Bad News Thread

Quick analysis of b.1.117 (UK variant), and the next 2 months.

Nationally- number of cases is doubling a bit faster than once per two weeks. (R = 1.4 or so.). Currently at 15K or so cases per day. Expect it to continue doubling until vaccines cover enough additional people to counteract the higher R. That is, we need to vaccinate 4/14 of those who are not yet immune. 2/7 x .84 = another 24% of the country. 80 M more people vaccinated. 2 months before it turns around for vaccines. 4 more doublings. 120K cases per day peak.

Big things I missed: 1- recovered b.1.117 cases will bring the peak lower. 2- Any vaccinations will slow the doubling, even if we don’t get to 80M more. 3- Over excited reopening will make the peak go higher. I am treating these as offsetting each other, but I suspect the third factor is bigger than the first or second.

California- b.1.117 has stalled at 15% of cases. Dad guess is that b.1.117 can’t make further inroads because it isn’t much stronger than the already dominant LA variant. If true, it means CA won’t have a b.1.117 peak. However, CA is opening dining, theaters, and stadiums, so expect case counts to remain high for a while. Case counts can’t go up too far without putting us back in purple and closing it all down again.

So, another national peak in the 100K-150K cases per day range. CA hanging out at the red/purple boundary. (Cases go down, open something stupid. Our stupid thing forces cases back up, close down the stupid. Repeat.)

Be glad the line for soccer is at 14 instead of at yellow. With dining open, I am no longer optimistic that we can hit yellow this spring.

(again, not an epidemiologist. So don’t take this too seriously.)
By the way. We will watch TX and the other open states. Based on what we have seen over the last yr, there won't be a spike.

References...90% percent of kids are in schools in FL and TX. CA is about 5%

These states didn't shut down restaurants and biz. CA did.

Today all are about equal.

CA screwed the pooch.

Oh yeah the latest excuse for the reason the numbers are the same is that CA has a variant. Well FL does too. In theory their UK variant is worse vs the standard one as well.

Either way in about 4-6 weeks I lay money TX/FL don't have numbers and different vs CA.

At that point what will @dad4 have to say?

He out a marker out per say when he said TX abandoning masks and allow biz full capacity was a big problem.

We are just weeks away from seeing what happens...right?
 
One of the great disconnects here I suspect is we have a lot of i (introverted health policy experts who went into their fields because it offered a way to manage data and policy instead of patients and staff) who have very little idea or empathy of what the es (highly extroverted people) are going through. Really think about it....the idea that 20 somethings who aren’t married or cohabitating are going to go a year without dating Or have a fling...does anyone really imagine that’s possible?
It's also the difference between those that work in a lab, clinical situation or research environment where you can control or eliminate variables vs. those that work in the real world where you can't control variables and instead have to make cost benefit decisions based on best available evidence, experience, probabilities and gut instinct. Not only is Covid not a math problem, neither is real life.
 
By the way. You know which state has a big rise in the UK variant?

FL.
Yes. FL is up to about 30%.

It makes it hard to compare FL to other states, for the same reason as socal. Different variant, but same logic.

If you want to bet on TX/FL versus CA, you'll have to define what you mean by "different". If FL ha 30% higher cases in early April, does that count as "same" or "different"?

And CA is opening indoor dining, so the comparison may be moot. It is not unlikely that we see 3 different outcomes, but one set of policies.
 
By the way. We will watch TX and the other open states. Based on what we have seen over the last yr, there won't be a spike.

References...90% percent of kids are in schools in FL and TX. CA is about 5%

These states didn't shut down restaurants and biz. CA did.

Today all are about equal.

CA screwed the pooch.

Oh yeah the latest excuse for the reason the numbers are the same is that CA has a variant. Well FL does too. In theory their UK variant is worse vs the standard one as well.

Either way in about 4-6 weeks I lay money TX/FL don't have numbers and different vs CA.

At that point what will @dad4 have to say?

He out a marker out per say when he said TX abandoning masks and allow biz full capacity was a big problem.

We are just weeks away from seeing what happens...right?
With respect to schools, I mostly agree. CA could and should have opened schools months ago.

Of course, the smart way to do it is in cohorts. Unfortunately, at many schools, the teachers aren't exactly polymaths. Asking them to cover 6 topics is kind of crazy.

With respect to Dad4 predictions, I will make my own, thanks. My December line held up until early March when indoor dining opened and invalidated the assumptions. I think I did pretty well with that one.

Current Dad4 prediction is a small national bump in April, topping out between 100k and 150k cases per day. CA prediction is we hang out at the red/purple boundary : more than 4 and less then 14 cases per 100k per day. CA Prediction becomes invalid if indoor dining, amusement parks, and stadiums stay open as cases rise.
 
Quick analysis of b.1.117 (UK variant), and the next 2 months.

Nationally- number of cases is doubling a bit faster than once per two weeks. (R = 1.4 or so.). Currently at 15K or so cases per day. Expect it to continue doubling until vaccines cover enough additional people to counteract the higher R. That is, we need to vaccinate 4/14 of those who are not yet immune. 2/7 x .84 = another 24% of the country. 80 M more people vaccinated. 2 months before it turns around for vaccines. 4 more doublings. 120K cases per day peak.

Big things I missed: 1- recovered b.1.117 cases will bring the peak lower. 2- Any vaccinations will slow the doubling, even if we don’t get to 80M more. 3- Over excited reopening will make the peak go higher. I am treating these as offsetting each other, but I suspect the third factor is bigger than the first or second.

California- b.1.117 has stalled at 15% of cases. Dad guess is that b.1.117 can’t make further inroads because it isn’t much stronger than the already dominant LA variant. If true, it means CA won’t have a b.1.117 peak. However, CA is opening dining, theaters, and stadiums, so expect case counts to remain high for a while. Case counts can’t go up too far without putting us back in purple and closing it all down again.

So, another national peak in the 100K-150K cases per day range. CA hanging out at the red/purple boundary. (Cases go down, open something stupid. Our stupid thing forces cases back up, close down the stupid. Repeat.)

Be glad the line for soccer is at 14 instead of at yellow. With dining open, I am no longer optimistic that we can hit yellow this spring.

(again, not an epidemiologist. So don’t take this too seriously.)
"2/7 x .84"

Are you are saying only 16% of the nation is currently immune? A higher percentage than that already has their first shot (about 17.5%). Don't people that already had it also "count"?
 
So, another national peak in the 100K-150K cases per day range. CA hanging out at the red/purple boundary. (Cases go down, open something stupid. Our stupid thing forces cases back up, close down the stupid. Repeat.)

(again, not an epidemiologist. So don’t take this too seriously.)
Yeah, this is kind of weak, @dad4. Below is what real epidemiologists are predicting. We should take him seriously, right?


Osterholm predicted that B117, the more contagious strain of the virus that is sweeping England and has been found in pockets of the United States, will become the dominant strain of the virus in the country. “If we see that happen, which my 45 years in the trenches tell us we will, we are going to see something like we have not seen yet in this country,” he said. “That hurricane is coming. We have to understand that because of this surge, we do have to call an audible.”

The epidemiologist said if we see a surge of the new variant this spring, it will be worse than the previous surges. “We saw our health care system literally on the edge of not being able to provide care,” Osterholm said. “Imagine if we have what has happened in England, twice as many of those cases
 
"2/7 x .84"

Are you are saying only 16% of the nation is currently immune? A higher percentage than that already has their first shot (about 17.5%). Don't people that already had it also "count"?

This is my critique as well. By all indications people that have had it have at least partial immunity. There haven’t been a lot of reinfections in the uk from the group that got it early on.

I do think he is right there will be another surge in the us (based alone on what’s happening in europe. Interestingly hard hit Belgium Spain and Switzerland are not part of the surge). Florida is a likely candidate not just because of variants but because of the seasonality effect.
 
This is my critique as well. By all indications people that have had it have at least partial immunity. There haven’t been a lot of reinfections in the uk from the group that got it early on.

I do think he is right there will be another surge in the us (based alone on what’s happening in europe. Interestingly hard hit Belgium Spain and Switzerland are not part of the surge). Florida is a likely candidate not just because of variants but because of the seasonality effect.
Yes, I wouldn't be surprised to see another "surge" such as @dad4 predicts. The sad thing is there will be a lot of older folks who declined the vaccine that will needlessly die if we have any surge. We'll see the rate of death for those that had the vaccine and those that didn't. I don't believe that will be pretty. There will also likely be older folks that get it from healthcare workers who had the opportunity to get the vaccine and refused.
 
About whether people who have already had it also count:

They would count, if we knew who they are. For most of them, we do not know.

As a result, when we vaccinate, we don't get to choose whether we vaccinate people with natural immunity. We vaccinate the immune and non-immune equally, without knowing which is which.

We have 16% who have been vaccinated. The other 84% are, in some sense, in line for the vaccine. The remaining infectable population lies within that 84%.

If you want to innoculate 2/7 of the infectable population, you do that by innoculating 2/7 of the people in line for the vaccine. (Some of whom were already immune, but didn't know it.). That's how I got 2/7 of 84%.

Now, if we are delaying vaccines for all known recovered patients, then 84% is the wrong number. It's more like 75%, because you get to subtract out known recovered patients before you start vaccinating. This would drop the peak slightly.
 
About whether people who have already had it also count:

They would count, if we knew who they are. For most of them, we do not know.

As a result, when we vaccinate, we don't get to choose whether we vaccinate people with natural immunity. We vaccinate the immune and non-immune equally, without knowing which is which.

We have 16% who have been vaccinated. The other 84% are, in some sense, in line for the vaccine. The remaining infectable population lies within that 84%.

If you want to innoculate 2/7 of the infectable population, you do that by innoculating 2/7 of the people in line for the vaccine. (Some of whom were already immune, but didn't know it.). That's how I got 2/7 of 84%.

Now, if we are delaying vaccines for all known recovered patients, then 84% is the wrong number. It's more like 75%, because you get to subtract out known recovered patients before you start vaccinating. This would drop the peak slightly.
Apparently in California at least the advice is no vaccine if you’ve had covid in the last 90 days. My friend was scheduled to have the shot next week but came down with covid two weeks ago and his appointment canceled through his employer. I don’t know however how tough the screening questions are or if the protocol is the same in all states.
 
About whether people who have already had it also count:

They would count, if we knew who they are. For most of them, we do not know.

As a result, when we vaccinate, we don't get to choose whether we vaccinate people with natural immunity. We vaccinate the immune and non-immune equally, without knowing which is which.

We have 16% who have been vaccinated. The other 84% are, in some sense, in line for the vaccine. The remaining infectable population lies within that 84%.

If you want to innoculate 2/7 of the infectable population, you do that by innoculating 2/7 of the people in line for the vaccine. (Some of whom were already immune, but didn't know it.). That's how I got 2/7 of 84%.

Now, if we are delaying vaccines for all known recovered patients, then 84% is the wrong number. It's more like 75%, because you get to subtract out known recovered patients before you start vaccinating. This would drop the peak slightly.
We are primarily vaccinating old folks. We know they didn't already have it because they are still alive to get it. C'mon man, you didn't really say, "they would count if we know who they were", did you? You created an upper bound. Why don't you finish your analysis and give a lower bound?
 
We are primarily vaccinating old folks. We know they didn't already have it because they are still alive to get it. C'mon man, you didn't really say, "they would count if we know who they were", did you? You created an upper bound. Why don't you finish your analysis and give a lower bound?
2/7 of .75 is about 22% instead of 24%.

Works out about the same. Moves it up a few days.

The other compromises and numeric cheats I made are much worse than that one. That's why I don't treat it as an upper or lower bound. It was a crude SWAG.
 
Storm definitely threw a monkey wrench into the data.

But the storm doesn’t explain the drift in sequencing results. Nor does the storm explain the level spot in national numbers the last 2 weeks. Or the fact that other countries with high past caseloads (like Brazil) are also seeing an increase.

The simplest explanation for all three is that some variants have a higher transmissibility than others. The same behavior which leads to Rt=0.8 for vanilla covid may mean Rt=1.1 or 1.2 for some of the new variants. (transmission is higher by 35-45% for the UK one.)

So, it isn't the storm. It's the variant. And, if that is correct, the national numbers will go back up over the next 3-4 weeks. (Then drop, as total immunity gets high enough to offset the higher transmissibility.)

Which means this comment is in the correct thread.
It's only been 6 days but the cases don't really support that: "It's the variant." If the variant pushed the graph from falling quickly to concave up and even rising, why has the graph been dropping since Feb 26 and concave down since Feb 24? if the variant is taking over, we would see an acceleration in cases due to the R being > 1. So, maybe it is the Super Bowl effect. That would explain a short bump up then a continued downward, trend that is concave down. I'm not denying that the variant won't eventually take over and may cause a rise in cases, but the data doesn't appear to be supporting that yet.

1615099191271.png
 
It's only been 6 days but the cases don't really support that: "It's the variant." If the variant pushed the graph from falling quickly to concave up and even rising, why has the graph been dropping since Feb 26 and concave down since Feb 24? if the variant is taking over, we would see an acceleration in cases due to the R being > 1. So, maybe it is the Super Bowl effect. That would explain a short bump up then a continued downward, trend that is concave down. I'm not denying that the variant won't eventually take over and may cause a rise in cases, but the data doesn't appear to be supporting that yet.

View attachment 10321
the NYT has some graphs that break out the variant cases from the normal cases. Variant is still exponentially growing outside of CA. Think of it as two different diseases with two different R. the above graph shows their sum.

It’s roughly similar to 4(0.9)^T + 1(1.1)^T near T=0. first term is regular covid, second term is UK.

the sum slopes down for now, but that will change as the variant grows from 20% to over 50%. 2 weeks?
 
the NYT has some graphs that break out the variant cases from the normal cases. Variant is still exponentially growing outside of CA. Think of it as two different diseases with two different R. the above graph shows their sum.

It’s roughly similar to 4(0.9)^T + 1(1.1)^T near T=0. first term is regular covid, second term is UK.

the sum slopes down for now, but that will change as the variant grows from 20% to over 50%. 2 weeks?
This is good stuff - and I understand it. My point was simply that the "bump" we saw isn't supported by the variant taking over as once it takes over, it should accelerate overall cases. The fact that the growth didn't increase and actually started to fall again indicates the bump-up was caused by something else.
 
Quick analysis of b.1.117 (UK variant), and the next 2 months.

Nationally- number of cases is doubling a bit faster than once per two weeks. (R = 1.4 or so.). Currently at 15K or so cases per day. Expect it to continue doubling until vaccines cover enough additional people to counteract the higher R. That is, we need to vaccinate 4/14 of those who are not yet immune. 2/7 x .84 = another 24% of the country. 80 M more people vaccinated. 2 months before it turns around for vaccines. 4 more doublings. 120K cases per day peak.

Big things I missed: 1- recovered b.1.117 cases will bring the peak lower. 2- Any vaccinations will slow the doubling, even if we don’t get to 80M more. 3- Over excited reopening will make the peak go higher. I am treating these as offsetting each other, but I suspect the third factor is bigger than the first or second.

California- b.1.117 has stalled at 15% of cases. Dad guess is that b.1.117 can’t make further inroads because it isn’t much stronger than the already dominant LA variant. If true, it means CA won’t have a b.1.117 peak. However, CA is opening dining, theaters, and stadiums, so expect case counts to remain high for a while. Case counts can’t go up too far without putting us back in purple and closing it all down again.

So, another national peak in the 100K-150K cases per day range. CA hanging out at the red/purple boundary. (Cases go down, open something stupid. Our stupid thing forces cases back up, close down the stupid. Repeat.)

Be glad the line for soccer is at 14 instead of at yellow. With dining open, I am no longer optimistic that we can hit yellow this spring.

(again, not an epidemiologist. So don’t take this too seriously.)
This is very interesting data, @dad4. Thanks for posting it. After some sleep and coffee, I have some “I’m not an epidemiologist and I didn’t even stay in a Holiday Inn Express” thoughts.

What is the population distribution for the variant? The distribution of the population who are susceptible to the virus has changed dramatically with the vaccine. While the case rate is important, it is much less important than the rate of death and hospitalization. Since last Tuesday, AZ was vaccinating 55 and older. Nationally, 80% of the deaths have come from 65 and older. So, as long as we are “spitballing”, let’s say 70% of those over 65 got a vaccine and it protects them from serious illness 90% of the time (that may be high for older folks).

% of 65 and older protected from serious illness = 0.7*0.9 = 0.63 —> 0.37 of over 65’s can still get a “serious” infection

So, where we would normally expect 80 deaths of the 100 total, we get 0.37*80 or about 30 deaths. This effectively cuts the rate of death by 50%. There is a belief that the variant is more deadly. My guess is, as with most initial numbers on the disease, they are overestimating considerably. Let’s say it’s 20% more. That would raise deaths to 1.2*30 = 36 and the effective drop is 44%, not 50%. Of course, the percent of olders getting vaccinated is increasing daily. Once we get to all the 55 year olds, that’s about 90% of the deaths. I’m calling this a wash given the numbers of the variant are still relatively low. You also mention that you have a constant “doubling” every two weeks and that will obviously slow with vaccinations.

On the “bad” end, as you state, behavior can change effective R. I tend to be optimistic that this will not be a significant factor. I believe most people’s behavior is pretty much “baked-in” and not subject to external restrictions as much as those who make the restrictions would like to believe. People that want to get the vaccine (about 2/3?) will likely be cautious until they get it. Those willing to be involved in riskier behaviors are already doing so. Unfortunately, the variant will likely affect the poorer, more crowded areas even more inordinately than the initial strain. To begin with, the virus is spreading faster there - at least in our home area - and those folks appear to be getting vaccinated at a lower rate than the population.

One other thought. The variant will likely run through the younger population at a much higher rate than the original virus as they are vaccinated at a much lower rate.
 
This is very interesting data, @dad4. Thanks for posting it. After some sleep and coffee, I have some “I’m not an epidemiologist and I didn’t even stay in a Holiday Inn Express” thoughts.

What is the population distribution for the variant? The distribution of the population who are susceptible to the virus has changed dramatically with the vaccine. While the case rate is important, it is much less important than the rate of death and hospitalization. Since last Tuesday, AZ was vaccinating 55 and older. Nationally, 80% of the deaths have come from 65 and older. So, as long as we are “spitballing”, let’s say 70% of those over 65 got a vaccine and it protects them from serious illness 90% of the time (that may be high for older folks).

% of 65 and older protected from serious illness = 0.7*0.9 = 0.63 —> 0.37 of over 65’s can still get a “serious” infection

So, where we would normally expect 80 deaths of the 100 total, we get 0.37*80 or about 30 deaths. This effectively cuts the rate of death by 50%. There is a belief that the variant is more deadly. My guess is, as with most initial numbers on the disease, they are overestimating considerably. Let’s say it’s 20% more. That would raise deaths to 1.2*30 = 36 and the effective drop is 44%, not 50%. Of course, the percent of olders getting vaccinated is increasing daily. Once we get to all the 55 year olds, that’s about 90% of the deaths. I’m calling this a wash given the numbers of the variant are still relatively low. You also mention that you have a constant “doubling” every two weeks and that will obviously slow with vaccinations.

On the “bad” end, as you state, behavior can change effective R. I tend to be optimistic that this will not be a significant factor. I believe most people’s behavior is pretty much “baked-in” and not subject to external restrictions as much as those who make the restrictions would like to believe. People that want to get the vaccine (about 2/3?) will likely be cautious until they get it. Those willing to be involved in riskier behaviors are already doing so. Unfortunately, the variant will likely affect the poorer, more crowded areas even more inordinately than the initial strain. To begin with, the virus is spreading faster there - at least in our home area - and those folks appear to be getting vaccinated at a lower rate than the population.

One other thought. The variant will likely run through the younger population at a much higher rate than the original virus as they are vaccinated at a much lower rate.
By May, the death rate is on the floor. The emergency will be effectively over ( at least until fall when some of the variants may have gotten away from the vaccine and even then the vaccine seems to help against death/serious illness at least so far). The question then is do we allow cases to continue to drive policy, even though by then the death rate is essentially that of a moderately bad flu season
 
By May, the death rate is on the floor. The emergency will be effectively over ( at least until fall when some of the variants may have gotten away from the vaccine and even then the vaccine seems to help against death/serious illness at least so far). The question then is do we allow cases to continue to drive policy, even though by then the death rate is essentially that of a moderately bad flu season
If case rates had no consequences, then you could drop all precautions.

However, running high case rates over summer also means that you are creating more new variants.

The more new variants you make, the higher the probability that one of them is seriously immune to the vaccine. Which would put us right back where we were in Feb 2020.

I'd really rather not do that.

Not that I have any choice. We seem to be dropping masks and opening up right now, even though we still have 1500 deaths per day.

At least we have priorities straight. Classes are by zoom, but I can eat at my favorite restaurant. Makes sense if my children hope to wait tables at Denny's some day.
 
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