Coronavirus

[bkp_duke]

How bad are the PCR tests we're using in the US? That seems really bad and there would be no way to stop the spread by testing.
This LabCorp PCR test looks like it has 100% sensitivity (small sample size): https://www.fda.gov/media/136151/download

@EVNow 's test comparison is a tad flawed in that paper, but does bring up one of the finer points of medicine. The reason why: SAMPLE COLLECTION. I don't doubt the published results (for THAT specific institution only), but there is a very large assumption being made that I didn't see the paper describe.

The PCRs are being run on nasal and throat swabs. That takes a TRAINED person to do that properly, so the quality of the results is dependent upon sample collection. Someone that doesn't know how to properly swab a throat is not going to pick up a true positive, even though the PCR test itself is nearly 100% sensitive and 100% specific.

The IgG and IgM tests have lower sensitivity and specificity, but they are run on blood samples. Blood is pretty much binary (you get it, or you don't and the person collecting it can readily see that in the sample tube).

There is also a timing effect that has to be considered. The PCRs are being run and looking at ONE point in time to see if you are infected by picking up viral RNA. There is a window of opportunity of only a few days to 2 weeks (depending upon how fast the host fights off the infection).

Conversely, the IgG and IgM test is being run at a point when you have likely produced antibodies. ANYTIME after the start of antibody production (which is later in the course of the disease), and also anytime AFTER the infection is cleared, this test should be positive for months.


So, you order the test based upon what you are looking for:
1) Active infection - order a PCR (preferably more than one sample - nasal and throat are what I would start with)
2) Looking for immunity - order the IgG / IgM antibody blood test


BTW, the false negative rate can be greatly reduced on the PCR, even by a bad sample collection, by repeating the test. This is where the training of the physician ordering it is important: clinical suspicion. If the case looks like COVID-19, and the PCR is negative, and a flu test is negative (because flu looks a lot like COVID-19), you would presumptively treat for both conditions, and repeat both tests (preferably with a different technician doing the collection

 

[FoverM]

It *really* looks like Italy's new daily cases curve peaked on Mar 23/24. That would put their total cases around 150K. Daily deaths should peak later this week, with an overall total of around 20K.

Spain looks like its daily new cases is peaking right now. That would put their total cases around 160K. They'll total at least 20K dead.

I'm sure a mathematician could figure it out analytically based on an assumed curve ... but it looks like the peak happens at the 10% daily new cases growth level => cases[ i ] / cases[ i-1 ] -1 <= 0.10. Italy was in the teens for a week before dropping into the single digits. According to worldometer.info, we've been in the teens for three days so far but I don't trust the data. It looks weird plus testing has been ramping up tremendously. My guess is that the US, being much larger than most of the other countries, will have a rolling peak through the states, so we'll have a wider+flatter curve overall.

 

[Unpilot]

That doesn't do it for me. As far as I can tell the website is saying there are 718 ICU beds available at all times for NY. Which isn't true.

Yeah there is something wrong with that model. The 718 beds available never change on the time line.

 

[SMAlset]

CV found in sewage in Netherlands city ahead of outbreak there.

Coronavirus in Sewage Portended Covid-19 Outbreak in Dutch City
Bloomberg - Are you a robot?

Stool sample tests as early indicators of carriers?

 

[AlanSubie4Life]

Well if the models say we're going to hit 200k deaths then that is going to happen unless it stays flat for a couple years.

Yeah definitely if we hit 200k it is a sure thing. Just trying to be optimistic here, man. Even though there continues to be no reason for optimism due to continued flailing and deep ineptitude.

 

[wdolson]

That's based on a new Imperial College report that is just as flawed as the one 2 weeks ago that said 2.2M was worst case.

This virus is spreading freely in all regions of the country and will end up infecting tens of millions or more. We've "flattened the curve", but that's not really impacting total deaths. At the end of the day, everyone's still getting it and those at high risk will die.

I found it a little ridiculous that Birix would say 100k if we do "everything perfectly". We are quite literally doing nothing even modestly well.

With proper medical care quite a few of those hospitalized will recover, though some may have lifelong health problems. If we keep the hospital load down, the deaths will be limited to those who were unsavable under any conditions. If hospital load gets too great, many who need the ICU but might recover won't make it. The 100K assumes a minimal number of hospital systems get overloaded, the 2.2 million is what happens if they all get overloaded. The best case death toll has gone up a bit because it's now inevitable some hospital systems is going to become overloaded before this is over. At this point the 2.2 million is not a realistic worst case because several places locked things down early enough to prevent the worst case in those places.

 

[Norbert]

Looks like the Bay Area may have reason to be cautiously optimistic:

Bend it like the Bay Area: Doctors see flatter curve after 2 weeks of social isolation

That I can believe, that after two weeks of isolation, there is a "slower upswing". That sounds cautious enough.

 

[SMAlset]

Looks like the Bay Area may have reason to be cautiously optimistic:

Bend it like the Bay Area: Doctors see flatter curve after 2 weeks of social isolation

Uptick today in Bay Area. Hospital news stories I’ve seen have said they are expecting this and expect it to get worse.

from San Francisco Chronicle (CDC et al statistics):

 

[Norbert]

Uptick today in Bay Area. Hospital news stories I’ve seen have said they are expecting this and expect it to get worse.

from San Francisco Chronicle (CDC et al statistics):

View attachment 527808

Just when I tried to be more optimistic....

 

[Norbert]

Social distancing was never well explained. It slows down transmission when you do it, but until you have a vaccine or herd immunity, it will start to come back when you relax social distancing. It's like hitting the brakes from time to time when coasting down a mountain, you don't want to stop the car entirely, or get going too fast, so you pump the brakes.

If we could lock up the entire population of the world entirely for a few weeks, we could make the virus extinct, but that's physically impossible. People need to move about who have critical jobs needed to keep the rest of the country alive and everyone needs to get supplies from time to time, and then there are those who will just disobey the orders. In places where there are no stay at home orders the virus is spreading rapidly around the population.

All the infectious disease experts I heard when China was locked down expected it to come back as soon as they let up on it. Stories I'm hearing about China now are that the government is working hard to hide all new infections. They are desperate to get the economy going again. This is the descendant of the same government that ruled through the greatest genocide in history (Mao's Great Leap Forward that killed 45 million in 4 years).



Missouri saw a 600% increase in cases last week and they still don't have a statewide stay at home order.

I feel more like describing it as the need to come to full stop, make sure the car doesn't overheat, and when it has cooled down, everything is refilled, sorted out, slowly try get going again.

 

[Norbert]

With proper medical care quite a few of those hospitalized will recover, though some may have lifelong health problems. If we keep the hospital load down, the deaths will be limited to those who were unsavable under any conditions. If hospital load gets too great, many who need the ICU but might recover won't make it. The 100K assumes a minimal number of hospital systems get overloaded, the 2.2 million is what happens if they all get overloaded. The best case death toll has gone up a bit because it's now inevitable some hospital systems is going to become overloaded before this is over. At this point the 2.2 million is not a realistic worst case because several places locked things down early enough to prevent the worst case in those places.

To assume that we could get as low as 100K just by avoiding an overload of hospitals, but still reach herd immunity, for which an infection rate of 50% estimate is on the low side AFAIK, that implies an IFR below 0.1%. I'm not aware of anyone thinking it is that low, at this point. You are usually one of my favorite posters, so I'd like to urge you to reconsider this point.

 

[Norbert]

It *really* looks like Italy's new daily cases curve peaked on Mar 23/24. That would put their total cases around 150K. Daily deaths should peak later this week, with an overall total of around 20K.

Spain looks like its daily new cases is peaking right now. That would put their total cases around 160K. They'll total at least 20K dead.

I'm sure a mathematician could figure it out analytically based on an assumed curve ... but it looks like the peak happens at the 10% daily new cases growth level => cases[ i ] / cases[ i-1 ] -1 <= 0.10. Italy was in the teens for a week before dropping into the single digits. According to worldometer.info, we've been in the teens for three days so far but I don't trust the data. It looks weird plus testing has been ramping up tremendously. My guess is that the US, being much larger than most of the other countries, will have a rolling peak through the states, so we'll have a wider+flatter curve overall.

Italy does seem to be at a point where the *new cases* may have peaked, but only if there is no new hot spot in another region.

I like the expression "rolling peak". That seems likely for the US at this point.

 

[wdolson]

To assume that we could get as low as 100K just by avoiding an overload of hospitals, but still reach herd immunity, for which an infection rate of 50% estimate is on the low side AFAIK, that implies an IFR below 0.1%. I'm not aware of anyone thinking it is that low, at this point. You are usually one of my favorite posters, so I'd like to urge you to reconsider this point.

I didn't run the numbers, I thought 100K was optimistic. All these models have a lot of assumptions cooked in. There is a lot of talk that the first peak is going to be it. In some pandemics that is the case, but that's either with a disease the doesn't spread very well and can be contained, or a disease in which there is already some herd immunity at the start. This spreads very easily and we're starting with essentially zero herd immunity (there is speculation SARS survivors might be immune, but they are a tiny minority of the world's population).

If we do everything right, we might get over the first maximum with about 100K dead. But there comes a point where isolation needs to be relaxed. Out of necessity people are going to need to do some things that require getting less than 6 feet from someone else again like getting your dental checkup or a dental procedure, there are surgeries being put off that can't wait, even haircuts. Plus the isolation is taking a heavy psychological toll on people.

Some models are assuming that once we're over the first hump we'll see a steady decline and be able to keep it there until there is a vaccine. But that's unlikely in a population that has any kind of porosity to their borders. Iceland, Australia, New Zealand, and other places similarly isolated may be able to do this by forcing anybody coming in into mandatory quarantine. It's going to be impossible in any land mass with a large population, especially with easy to cross borders with other countries.

The 1918 flu had a double peak with the second peak being much worse than the first. In the 1918 flu the total death toll in the US was about 0.6% of the population. Medicine has advanced quite a bit and we can save people who get sicker than 1918, but we could see 0.6% again, or a little less. While we have better medical tech, this is deadlier to the vulnerable population than the 1918 flu was.

The 100K best case scenario is basically impossible to achieve with the vaccine out a year or more, the current government lack of coordination, resource shortages, and a segment of the population who still don't believe this is real. The real scenario is probably going to be somewhere in the middle.

In the end the death toll is going to be a punch in the gut psychologically all over the world. the last time this happened, a lot of kids still died before age 5 from childhood diseases. My father was born in 1920 and my mother in 1925. My father was considered a lucky kid because he caught none of the diseases the other kids caught. My mother got a few of them. She used to talk about how whooping cough felt. Both knew kids who died of childhood diseases.

Up until this pandemic the only people most of us knew who died of an infectious disease were old or had some kind of serious health condition. It's alien to most of us to have someone perfectly healthy one day and dead a couple of weeks later from an infectious disease. In the arc of history this isn't new, but it is to almost everyone alive in the developed world today.

 

[deonb]

To be fair that was March 6th. That story is terrifying.

That date is wrong. Didn't notice. It happened on March 10th. Here is another source with the right date:
COVID-19 infiltrated Mt. Vernon choir, killing 2 members and infecting others

Keep in mind, this is WA state. By that time it was already past the Life Care outbreak, Microsoft, Amazon, Nordstrom and Starbucks were already working from home. UW went online only. We had 269 cases, and 22 deaths at that time.

So everybody here knew the recommended hygiene and 6-foot rule to be followed very well. It wasn't lock down yet, but people were very careful already. And the choir followed all the rules and recommendations that was given to them, which unfortunately didn't (and doesn't) include airborne virus precautions.

 

[RobStark]

If the Trump Administration set the bar at 100k-200k to me that means their internal models has total death count below that.

My guess it will be ~90k and they will call that a victory in the Presidential campaign.

 

[Thekiwi]

If the Trump Administration set the bar at 100k-200k to me that means their internal models has total death count below that.

My guess it will be ~90k and they will call that a victory in the Presidential campaign.

had a similar thought - but I’m sure they will just keep moving the goalposts, so it will become something like “100K-200k before it peaked”.

 

[Norbert]

Miami VA hospital employees are being told to wear, reuse one surgical mask per week

 

[EinSV]

Uptick today in Bay Area. Hospital news stories I’ve seen have said they are expecting this and expect it to get worse.

from San Francisco Chronicle (CDC et al statistics):

View attachment 527808

I wouldn't read too much into the uptick on Monday after the drop over the weekend, especially since weekend reporting can be spotty.

For example, the health department in Santa Clara County, which has the most reported cases in the Bay Area, mentioned on its website that there were reporting glitches over the weekend:

"March 30, 2020 Update: The 202 new confirmed cases reported today include some results that were not previously reported over the past two days. This increase reflects a reporting delay, not necessarily a significant single day increase." Coronavirus (COVID-19) Data Dashboard - Public Health Department - County of Santa Clara

So we may not have turned the corner on new confirmed cases yet but yesterday's increase may just be due to reporting delays.

 

[defc0n]

If the Trump Administration set the bar at 100k-200k to me that means their internal models has total death count below that.

My guess it will be ~90k and they will call that a victory in the Presidential campaign.

Exactly same thing I was thinking. Except I think it will be a bit lower than that even.

 

[EinSV]

Oxford's Centre for Evidence-Based Medicine has a nice summary of the scientific analyses of the impact of weather conditions on transmission of coronavirus.

Their verdict (as of March 22) was:

"Although much of the data has not been peer-reviewed yet, emerging evidence appears to suggest that weather conditions may influence the transmission of the novel coronavirus (SARS-CoV-2), with cold and dry conditions appearing to boost the spread. This phenomenon may manifest itself through two mechanisms: the stability of the virus and the effect of the weather on the host. The weather effect is minimal, and all estimates are subject to significant biases reinforcing the need for robust public health measures."

Do weather conditions influence the transmission of the coronavirus (SARS-CoV-2)? - CEBM

Another pre-publication study is out concluding that increasing temperatures could help reduce covid-19 transmission, at least in the Northern Hemisphere. The punch line is:

We find robust statistical evidence that a 1 degree C increase in local temperature reduces transmission by 13% [-21%,-4%, 95%CI]. In contrast, we do not find that specific humidity or precipitation influence transmission. Our statistical approach separates effects of climate variation on COVID-19 transmission from other potentially correlated factors, such as differences in public health responses across countries and heterogeneous population densities. Using constructions of expected seasonal temperatures, we project that changing temperatures between March 2020 and July 2020 will cause COVID-19 transmission to fall by 43% on average for Northern Hemisphere countries and to rise by 71% on average for Southern Hemisphere countries. https://www.medrxiv.org/content/10.1101/2020.03.26.20044420v1.full.pdf
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