Tag Archives: ncov19

SARS2 and Animals

Posted by xaminmo
This CNET Article discusses research on SARS-CoV-2 in several common animals, as well as a bit of history on the virus.  The article also discusses the animal origins of this virus, and a quick summary to date. A limited number of animals have been tested for and proven to be infected by the virus.  No proof of humans catching it back from animals has happened.  Very little study has occurred on the communicablility, and it was initially thought to be no risk.
 
The jist of the research paper is that adults and juvenile cats can get it the same as humans; young cats and ferrets can get it just in the upper respiratory tract (sinuses, tonsils), but not the lower respiratory tract. Dogs can technically get it, but are not very susceptible. It does not stay in them long. Ducks, pigs, pidgeons, etc are not susceptible at all. 
 
Another group did computer modeling of 253 animals’ ACE2 receptors to see what other animals we should investigate as possible transmission vectors.  
  • Human, Flying Fox, Horseshoe Bat, Lynx, Civet, Cat, Swine, Pangolin, Cow, Buffalo, Mustela (ferrets, weasles, etc), Goats, Sheep, ACE2 were clustered with humans.
  • Mice, birds, reptiles, etc were not, and mice were proven not susceptible.
  • Civet and Bat have been implicated in SARS1 sources, and Pangolin and Bat for SARS2 sources.

     SARS2 ACE2 Phylology Chart

This chart shows the ACE2 receptors that conserve the same binding sites as humans. They suspect that 50% and above “could” harbor the virus, but that birds generally are not a reservoir for betacoronaviruses. We see in other research that dogs, at 90%, are poor carriers, and clear the virus within 4 days. Swine were not actually susceptible, and ferrets were not able to get it into their lungs. The mechanism of those differences is unknown.

SARS2 ACE2 Phylology similarities


CV19 April 3

Posted by xaminmo

CV19 Pandemic Update for 2020-04-03

I did not make screenshots of my favorite graphs, but check out http://91-divoc.com/pages/covid-visualization/ and play with log vs normal, and etc on the interactive graphs.  Deaths and confirmations log chart is very visibly bending in the right direction. We still have a ways to go.

Executive Summary:

  • Worldwide, 1,095,917 confirmed cases and 58,787 deaths, which is within 1% of the 1-day estimate.
  • US is 275k infected, and 7382 dead, which is also within 1% of 1-day estimates.
  • China probably has ~400k unconfirmed cases, and ~16,500 unconfirmed deaths.
  • We need our confirmed and death exponents to fall to as close to 100% as possible. (vs 113% & 119% respectively).
  • US & TX confirmed exponents are stalled in the 113% range. The death date exponent has not yet fallen, averaging over 120%.
  • US deaths per confirmed case continues to increase, and will do so until as far as 47 days after the last new infection.
  • Many places in the US extended their stay-at-home plans to May 20.

1-Day Estimate for April 3
Non-China 1,018,824/56,704; Italy 120,107;14,719; USA 277,775/7,382; TX 5,900/90; ME 411/8
SD Adjusted USA 287,625/7,557; Texas 6,139/100

Actual April 3
Non-China 1,013,406/55,461; Italy 119,827/14,681; USA 275,586/7,087; TX 5,734/100; ME 432/9

1-Day Estimate for April 4
Non-China 1,103,432/61,938; Italy 124,594/15,489; USA 311,960/8,475; TX 6,486/130; ME 496/9
SD Adjusted USA 318,885/9,052; Texas 6,853/129

7-day Estimate for April 8
non-China 1,917,505/109,549; Italy 169,991/23,851; USA 745,176/25,239; Texas 15,874/306; Maine 656/26
SD Adjusted USA 707,819/21,874; Texas 14,357/317
This is falling due to our curve getting flatter. US 500k, TX 11.2k

Commentary:

Day to Day deaths are still climbing nationally. No consistent major slowing there. CA and NY/NJ/MA areas have a lot going on. It may take some time for them to dig out of this.

After lockdown, confirmed cases take 9-12 days to be affected, and deaths another 8-11 days after that. Anywhere that is overloaded will have a higher death rate, which may offset this prediction

As expected with the slow-down in spread, our mortality rate keeps climbing. 1.44%, 1.55%, 1.67%, 1.75%, 1.84%, 2.06%, 2.23%, 2.43%, 2.57%.

Inflection point for outbreaks with an R0 of 2.2 is 60% of the population becoming immune. Divide that by whatever you think our detection rate is. I think we get about 38%, so maybe 75m people in the US showing as confirmed. In other words, we are clamping down on the spread. It is not slowing due to going through the bulk of the population. If we all started mingling again tomorrow, we would see a big surge in cases 2 weeks later.

Average is 6 days to onset and 14 days from onset to death for those who do not survive. Social distancing data lags by 3-5 days. Statistics lag by 1 day. Detection lags by 9-12 days. Impact delay of social distancing on confirmations MAY BE 9 days. The correlation is fuzzy, but may be around 9 days lag.

Research for improving mortality rates could put things back to normal, but we are not there yt. Even if it is solved now, logistics of getting it deployed are not instantaneous.

Spreadsheet is updated, and downloadable here:
https://drive.google.com/file/d/1vocCN445AZyVBBLsv0kJR8ZDP9DM0UST/view

My favorite charts:
http://91-divoc.com/pages/covid-visualization/
https://www.unacast.com/covid19/social-distancing-scoreboard

Additional Data Sources:
https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data
https://github.com/COVID19Tracking/covid-tracking-data/tree/master/data
https://ourworldindata.org/covid-testing

China Underreporting Claims:
I do not think this is willful deception, so much as, they are only reporting what they can confirm. It just happens that they can confirm only a small subset of the infections prior to March.

China cremation rates, I lost the URL for the older data, but current data is here:
http://mzj.wuhan.gov.cn/tjxx/387166.jhtml
2019    Number of cremated remains    JZH014221000    56,007
It varies by about 2500 per quarter, so roughly 5k per month in Wuhan province.

The number of urns and cremations are very high, and “the funeral homes are unable to keep up.”
https://www.bloomberg.com/news/articles/2020-03-27/stacks-of-urns-in-wuhan-prompt-new-questions-of-virus-s-toll
https://english.alarabiya.net/en/features/2020/03/31/Delivery-of-5-000-urns-undermines-China-s-coronavirus-official-death-toll-Report
http://www.asianews.it/news-en/Wuhan,-endless-queues-for-ashes-of-coronavirus-dead-cast-doubts-on-numbers-49673.html

There are multiple sources indicating people who were not checked into a hospital were not counted.
Journalistic sources include
https://www.rfa.org/english/news/china/cremate-02142020105822.html
https://www.scmp.com/news/china/society/article/3050311/its-pneumonia-everybody-china-knows-about-many-deaths-will-never
https://www.who.int/bulletin/volumes/84/3/news30306/en/

I did not save teh ones from February where the WHO felt they were underestimating because they had no way to count those otuside of the hospitals. They said 4-8 times higher rates were likely.

This exclusion has been common in other countries, including Italy, Iran, etc:
https://www.wsj.com/articles/italys-coronavirus-death-toll-is-far-higher-than-reported-11585767179
https://www.space.com/iran-coronavirus-graves-satellite-images.html


CV19 US Hospitalization Rates

Posted by xaminmo

CV19 Pandemic Update!

US has stepped up testing rapidly, and so while social distancing is at -40%, we still show +1% of the new model prediction.

03-26 Thursday
1-day Projection: WW 524523/24175; PRC 81731/3289; NON 442792/20886; IT 79988/8254; US 80513/1257; TX 1582/19 non+IT 1.2%, US 5.1%
1-Day Distancing: WW 524523/24175; PRC 81731/3289; NON 442792/20886; IT 79988/8254; US 82170/1244; TX 1632/20 TX 5% high, US 2% low
Actual Numbers: WW 529591/23970; PRC 81782/3291; NON 447809/20679; IT 80589/8215; US 83836/1209; TX 1563/21

The rapid rise in US testing (127% per day average) may numerically counter the decrease in disease spread from social distancing (-40%). I hope that is factored into the policy plans, because it may look a lot more spooky over the next week than it really is.

03-27 Friday
1-Day Projection: WW 601509/27192; PRC 81903/3297; NON 519605/23895; IT 87309/8995; US 106851/1552; TX 1988/29
1-Day Distancing: WW 601509/27192; PRC 81903/3297; NON 519605/23895; IT 87309/8995; US 103554/1554; TX 1971/27
1=Day US Prototype: Positive: 89,618 Negative: 486,863 Pending: 66,880 Hospitalized: 13,923 Dead: 1,471

I added the Number of Tests and number hospitalized in the US to the spreadsheet. This is somewhat complete for the US and TX, but other countries are hit or miss. Those checkpoint earlier in the day than other stats, but that is fine. Those are much better numbers to track hospital overload than trying to extrapolate from confirmed cases, but much less data. I am still tweaking it all.

Midday Thursday, the US had 10131 hospitalized, and 1163 dead from COVID-19. The rates of increase of these are still climbing at the typical 135% per day. There is not yet a clear correlation between social distancing and death or hospitalization rates, but I am still testing ideas.

Since I only have that for the whole US, I am still tracking confirmed, death, and projecting with social distancing in the main sheet.

2020-04-01 7-day Comparison
7-Day Projection: WW 1169645/61852; PRC 82134/3338; NON 1087512/58514; IT 157313/19560; US 477863/6398; TX 9131/162
7-Day Distancing: WW 1169645/61852; PRC 82134/3338; NON 1087512/58514; IT 157313/19560; US 232880/4603; TX 5875/72
7-Day US Prototype: Positive: 134,035 Negative: 728,160 Pending: 100,028 Hospitalized: 68,262 Dead: 4,770 Overrun: 04-06 295-335k

The old formula pushes Texas overrun slightly further out for late-stage events:

04-06 29k TEXAS ICU OVERRUN STAGE 1
04-07 36k TEXAS VENT OVERRUN STAGE 1
04-12 146k TEXAS ICU STG3
04-13 178k TEXAS VENT STG3 & Hosp STG1
04-16 400k may be the inflection point for Texas if 14% like China, but our death rate is lower than theirs or the world.
04-17 532k TEXAS HOSP STG3
04-20 1.2m Inflection point for R0 of 2.2 is 60% with detection rate of 39.08

The new distancing prototype formula looks like this after tweaking:

04-15 2929 TEXAS ICU OVERRUN STAGE 1
04-17 1787 TEXAS VENT OVERRUN STAGE 1
05-02 2929 TEXAS ICU OVERRUN STAGE 3
05-03 1787 TEXAS VENT OVERRUN STAGE 2
05-04 26633 TEXAS HOSPITAL OVERRUN STAGE 1
05-09 4550 TEXAS VENT OVERRUN STAGE 3
05-09 400k may be the inflection point for Texas if 14% like China, but our death rate is lower than theirs or the world.
05-16 26633 TEXAS HOSPITAL OVERRUN STAGE 2
06-05 47441 TEXAS HOSPITAL OVERRUN STAGE 3
05-21 1.2m Inflection point for R0 of 2.2 is 60% with detection rate of 39.08

The growth in hospitalizations puts overrun at 04-06. I do not know what to believe.

Here are the milestones from 04-23 data for comparison to track our progress flattening the curve:

04-06 33k TEXAS ICU OVERRUN STAGE 1
04-07 45k TEXAS VENT OVERRUN STAGE 1
04-10 150k TEXAS VENT/ICU STG2 & Hosp STG 1
04-13 366k TEXAS VENT/ICU STG3 & Hosp STG 2
04-15 660k TEXAS Hosp STG 3

Milestones are based on guesstimates: TX 28.7m pop; 2.9 beds per 1000 in TX (83230); 32% unoccupied (26633) / 11% are ICU (2929); 6.7% ventilators (1787); 10% limited function ventilation (2663) / 5-15% conf need hosp(532k-177k @ overrun); 2-10% ICU (29k-146k); 1-5% need vent (36k-178k)

Testing has ramped up substantially, and the US has a capacity around 350k tests per week, or 50k per day. The increased testing, and the shift in social distancing makes these numbers more fuzzy. I tweaked my multipliers for regression testing.

Our hospital load may be 31.86% of the world average for the same number of confirmed. Korea had 8652 confirmed from 316664 tests on 03-20 with 94 deaths. Their death rate is 1.42%. Ours is 1.44% with 579k tests, 83836 confirmed, 1209 deaths. The world rate is 4.52% I suppose that the death to confirmed case is tied to the test percentage.

Inflection point for R0 of 2.2 is 60% of the population, times the percentage of infected people who get confirmed. It was estimated elsewhere that China at 4.02% mortality rate per confirmed was 14% tested. That means our hospital load will be 35.82% for the same number of confirmed, or that our confirmed cases are 39.08% of our total cases.

TX has 28.7 million, and 39.08% of that is 1.12 million as our inflection point.

Unknown accuracy because testing inputs are changing, and I am just making things up.

Social distancing data lags by 3 days. Statistics lag by 1 day. Detection lags by 9-12 days. Impact delay of SD on Confirmations is 9 days.

https://drive.google.com/file/d/1vocCN445AZyVBBLsv0kJR8ZDP9DM0UST/view


Social Distancing Dashboard

Posted by xaminmo
This site uses anonymous mobile phone data to calculate the change in miles traveled, and the change in number of mobile phone encounters. It is an earlier predictor of how well social distancing is working, without having to wait 12 days for the confirmed cases stats to change, nor worry about changes in testing frequency or methodology.
 
It’s really a green-light instantaneous dashboard kind of thing. They don’t expose trending data, or even numerical data, so you cannot chart, trend, or predict off of this.
 

CV19 no big deal

Posted by xaminmo
A good question I saw and responded to is “Hardly anyone is sick, and hardly anyone has died. Why is everyone all panicky about CV19? What’s missing?”
 
TLDR: It spreads exponentially, and while you have no symptoms. Listen to the experts if you don’t understand. Don’t be a party to manslaughter.
 
NARRATIVE: The missing part is that it’s an exponential spread. It’s like the old puzzle, there’s one lily pad on a pond, and every day, each lily pad becomes two. It takes 30 days to cover the pond. When is the pond half covered? 29 days.
 
Today, the absolute numbers look very mild right now, and that’s what we like. We want them to stay mild, but any action we take will not have an effect for 12 days. Also, number reporting lags by 1 day. 13 days before the end looks like just any other day in paradise. We’re not doubling every day. We’re doubling every 2.2 days.
 
For the US, we are 10 days from overloading hospital capacity, and 14 days from overloading even reserve, crappy capacity. When we overload the hospital capacity, the death rate quadruples. That’s why it became such a panic.
 
Luckily, the declaration of pandemic was on the 11th, which just started to show up in the numbers yesterday. We’ll know by late Thursday if the declaration of national emergency made an impact. The goal is to keep the number of people in the hospital below the threshold where a lot of extra people die. Right now, that looks so far off, but if we didn’t drastically slow the spread, that would start to look grim for the worst survivable cases around April 5, and by April 15 would be just letting the really sick asphyxiate. I say “didn’t” rather than “don’t” because the time to take action has already passed.
 
It’s easy to ignore when 85% of the people infected simply are not counted, and when only 10% of the counted people are at risk of dying from a hospital overload. However, that amounts to 2-5 million people in the US potentially dying from this. With that many, chances are one of them would be a close friend or family member. If it happens to you, then you would definitely care, and you would not care that it was because a bunch of people didn’t understand exponential math.
 
The panic is because a bunch of us care even when it’s not someone close to us, or we can see that it could happen to us. There are a lot of asymptomatic carriers, spreading the disease. So “I feel fine, I don’t need to quarantine” has already lead to deaths, and will lead to many more deaths.
 
It wouldn’t be God’s Will, or bad luck. It would be a willful choice of people to ignore the experts because the non-experts didn’t understand, and therefore decided the experts were not actually experts. Reckless action leading to the death of others is called manslaughter, and negligent action leading to death is called negligent homicide. Purposefully infecting someone would be called murder.
 
Lag times per Feb 7 study in JAMA from Wang et al:
Median time from first symptom to dyspnea was 5.0 days
to hospital admission was 7.0 days
to acute respiratory distress syndrome was 8.0 days.
For survivors, the median hospital stay was 10 days.
https://jamanetwork.com/journals/jama/fullarticle/2761044
 
Lag times per Jan 22 report by China National health:
Median days from first symptom to death were 14 (range 6-41)
70 year old or above (11.5 [range 6-19] days)
below 70 year old (20 [range 10-41] days.
https://onlinelibrary.wiley.com/doi/full/10.1002/jmv.25689?af=R
 
The average is 12 days to show up in the stats, and 20 days start to finish, so that’s what most stats focus on. Policy changes consistently take 12 days to show up in the stats. I’m not sure where that first started, but you can look at the raw numbers and see it. It is self evident.

SARS-2 March 24 Update

Posted by xaminmo

First, the update:

03-24 Tuesday
1-day Projection: WW 425953/18600; PRC 81595/3283; NON 346031/15382; IT 69104/6744; US 57310/731; TX 916/10
Actual Numbers: WW 417966/18615; PRC 81591/3281; NON 336375/15334; IT 69176/6820; US 53740/706; TX 955/12

03-25 Wednesday
1-day Projection: WW 461807/21005; PRC 81686/3288; NON 381238/17782; IT 74856/7654; US 66137/903; TX 1203/16

Infection spread appears to be reducing in US and TX, even though TX was above projections for yesterday.
US shows 134% instead of 135%, and the last 3 days were 130%, 131%, and 123%.
TX shows 135% instead of 147%, and the last 3 days were 108%, 121%, and 126%.

This implies that the declaration of pandemic may have had positive effect.

The numbers from tonight or tomorrow will start reflecting any changes caused by the declaration of national emergency.

Milestones would have pushed out a day, but my methodology was poor. I now show the number for the condition in the left of the note, not the estimated number for that day. Also, I dropped stage 2 here, and just show worst case reserve (smallest number) and best case reserve (largest number). I do not have proper numbers to separate stage 1 (over standard) vs stage 2 (over minimum reserve).

04-05 29k TEXAS ICU OVERRUN STAGE 1
04-06 36k TEXAS VENT OVERRUN STAGE 1
04-10 146k TEXAS ICU STG3
04-11 178k TEXAS VENT STG3 & Hosp STG1
04-14 400k may be the inflection point for Texas
04-15 532k TEXAS HOSP STG3

Milestones are based on guesstimates, because the exact number of ICU beds and placement of ventillators is proprietary data that is hard to find and confirm. My estimates are based on: TX 28.7m pop; 2.9 beds per 1000 in TX (83230); 32% unoccupied (26633) / 11% are ICU (2929); 6.7% ventilators (1787); 10% limited function ventilation (2663) / 5-15% conf need hosp(532k-177k @ overrun); 2-10% ICU (29k-146k); 1-5% need vent (36k-178k)

Testing infrastructure may fail before the inflection point, leading to a false decrease in numbers reported. If that happens, we may not numerically reach the inflection point, which is 60% of the population for R0 of 2.2. Remember, we only confirm 12-15% of the actual cases, as many are mild or even asymptomatic, but are still infectious to others.

I expect these to move further out each of the next few days, and then it will probably look like it levels off a bit for several days before reducing further.

We are not out of the woods. Hospital usage is 1-4 weeks. Average infection course is 20 days with no hospitalization, but once people are bad enough to need O2 or ventilation, it takes longer to recover well enough to not need it anymore.  If we were to fall to 112% today (unrealistic extreme) and stay there, the milestone dates become 04-23, 04-25, 05-07, 05-09, 05-16, 05-18. That spreads out enough that we may gain an extra couple of days on each due to early cases resolving (people do not stay in the hospital forever).

The current milestones for the US, since TX is about 9% of the US:
03-31 29k -> 322k US ICU OVERRUN STAGE 1
03-31 36k -> 400k US VENT OVERRUN STAGE 1
04-05 146k -> 1622k US ICU STG3
04-06 178k -> 1977k US VENT STG3
04-08 400k -> 4444k US inflection point
04-09 532k -> 5800k US HOSP STG 2

These are MUCH more fuzzy, since it is not exactly 9%, and ICU, Vent and bed capacities vary. That adds 1-2 days uncertainty. This also will be affected by any changes in the numbers as discussed above.

Here are the milestones from 04-23 data for comparison to track our progress flattening the curve:
04-06 33k TEXAS ICU OVERRUN STAGE 1
04-07 45k TEXAS VENT OVERRUN STAGE 1
04-10 150k TEXAS VENT/ICU STG2 & Hosp STG 1
04-13 366k TEXAS VENT/ICU STG3 & Hosp STG 2
04-15 660k TEXAS Hosp STG 3

NOTE that the very first milestone was 04-02 based on 570 ICU beds, and was abandoned as a predictor.

When testing and behavior are nonchanging:
Model is +/- 25% per week
That is +/- 1.5 days for stage 1
That is +/- 2.5 days for stage 2
That is +/- 3.5 days for stage 3

Inflection point for R0 of 2.2 is 60%.
Current reporting rate is 12-15%.
Assuming we keep testing by same criteria, the Tx inflection point is 400k confirmed.
We may not reach this numerically due to testing/infrastructure failure.
eg, we may reach stage 3 while our confirmed rate is much lower, but still around the same days.

This is all bistromath, and both reporting rates, and trends are changing daily at this point.

Also note that the numbers lag by up to 24 hours based on reporting systems.

Also Also note that it still takes around 12 days for action changes to affect trends, since people infected today will not be detected for a while.

Also Also Also note that there are many people who have NO symptoms at all, but are still infecting others. This, along with poor testing, explains the 12-15% confirmation rate.

https://drive.google.com/file/d/1vocCN445AZyVBBLsv0kJR8ZDP9DM0UST/view


Overrun Planning

Posted by xaminmo

Stats for Sunday, Monday, and predictions for Tuesday, and Texas hospital overruns.

03-22 Sunday

  • 7-day Projection: WW 262771/11285; PRC 81266/3324; NON 259371/14696; IT 78550/8986; US 25567/280; TX 521/21. plus or minus 25%.
  • 1-day Projection: WW 340729/14895; PRC 81360/3265; NON 260988/11728; IT 61049/5774; US 34015/386; TX 857/5.
  • Actual Numbers: WW 335955/14632; PRC 81397/3265; NON 254558/11367; IT 59138/5476; US 33272/417; TX 627/8

03-23 Monday

  • 1-day Projection: WW 370630/16503; PRC 81489/3271; NON 290297/13301; IT 65275/6215; US 43432/566; TX 627/13. TX Deaths is Still early and erratic
  • Actual Numbers: WW 378287/18600; PRC 81496/3274; NON 296791/13223; IT 63927/6077; US 43667/552; TX 758/9. IT is slowing, which is good. JHU new dataset.

03-24 Tuesday

  • 1-day Projection: WW 425,953/18,600; PRC 81,595/3,283; NON 346,031/15,382; IT 69,104/6,744; US 57,310/731; TX 916/10
  • Actual Numbers: To be determined.  Infection spread for US is fluctuating slightly.

The following major milestones assume no gross change in testing rates nor confirmed infection rates.  Stage 1 is over standard capacity.  Stage 2 is over worst case reserve capacity.  Stage 3 is over best case reserve capacity.  This does not cover additional production, but does cover identified lower-function and out-of-date equipment from federal, military, and major hospital stockpiles.  At Stage 1, alternative locations are getting converted for use by patients, such as closed medical buildings.  At stage 2, we’re relying on medical and nursing students as front-line caregivers, and MASH style pop-up tent hospital expansions start getting deployed where possible. At stage 3, we’re draping parking garages, and getting scouts with first-aid badges to help.  Elderly or anyone with comorbidities will be comforted, but won’t get access to mechanical ventilation.  Only those with the best chance of survival with, and a high risk of death without, would get advanced care.

  • 04-05 33k TEXAS ICU OVERRUN STAGE 1 / 28.7m pop; 2.9 beds per 1000 (83230); 32% unoccupied (26633) / 11% are ICU (2929); 6.7% ventilators (1787) and 10% limited function ventilation (2663) / 5-15% conf need hosp(532k-177k @ overrun); 2-10% ICU (29k-146k); 1-5% need vent (36k-178k)
  • 04-06 45k TEXAS VENT OVERRUN STAGE 1 / 28.7m pop; 2.9 beds per 1000 (83230); 32% unoccupied (26633) / 11% are ICU (2929); 6.7% ventilators (1787) and 10% limited function ventilation (2663) / 5-15% conf need hosp(532k-177k @ overrun); 2-10% ICU (29k-146k); 1-5% need vent (36k-178k)
  • 04-10 150k TEXAS VENT/ICU STG2 & Hosp STG 1 / 28.7m pop; 2.9 beds per 1000 (83230); 32% unoccupied (26633) / 11% are ICU (2929); 6.7% ventilators (1787) and 10% limited function ventilation (2663) / 5-15% conf need hosp(532k-177k @ overrun); 2-10% ICU (29k-146k); 1-5% need vent (36k-178k)
  • 04-13 366k TEXAS VENT/ICU STG3 & Hosp STG 2 / 28.7m pop; 2.9 beds per 1000 (83230); 32% unoccupied (26633) / 11% are ICU (2929); 6.7% ventilators (1787) and 10% limited function ventilation (2663) / 5-15% conf need hosp(532k-177k @ overrun); 2-10% ICU (29k-146k); 1-5% need vent (36k-178k)
  • 04-15 660k TEXAS Hosp STG 3 / 28.7m pop; 2.9 beds per 1000 (83230); 32% unoccupied (26633) / 11% are ICU (2929); 6.7% ventilators (1787) and 10% limited function ventilation (2663) / 5-15% conf need hosp(532k-177k @ overrun); 2-10% ICU (29k-146k); 1-5% need vent (36k-178k)

The inflection point for R0 of 2.2 is 60%. Current reporting rate is 12-15%. Assuming we keep testing by same criteria, the Tx inflection point is about 400k confirmed. We may not reach this numerically due to testing/infrastructure failure. eg, we may reach stage 3 while our confirmed rate is much lower, but still around the same day, and still around the same number of actual infected.  Also, there are different groups between spreaders and isolators.  I don’t know the balance of those two groups. They could be 20/80 or 50/50.

Barring major changes, the model is +/- 25% per week.  That is +/- 1.5 days for stage 1. That is +/- 2.5 days for stage 2. That is +/- 3.5 days for stage 3.

If the Pandemic declaration helped, then 03-24 will be at least 2% low for US and TX. If the Emergency declaration helped, then 03-25 will be at least 2% low for US and TX.  Either of those should show a continual downward trend.  We have had a lot of people ignoring expert and government recommendations, so I do not expect an abrupt change.

If we did abruptly fall to, say, 112% on 03-24 and stay there, then Stage 1 starts April 23-26; then Stage 2 starts May 7-11; Stage 3 may never happen due to average disease cycle of 20 days, and ICU cycle of 30 days.  This would be a dream scenario, and is unlikely.  More likely to see a 5% drop several days in a row.  It’s unlikely to see the clam-down go below 110% until it looks really bad (and then it’s too late).

Texas is about 9% of the US capacity and slightly more capacity than average.  Look for 11x numbers in the US column for similar problems.

  • 33k -> 363k on 03/30 Stage 1 ICU
  • 45k -> 495k on 03/31 Stage 1 Vent
  • 150k -> 1650k on 04/04 Stage 2 / Stage 1 Hosp
  • 366k -> 4026k on 04/07 Stage 3 / Stage 2 Hosp
  • 660k -> 7260k on 04/09 Stage 3 Hosp

112% projections:

  • 112% ICU Stage 1 is 04/10
  • 112% Vent Stage 1 is 04/12
  • 112% V2 / Hosp Stage 1 is 04/23
  • 112% V3/H2 is 05/01
  • 112% H3 is 05/06
  • 112% numbers are +/- 3, 5, and 7 days.

This is all bistromath, and really, anything more than a week out is just guesswork. A lot can change in a week, and I’m expecting substantial changes over the next 3 days based on the activities 10-14 days ago.

The Spreadsheet has been updated. JHU replaced some data sources, so it was a little annoying, and a little more manual entry.

https://drive.google.com/file/d/1vocCN445AZyVBBLsv0kJR8ZDP9DM0UST/view


Projection Spreadsheet

Posted by xaminmo

Google link is https://drive.google.com/file/d/1vocCN445AZyVBBLsv0kJR8ZDP9DM0UST/view View/comment only. I don’t know what broke yet, or if everything works right.


Tsunami

Posted by xaminmo

I have been maintaining projections on omnitech.net/blog and fb.com/xaminmo .

Basically, it is time to hide from society right now. There are a lot of people still spreading it because it is their right to be free. If you get it now, there will be no resources to help you if you get very sick.

Projections may change by Wednesday, since that is 12 days after the national emergency was declared. If we cut our spread in half, then we get almost an extra week of respite.

Except, I know groups of people who were congregating for public meals as recently as Wednesday, and group exercise just Friday. 6 feet at 14mph is not enough. I don’t have the ability to get people to trust me. Either they see, or they don’t. Plenty actively disbelieve. It’s core to their being to believe exactly opposite of me.

We got complacent, because we’re “not like Italy. Look, they are older, and we were infected sooner. We’re so much better, and our death rate is lower.”

Italy started at +25% per day, and brought it down to +12% per day.

The US started at +5-10%, but for weeks has been spreading at +35% per day. Texas, my state, has to do it bigger. We’re spreading at +47%.

So, April 2, Texas ICU reserve capacity is overrun. A week later, all Texas hospital reserve capacity is overrun. I don’t know where in there we run out of trained medical professionals and supplies to treat safely.

If we did a great job when the pandemic was declared, we get 4-6 more days. A week prior, it will look like a normal day, a little busy, and probably still no toilet paper.

I wish it were not so, but the window of opportunity to change this course is almost closed, and we seem to be accelerating towards it, not slowing.

A tsunami is coming, and we have not even felt the tremor yet.


SARS2 not from a lab

Posted by xaminmo

Two bits of info indicating extremely unlikely that this was engineered in a laboratory: A) Computer models show the binding function would be very poor for how it binds; B) The core code of the virus matches animal versions, not versions known to make humans sick.

Here's why: SARS-CoV-2 is very closely related to the virus that causes severe acute respiratory syndrome (SARS), which fanned across the globe nearly 20 years ago. Scientists have studied how SARS-CoV differs from SARS-CoV-2 — with several key letter changes in the genetic code.

Yet in computer simulations, the mutations in SARS-CoV-2 don't seem to work very well at helping the virus bind to human cells. If scientists had deliberately engineered this virus, they wouldn't have chosen mutations that computer models suggest won't work.

https://www.livescience.com/coronavirus-not-human-made-in-lab.html

This evidence for natural evolution was supported by data on SARS-CoV-2’s backbone – its overall molecular structure. If someone were seeking to engineer a new coronavirus as a pathogen, they would have constructed it from the backbone of a virus known to cause illness. But the scientists found that the SARS-CoV-2 backbone differed substantially from those of already known coronaviruses and mostly resembled related viruses found in bats and pangolins.
https://www.scripps.edu/news-and-events/press-room/2020/20200317-andersen-covid-19-coronavirus.html