Coronavirus

[EVNow]

The accepted theory that this jumped from animals to humans in a wet market in Hunan both fits the known data well and is very plausible. Sometimes viruses in animals that may or may not not cause serious illness in the animals figures out how to jump species and infects us. MERS and SARS are two previous coronaviruses that jumped species.

Coronavirus Could Be a 'Chimera' of Two Different Viruses, Genome Analysis Suggests : COVID19

As you know, a cell infected with a virus is "hijacked" and becomes a factory that makes copies of the virus. It's possible to be infected by two different viruses at the same time. And it's possible that the hijacked cell creates a virus that is a combination of both viruses which infected it.

The article suggests that's what must have happened to create SARS-CoV-2

Keep in mind, every "combination" created by a doubly infected cell is a "mistake." Neither virus wants the cell to do that. They both want the cell to faithfully replicate it. And cellular machinery being what it is (that is to say, really quite good), most copies are faithful to one or the other virus.

And most mistakes are undoubtedly jumbled messes - viruses that don't actually work.

Therefore, the chance that any particular virus emerging from an infected cell is a viable, working hybrid is incredibly low - like winning lottery ticket low. But, when you're infected, millions of cells are infected and they're pumping out billions of viruses. Somewhere in there, someone won that lottery.​

cue : If the chance of it happening is low, it must have been created in a lab. Because conspiracy theories don't need any proof.

 

[EVNow]

This is wild and interesting.

Asymptomatic and Presymptomatic SARS-CoV-2 Infections in Residents of a Long-Term Care Skilled Nursing Facility — King County, Washington, March 2020 : COVID19

Demographic characteristics were similar among the 53 (69.7%) residents with negative test results and the 23 (30.3%) with positive test results (Table 1). Among the 23 residents with positive test results, 10 (43.5%) were symptomatic, and 13 (56.5%) were asymptomatic. Eight symptomatic residents had typical COVID-19 symptoms, and two had only atypical symptoms; the most common atypical symptoms reported were malaise (four residents) and nausea (three). Thirteen (24.5%) residents who had negative test results also reported typical and atypical COVID-19 symptoms during the 14 days preceding testing.

Demographic characteristics were similar among the 53 (69.7%) residents with negative test results and the 23 (30.3%) with positive test results (Table 1).

Sixteen days after introduction of SARS-CoV-2 into facility A, facility-wide testing identified a 30.3% prevalence of infection among residents, indicating very rapid spread, despite early adoption of infection prevention and control measures. Approximately half of all residents with positive test results did not have any symptoms at the time of testing, suggesting that transmission from asymptomatic and presymptomatic residents, who were not recognized as having SARS-CoV-2 infection and therefore not isolated, might have contributed to further spread.​

 

[linux-works]

I ventured out to the food store, last nite, for the first time in almost 3 weeks (wow). the world changed out from under me! what was once a 24 hour store (safeway, sunnyvale) is now 6am-9pm only. I got there at 10.45pm and it was ultra closed (yeah, lets go with ultra closed, that describes it). got back in my car, drove to one other store that still had 5 minutes left. got what I could and left. the TP isle was empty, I think there might have even been IOU notes left

ok, how about amazon? anything there? not really. and, well, a strange recommendation....

the newer item is.... well, not really the same thing, now, is it?

(is it? I've been away so long, maybe this IS the new normal??)

 

[Daniel in SD]

Since we have discussed sensitivity of PCR tests. Here is an interesting paper.

The comparative superiority of IgM-IgG antibody test to real-time reverse transcriptase PCR detection for SARS-CoV-2 infection diagnosis : COVID19

Of 133 patients with SARS-CoV-2 infection, there were 44 moderate cases, 52 severe cases, and 37 critical cases with no significant difference of gender and age among three subgroups. Overall, the positive ratio in IgM antibody test was higher than in RT-PCR detection. In RT-PCR detection, the positive ratio was 65.91%, 71.15%, and 67.57% in moderate, severe, and critical cases, respectively. Whereas, the positive ratio of IgM/IgG antibody detection in patients was 79.55%/93.18%, 82.69%/100%, and 72.97%/97.30% in moderate, severe, and critical cases, respectively. Moreover, the concentrations of antibodies were also measured in three subgroups.​

Seems like the number that matter is the accuracy for moderate cases.
RT-PCR 66% (this was for "real time" PCR not conventional PCR. They used conventional PCR to get the positive samples)
IgM 80%
IgG 93%
What's the difference between IgM and IgG? Is the test accuracy between them correlated?
Also, they don't have a false negative rate for this test because they only tested positive samples.

 

[EVNow]

Seems like the number that matter is the accuracy for moderate cases.
RT-PCR 66% (this was for "real time" PCR not conventional PCR. They used conventional PCR to get the positive samples)
IgM 80%
IgG 93%
What's the difference between IgM and IgG? Is the test accuracy between them correlated?
Also, they don't have a false negative rate for this test because they only tested positive samples.

No - RT-PCR is the one everyone has been using.

Reverse transcription polymerase chain reaction (RT-PCR) is a laboratory technique combining reverse transcription of RNA into DNA (in this context called complementary DNA or cDNA) and amplification of specific DNA targets using polymerase chain reaction (PCR).​

 

[SageBrush]

I updated the data for the daily hospitalization change for large US states with available data.
Consistent with arguably inaccurate infection rate data, the growth is reducing.
Data is sourced from The COVID Tracking Project.

Caveat: data quality might not be great and some states only update every second day (adjusted in the data)

View attachment 527704

Included data attached.

Nice !
Are these Covid-19 related hospitalizations ?

 

[Norbert]

I updated the data for the daily hospitalization change for large US states with available data.
Consistent with arguably inaccurate infection rate data, the growth is reducing.
Data is sourced from The COVID Tracking Project.

Caveat: data quality might not be great and some states only update every second day (adjusted in the data)

View attachment 527704

Included data attached.

Consistency with infection rate data is not a good sign. Both are subject to the limitations of processing capacity in hot spots.

I believe that underestimating the problem is still the larger danger.

 

[Daniel in SD]

No - RT-PCR is the one everyone has been using.

I may be confused because it's really confusing. I think they were testing "real time RT-PCR" and IgM-IgG vs. samples tested with conventional RT-PCR. If everyone were using a test with 66% sensitivity that would be really bad.
From you link:

Method: We retrospectively and observationally studied 133 patients diagnosed with SARS-CoV-2 and admitted in Renmin Hospital of Wuhan University, China, from Feb 17 to Mar 1, 2020. Demographic data, symptoms, clinical examination, laboratory tests, and clinical outcomes were collected. Data were compared between IgM-IgG antibody test and real-time RT-PCR detection for COVID-19 patients.

 

[deonb]

You're describing the usual platinum-plated clinical trials process, but that's almost completely useless here given the timelines involved.

Keep in mind that this is now an FDA approved treament, so clinical studies won't accelerate the use much more. If it makes as dramatic a difference as some people claim it does, doctors who have been treating patients before approval, and now after approval will start shouting it from the rooftop if they also personally observe that much of a difference. It would be like when antibiotics or steroids first started out.

If on the other hand, it makes only a marginal difference, then a longer term study that weighs positives vs. negatives is actually warranted.

 

[Todesbuckler]

Here's also the update for infection rates.
As mentioned and discussed in this forum, measurement error due to availability in testing kits is likely present biasing the growth rates for some countries downwards (e.g. most likely New York state) and for other countries upwards (e.g. Italy with decreasing positive rates, decreasing infection rates and on average increasing number of tests). However, even with a certain distortion, the growth seems to decrease.
Data from Coronavirus Update (Live): 783,812 Cases and 37,773 Deaths from COVID-19 Virus Outbreak - Worldometer

 

[deonb]

Sad milestone reached today:

US Deaths from COVID-19: 3146
US Deaths from 9/11 attacks: 2977

 

[TheTalkingMule]

John Prine is ok. Shocked and overjoyed.

 

[Todesbuckler]

Nice !
Are these Covid-19 related hospitalizations ?

Yes.
For some states the website also lists the sources of their data (e.g. official state reports)

 

[Papafox]

Keep in mind that this is now an FDA approved treament, so clinical studies won't accelerate the use much more. If it makes as dramatic a difference as some people claim it does, doctors who have been treating patients before approval, and now after approval will start shouting it from the rooftop if they also personally observe that much of a difference. It would be like when antibiotics or steroids first started out.

If on the other hand, it makes only a marginal difference, then a longer term study that weighs positives vs. negatives is actually warranted.

Getting word out to his peers is exactly what Dr. Zelenko was doing in this post. His hope is that other physicians will try the 3 drug cocktail of HCQ, Z-pack, and zinc in patients who are early enough in the COVID-19 progression that they are not yet hospitalized. I know of no clinical trials underway for the combination of the three drugs. He's saying to try these three together early in the disease progression because the results are excellent. Let's keep our ears open and see how this situation progresses. Fingers crossed.

 

[AlanSubie4Life]

John Prine is ok. Shocked and overjoyed.

Doesn't really sound like it, sorry to inform you. Hopefully he'll be successfully removed from the ventilator - the sooner the better.

Fiona Whelan Prine on Twitter

 

[Norbert]

The naive CFR (lacking adjustment for time infection to death) for South Korea is now at 1.6%.
The 14-day adjusted number is now at 1.9% and rising.

 

[AlanSubie4Life]

The naive CFR (lacking adjustment for time infection to death) for South Korea is now at 1.6%.
The 14-day adjusted number is now at 1.9% and rising.

And in other news that isn't news, the naive CFR for Germany is 0.96% and rising - in spite of the massive recent growth in case numbers (the denominator). 14-day lag number is 10%. Obviously that could be skewed by a number of factors. It's also likely that a 14-day lag is a bit too high. IIRC, the 14-day adjustment that papers use is from onset of symptoms to death. We're doing "logged as positive to death". Which is likely closer to 7 days for an appropriate lag (a day or two of symptoms at least + a few days for test results needs to be subtracted from 14).

For Germany, that 7-day lag works out to 2.5%. SK works out to about 1.7%.

An IFR of 1%, as mentioned in today's Imperial College study, increasingly looks quite reasonable.

 

[winfield100]

Tsa travel data March 2019 and 2020
(Vaguely 80-90+% drop)
TSA checkpoint travel numbers for 2020 and 2019

Date Total Traveler Throughput Total Traveler Throughput
(1 Year Ago - Same Weekday)
2020. 2019
3/29/2020 180,002 2,510,294
3/28/2020 184,027 2,172,920
3/27/2020 199,644 2,538,384
3/26/2020 203,858 2,487,162
3/25/2020 239,234 2,273,811
3/24/2020 279,018 2,151,913
3/23/2020 331,431 2,434,370
3/22/2020 454,516 2,542,643
3/21/2020 548,132 2,227,181
3/20/2020 593,167 2,559,307
3/19/2020 620,883 2,513,231
3/18/2020 779,631 2,320,885
3/17/2020 953,699 2,177,929
3/16/2020 1,257,823 2,465,709
3/15/2020 1,519,192 2,545,742
3/14/2020 1,485,553 2,274,658
3/13/2020 1,714,372 2,634,215
3/12/2020 1,788,456 2,503,924
3/11/2020 1,702,686 2,187,298
3/10/2020 1,617,220 2,122,898
3/9/2020 1,909,363 2,378,673
3/8/2020 2,119,867 2,485,430
3/7/2020 1,844,811 2,156,262
3/6/2020 2,198,517 2,543,689
3/5/2020 2,130,015 2,402,692
3/4/2020 1,877,401 2,143,619
3/3/2020 1,736,393 1,979,558
3/2/2020 2,089,641 2,257,920
3/1/2020 2,280,522 2,301,439

 

[ByeByeJohnny]

As someone who has has been really sick over the last 14 days my main concern and one that several people I've talked with who has had as much as a cold during the last two months seems to share is that it's a huge problem not knowing if I had the virus or not. Because now I'm so wishing the virus is actually what I had.

I've been way sicker than ever in my life and had several but not all of the virus effects. Just the odds of that happening right now makes me think I had it. And if I had it I want to know but there is no way I can find out. I would still be taking all precautions needed both tomorrow and six months from now but it would change my mindset if I knew. Right now I'm pretty sure I will thinking about how sick I was and worrying about getting even sicker a lot for months to come.

And I'm in a country with highly praised free medical treatment but I was actually told to call back in a few days when I contacted a hospital for the first time in 35 years. Telling them how horrible I felt they wouldn't even send a doctor because they were all needed at the hospital but I shouldn't come there because if I didn't have the virus that was a bad idea and they would probably just send me home again. So yeah, I know most cases are not found and never reported so any type of percentages are widely wrong and really just guesses. It's just impossible to say how wrong.

In most places in the world unless you go to a hospital and they can confirm that you have pretty severe symptoms you will not be tested. In my case It sounded like a good chance I wouldn't even be tested if I went to the hospital being very sick.

A vaccine is obviously a priority but some way to test who has actually already had this is much needed if life is to get back to normal anytime soon. It would also be way to figure out the real infection rates and death percentage.

People not knowing if they have been sick or not will have a huge impact on the economy.

Apologies if this has been discussed. Have had a hard time keeping up my reading habits the last few weeks.

 

[Daniel in SD]

Tsa travel data March 2019 and 2020
(Vaguely 80-90+% drop)
TSA checkpoint travel numbers for 2020 and 2019

Date Total Traveler Throughput Total Traveler Throughput
(1 Year Ago - Same Weekday)
2020. 2019
3/29/2020 180,002 2,510,294
3/28/2020 184,027 2,172,920
3/27/2020 199,644 2,538,384
3/26/2020 203,858 2,487,162
3/25/2020 239,234 2,273,811
3/24/2020 279,018 2,151,913
3/23/2020 331,431 2,434,370
3/22/2020 454,516 2,542,643
3/21/2020 548,132 2,227,181
3/20/2020 593,167 2,559,307
3/19/2020 620,883 2,513,231
3/18/2020 779,631 2,320,885
3/17/2020 953,699 2,177,929
3/16/2020 1,257,823 2,465,709
3/15/2020 1,519,192 2,545,742
3/14/2020 1,485,553 2,274,658
3/13/2020 1,714,372 2,634,215
3/12/2020 1,788,456 2,503,924
3/11/2020 1,702,686 2,187,298
3/10/2020 1,617,220 2,122,898
3/9/2020 1,909,363 2,378,673
3/8/2020 2,119,867 2,485,430
3/7/2020 1,844,811 2,156,262
3/6/2020 2,198,517 2,543,689
3/5/2020 2,130,015 2,402,692
3/4/2020 1,877,401 2,143,619
3/3/2020 1,736,393 1,979,558
3/2/2020 2,089,641 2,257,920
3/1/2020 2,280,522 2,301,439

SARS-CoV-2 going to win Nobel Peace Prize for fighting climate change.