the 634 confirmed cases, a total of 306 and 328 were reported to be
symptomatic and asymptomatic, respectively. The proportion of asymptomatic
individuals appears to be
16.1 % (35/218) before February 13,
25.6 % (73/285) on February 15,
31.2 % (111/355) on February 16,
39.9% (181/454) on February 17,
45.4% (246/542) on February 18,
51.9% (322/621) on February 19 and
51.7% (328/634) on February 20 (Table 1)
...

The reported asymptomatic cases consists of both true asymptomatic infections and
symptomatic cases that had not yet developed symptoms at the time of data collection,
i.e., the data is right-censored.
...

Our estimated asymptomatic proportion is at 17.9% (95% CrI: 15.5%–20.2%),
which overlaps with a recently derived estimate of 33.3% (95% CI: 8.3%–58.3%) from
data of Japanese citizens evacuated from Wuhan [13].
...

Our study is not free from limitations.

First, laboratory tests by PCR were
conducted focusing on symptomatic cases especially at the early phase of the quarantine.
If asymptomatic cases where missed as a result of this, it would mean we have
underestimated the asymptomatic proportion.

Second, it is worth noting that the data of
passengers and crews employed in our analysis is not a random sample from the general
population. Considering that most of the passengers are 60 years and older, the nature of
this age distribution may lead to underestimation if older individuals tend to experience
more symptoms. An age standardized asymptomatic proportion would be more
appropriate in that case.

Third, the presence of symptoms in cases with COVID-19 may
correlate with other factors unrelated to age including prior health conditions such as
cardiovascular disease, diabetes, immunosuppression. Therefore, more detailed data
documenting the baseline health of the individuals including the presence of underlying
diseases or comorbidities would be useful to remove the bias in estimates of the
asymptomatic proportion.

[Badger52]

Local/regional outlets have it also, this is from the AP. Some other scattered reports indicate that facility or area has upwards of 30 healthcare folks out on self-quarantine now as well.

MSM will be along in awhile to cover it after they sort out their Clown Show 2020 "March to Milwaukee!"™ coverage for the weekend. (What to tell you, when, by who, etc.)

Screw it; headed out to enjoy the day, kinda like yesterday.