The Coronavirus

[Bob Butler 54]

(05-25-2020, 07:48 AM)Mikebert Wrote: It's not the R0, its the R. R is the observed infection rate. R0 is the infection rate under natural conditions, typically at the beginning of an outbreak. That is, it is the base case, hence the subscript 0.

For Warren, R0 is a first order rate constant for infection kinetics.  R is the rate constant after you take into account various inhibitors like social distancing, mask-wearing and weather, plus mass-action effects like isolation & contact tracing or brute-force actions like shutdowns.

My point remains the same even with Warren using more numbers. If enough people are not taking isolation seriously, isolation will not have as much effect. Warren assumes isolation will have a factor of 10 effect, and is looking for a reason it is having a lesser effect. I assume that a great part of this lesser effect is Trump's narrative that this should not be taken seriously, that a robust economy is more important than saving lives. Thus, the difference between R0 and R is much smaller than the 10 it might presumably reach.

The key is that even with a lesser effect, we are driving R below below one. We have flattened the curve. That the reduction is smaller than 10 is not reason to go back to having R above one. It is regrettable. With a low enough infection rate, sufficient testing and repeated full isolation when the expected outbreaks occur, we could bring the economy back. As is, the federal lack of response makes this difficult.

[David Horn]

(05-24-2020, 01:20 PM)sbarrera Wrote: Using this sort of nuanced data to take intelligent, coordinated action is exactly what strong national leadership should/would be doing. But alas, we have a dumpster fire of a Federal government presided over by a criminal lunatic.

 
You know, if you have an opinion, you should share it. 

[David Horn]

(05-25-2020, 08:44 AM)Bob Butler 54 Wrote:

(05-25-2020, 07:48 AM)Mikebert Wrote: It's not the R0, its the R. R is the observed infection rate. R0 is the infection rate under natural conditions, typically at the beginning of an outbreak. That is, it is the base case, hence the subscript 0.

For Warren, R0 is a first order rate constant for infection kinetics.  R is the rate constant after you take into account various inhibitors like social distancing, mask-wearing and weather, plus mass-action effects like isolation & contact tracing or brute-force actions like shutdowns.

My point remains the same even with Warren using more numbers.  If enough people are not taking isolation seriously, isolation will not have as much effect.  Warren assumes isolation will have a factor of 10 effect, and is looking for a reason it is having a lesser effect.  I assume that a great part of this lesser effect is Trump's narrative that this should not be taken seriously, that a robust economy is more important than saving lives.  Thus, the difference between R0 and R is much smaller than the 10 it might presumably reach.

The key is that even with a lesser effect, we are driving R below below one.  We have flattened the curve.  That the reduction is smaller than 10 is not reason to go back to having R above one.  It is regrettable.  With a low enough infection rate, sufficient testing and repeated full isolation when the expected outbreaks occur, we could bring the economy back.  As is, the federal lack of response makes this difficult.

Report from the hinterlands: everyone (well, far too many anyway) are back to normal here in exurban Trumpland.  If this disease is less virulent in the summer months, and just the act of being outdoors will promote that to some extent, then we many see that large reemergence in the Fall that has been predicted.  People who don't agree with the CDC guidance, and there are huge numbers in that camp, are not going to go for Shutdown 2.0 no matter the need.  This can get really ugly by October, and ultimately affect the election.  

There are way too many moving parts to this story.

[Bob Butler 54]

(05-25-2020, 10:06 AM)David Horn Wrote: Report from the hinterlands: everyone (well, far too many anyway) are back to normal here in exurban Trumpland.  If this disease is less virulent in the summer months, and just the act of being outdoors will promote that to some extent, then we many see that large reemergence in the Fall that has been predicted.  People who don't agree with the CDC guidance, and there are huge numbers in that camp, are not going to go for Shutdown 2.0 no matter the need.  This can get really ugly by October, and ultimately affect the election.  

There are way too many moving parts to this story.

I agree there are lots of moving parts, but the key is that if you don’t take the isolation seriously, R stays higher than one. That means exponential growth. That to me means something must give, and likely long before October.

[sbarrera]

(05-25-2020, 09:52 AM)David Horn Wrote:

(05-24-2020, 01:20 PM)sbarrera Wrote: Using this sort of nuanced data to take intelligent, coordinated action is exactly what strong national leadership should/would be doing. But alas, we have a dumpster fire of a Federal government presided over by a criminal lunatic.

 
You know, if you have an opinion, you should share it. 

[David Horn]

(05-25-2020, 10:38 AM)Bob Butler 54 Wrote:

(05-25-2020, 10:06 AM)David Horn Wrote: Report from the hinterlands: everyone (well, far too many anyway) are back to normal here in exurban Trumpland.  If this disease is less virulent in the summer months, and just the act of being outdoors will promote that to some extent, then we many see that large reemergence in the Fall that has been predicted.  People who don't agree with the CDC guidance, and there are huge numbers in that camp, are not going to go for Shutdown 2.0 no matter the need.  This can get really ugly by October, and ultimately affect the election.  

There are way too many moving parts to this story.

I agree there are lots of moving parts, but the key is that if you don’t take the isolation seriously, R stays higher than one.  That means exponential growth.  That to me means something must give, and likely long before October.

So, when they all get sick. who gets; the blame?  Trump is the logical choice, but he's exempt, for some reason.  That leaves wild conspiracy theories, with nothing more behind them than rage.  Let's assume that the Trumpster is defeated and Biden is elected by a wide margin.  Some folks, including the Never Trumpers from the GOP, are getting scared that Trump will destroy the election, pardon every one including himself, and refuse to hand overpower.  It's hard to know how that plays prior to January 20, 2021.  Even then, it could be contentious.

[Warren Dew]

(05-24-2020, 09:46 PM)Bob Butler 54 Wrote:

(05-24-2020, 09:35 PM)Warren Dew Wrote:

(05-24-2020, 01:05 PM)sbarrera Wrote: Seems the lockdown measure are more neccessary in the hot zone, and should be continued.

I don't think it's obvious that the measures that are currently failing to control the number of cases in the "hot zone" are the ones that should be continued.

I live in an urban suburb of Boston, a hot area of a hot zone.  We had a fairly severe shutdown with people basically going to grocery and drug stores and nowhere else.  This reduced travel and should have reduced the viral reproduction rate R by a factor of 10, but the actual result of a new case reduction that's extremely gradual showed a reduction in R by a factor of 3 at most.  Something is going on beyond the shutdown.

Possibilities include a very high R on the subway system, which remained open, or transmission by some other vector, like food or something, or an external driver, like people travelling from New York.  We don't know what it was, but we need to find out, because we need for the interventions to become more effective, rather than just resorting to the ones that are most draconian but are of limited effectiveness.

I'm hoping masks will help, but masks will only address the same tranmission vectors that we thought we were already addressing.

I suspect a lot of it is individuals failing to take the precautions seriously enough.  Mothers holding sleepovers, or dropping kids off at shut down malls to socialize might be examples.

Have you seen a lot of people not taking the precautions seriously where you are, and where is that?  In my area, Cambridge/Somerville, people seemed to be very serious about observing the precautions, at least up until masks were required.  There are maybe 10% scofflaws regarding masks, either not wearing them at all, or wearing them around the neck only, or over the mouth but not the nose.  But it's early to see results from the May 6 mask requirement yet.

[Warren Dew]

(05-25-2020, 07:21 AM)Mikebert Wrote:

(05-24-2020, 09:35 PM)Warren Dew Wrote: I don't think it's obvious that the measures that are currently failing to control the number of cases in the "hot zone" are the ones that should be continued.

I live in an urban suburb of Boston, a hot area of a hot zone.  We had a fairly severe shutdown with people basically going to grocery and drug stores and nowhere else.  This reduced travel and should have reduced the viral reproduction rate R by a factor of 10,

I don't understand how it is obvious that the measures being used to control the number of cases in the "hot zone" are failing. Over the last month, the daily death rate has fallen by 75%. Over the same period of time in the rest of the country the death rate has been slightly up (6%).

Where are you getting your numbers?  Wikipedia numbers show the daily death rate, averaged over 7 days to smooth out low weekend reporting, is a little over 60.  A month ago, it was about 150.  That's a factor of 2.5 reduction, not a factor of 4 reduction.

In contrast, the previous month, there was about a factor of 40 increase.  If R is 3 for a factor of 40 increase in a month, then the factor of 2.5 reduction reflects an R of about 0.8.

If you look at South Korean numbers, their increase rate was even faster - a factor of 10 in new cases in a week - but their decrease rate was just as fast, with new cases falling by a factor of 10 the next week.  They cut their R to something like 0.3 or 0.4.  So what did they do that we didn't do?

[Bob Butler 54]

(05-25-2020, 05:53 PM)Warren Dew Wrote: Have you seen a lot of people not taking the precautions seriously where you are, and where is that?  In my area, Cambridge/Somerville, people seemed to be very serious about observing the precautions, at least up until masks were required.  There are maybe 10% scofflaws regarding masks, either not wearing them at all, or wearing them around the neck only, or over the mouth but not the nose.  But it's early to see results from the May 6 mask requirement yet.

Mostly I am staying in isolation. Most of the reporting I've heard comes from the Plymouth local group on Facebook. They are reporting a number of people who are not so serious about the isolation, leaving gaping holes, especially with letting kids socialize. If they are correct, that helps account for why you are seeing a lesser change in R. You give a number of other possible reasons for it.

Regardless, Trump's happy talk don't take it seriously propaganda does seem to be knocking a hole in the hot zone governor's alliance attempt at isolation. We seem to have knocked R down below one, but without cooperation among everybody we won't be able to open up the economy again without bringing R above one.

Notably, nursing home, meat packing plants and prisons are not the only places where a dense packing of people occurs. Opening up will mean restarting all sorts of problematic businesses. Without tests to pick up the local outbreaks, the outbreaks will tend do spread. We'll have to see the net balance.

[Eric the Green]

(05-25-2020, 05:53 PM)Warren Dew Wrote:

(05-24-2020, 09:46 PM)Bob Butler 54 Wrote:

(05-24-2020, 09:35 PM)Warren Dew Wrote:

(05-24-2020, 01:05 PM)sbarrera Wrote: Seems the lockdown measure are more neccessary in the hot zone, and should be continued.

I don't think it's obvious that the measures that are currently failing to control the number of cases in the "hot zone" are the ones that should be continued.

I live in an urban suburb of Boston, a hot area of a hot zone.  We had a fairly severe shutdown with people basically going to grocery and drug stores and nowhere else.  This reduced travel and should have reduced the viral reproduction rate R by a factor of 10, but the actual result of a new case reduction that's extremely gradual showed a reduction in R by a factor of 3 at most.  Something is going on beyond the shutdown.

Possibilities include a very high R on the subway system, which remained open, or transmission by some other vector, like food or something, or an external driver, like people travelling from New York.  We don't know what it was, but we need to find out, because we need for the interventions to become more effective, rather than just resorting to the ones that are most draconian but are of limited effectiveness.

I'm hoping masks will help, but masks will only address the same tranmission vectors that we thought we were already addressing.

I suspect a lot of it is individuals failing to take the precautions seriously enough.  Mothers holding sleepovers, or dropping kids off at shut down malls to socialize might be examples.

Have you seen a lot of people not taking the precautions seriously where you are, and where is that?  In my area, Cambridge/Somerville, people seemed to be very serious about observing the precautions, at least up until masks were required.  There are maybe 10% scofflaws regarding masks, either not wearing them at all, or wearing them around the neck only, or over the mouth but not the nose.  But it's early to see results from the May 6 mask requirement yet.

It doesn't matter what anyone has seen in person. I do get pictures on the news showing lots of people gathering too close in various situations now, especially in parks and beaches, and also demonstrations and celebrations. Now some churches and restaurants may be opened. It could be like Mardi Gras in New Orleans, after which one of the first big outbreaks in the USA happened.

[Eric the Green]

(05-25-2020, 07:17 AM)Mikebert Wrote:

(05-24-2020, 01:05 PM)Eric the Green Wrote: The graph compared the two zones, showing the rest of US now has a higher rate than the hot zone, but you say one trend line is 10X the other. The graph might be less confusing if it compared the two lines on the same scale.

Another observation from my daily observation of the stats: MD, VA and DC are also part of the hot zone.

The scale on the left is 1/10 the scale on the right. If both were plotted on the same axis it would make it hard to see the shape of the rest of the country.

I chose the top 7 states in terms of total deaths as the Hot Zone, when I started to track these. CA has since bumped CT to 8th place, but because CA is so large, its per capita death rates are very small, so I wouldn't include them any way. The next two states in the total death ranking are LA and MD, so if I chose to expand the Hot State category they would be next. Next after them would be FL, which I would exclude based on size, like CA. Then comes OH, IN, and GA, followed by TX (which I would exclude like CA and FL). Then comes CO and only then VA.  So VA is not really part of the hot zone.

DC is hot in terms of per capita deaths, but has a small number of total deaths, like RI. Consider how this graph is constructed. The Hot Zone is the sum of dealths in seven states with the highest deaths. Adding in more states with small numbers of death will not significantly change the plot, they will only serve to divide the total deaths by a bigger population and water down the finding. 

A key thing to remember is NY accounts for 29% of the deaths in the whole country and 45% of the deaths in the hot zone. I chose the other six states partly to reduce the dominance of NY in the data set, while removing their dynamics from the national data. When you plot the national data you see a peak and decline afterward. But this is misleading. It is an artifact of including NY and a handful of other states in the total. Take those out (i.e. the Hot Zone) and you get the profile in a majority of the country. There was no peak, no "first wave".  It's just a steady progression.  As states open up, the state and local health departments will be working to isolate infected people since we now have MUCH more testing that we did in March. There will probably be no "second wave".  The flat trend may be replaced by a slowly rising trend, but that is a lot less scary.

I would point out that the shape of the hot zone profile is also shown by 4 hot zone state that are not NY. Two are adjacent to NYC (NJ, CT) and so are really part of the NYC outbreak.  Another state (MA) may are may not have its own outbreak. Then there is my state (MI) which likely got its own innoculum from Europe or maybe even Wuhan because of the links between the auto industry and suppliers there. So I consider MI to be a separate outbreak, like the early ones in WA and CA. These outbreaks were crushed by the authorities, keeping these states from becoming part of the hot zone.

LA may have had its own outbreak too, I am not very familiar with their experience.

It's a good graph and method. THere's a difference between the "hot" states and the rest of the country.

I might think of the hot zone as the eastern seaboard from VA to MA, a contiguous territory being a "zone." VA and MD are hot because their # of new cases is frequently among the highest now. I would call that entire area the hot zone.

It has been hot because of its location and its demographic.

I don't think we still do enough testing. With so many infected people and newly infected people out there, a second wave could develop after too much opening up. Trump is pushing for a second wave. But predicting this thing is hard just based on what's happening and the surface stats.

[Bob Butler 54]

CNN is reporting on the lax attitude of many Americans, that even while cases are going up in some states the attitude is getting easier.  One comment...

Quote:"My family has the same mindset as me and we kind of just agreed that if we get it, we get it. We're going to handle it as a family and get over it," one beachgoer told CNN's Gary Tuchman.

This sort of reflects what I am hearing on the local Facebook group. Many are not taking this seriously, thus the R value is higher than it could be.

[Warren Dew]

(05-25-2020, 10:18 PM)Eric the Green Wrote: I might think of the hot zone as the eastern seaboard from VA to MA, a contiguous territory being a "zone."

Notably absent from Mikebert's "hot zone" is Rhode Island.  It's notable because, unlike the other northeastern states that are in the zone, Rhode Island imposed travel restrictions from New York.

[Mikebert]

(05-25-2020, 06:06 PM)Warren Dew Wrote:

(05-25-2020, 07:21 AM)Mikebert Wrote:

(05-24-2020, 09:35 PM)Warren Dew Wrote: I don't think it's obvious that the measures that are currently failing to control the number of cases in the "hot zone" are the ones that should be continued.

I live in an urban suburb of Boston, a hot area of a hot zone.  We had a fairly severe shutdown with people basically going to grocery and drug stores and nowhere else.  This reduced travel and should have reduced the viral reproduction rate R by a factor of 10,

I don't understand how it is obvious that the measures being used to control the number of cases in the "hot zone" are failing. Over the last month, the daily death rate has fallen by 75%. Over the same period of time in the rest of the country the death rate has been slightly up (6%).

Where are you getting your numbers?  Wikipedia numbers show the daily death rate, averaged over 7 days to smooth out low weekend reporting, is a little over 60.  A month ago, it was about 150.  That's a factor of 2.5 reduction, not a factor of 4 reduction.

In contrast, the previous month, there was about a factor of 40 increase.  If R is 3 for a factor of 40 increase in a month, then the factor of 2.5 reduction reflects an R of about 0.8.

If you look at South Korean numbers, their increase rate was even faster - a factor of 10 in new cases in a week - but their decrease rate was just as fast, with new cases falling by a factor of 10 the next week.  They cut their R to something like 0.3 or 0.4.  So what did they do that we didn't do?

I get my numbers of Worldometer, from Wikipedia and for some states from these guys. https://covidtracking.com/data

Are you talking about Massachusetts only? The hot zone is 7 states, not just one. For Massachusetts my most recent 7-day avg is 79, down from 167 a month ago, or 53% down.

But, Michigan is down 66%. New York is down 80%. New Jersey is down 61%, and Connecticut is down 65%. Pennsylvania is down 27% and Illinois is actually up 6%. So your state is in the middle of the pack.

[Mikebert]

(05-26-2020, 12:03 PM)Warren Dew Wrote:

(05-25-2020, 10:18 PM)Eric the Green Wrote: I might think of the hot zone as the eastern seaboard from VA to MA, a contiguous territory being a "zone."

Notably absent from Mikebert's "hot zone" is Rhode Island.  It's notable because, unlike the other northeastern states that are in the zone, Rhode Island imposed travel restrictions from New York.

I described why states like RI weren't included to Eric. it is so small its contribution would be completely overwhelmed by the other states so its not worth to track. It takes a bit of time to track all these states and a few countries.

[Mikebert]

(05-25-2020, 10:18 PM)Eric the Green Wrote:

(05-25-2020, 07:17 AM)Mikebert Wrote:

(05-24-2020, 01:05 PM)Eric the Green Wrote: The graph compared the two zones, showing the rest of US now has a higher rate than the hot zone, but you say one trend line is 10X the other. The graph might be less confusing if it compared the two lines on the same scale.

Another observation from my daily observation of the stats: MD, VA and DC are also part of the hot zone.

The scale on the left is 1/10 the scale on the right. If both were plotted on the same axis it would make it hard to see the shape of the rest of the country.

I chose the top 7 states in terms of total deaths as the Hot Zone, when I started to track these. CA has since bumped CT to 8th place, but because CA is so large, its per capita death rates are very small, so I wouldn't include them any way. The next two states in the total death ranking are LA and MD, so if I chose to expand the Hot State category they would be next. Next after them would be FL, which I would exclude based on size, like CA. Then comes OH, IN, and GA, followed by TX (which I would exclude like CA and FL). Then comes CO and only then VA.  So VA is not really part of the hot zone.

DC is hot in terms of per capita deaths, but has a small number of total deaths, like RI. Consider how this graph is constructed. The Hot Zone is the sum of dealths in seven states with the highest deaths. Adding in more states with small numbers of death will not significantly change the plot, they will only serve to divide the total deaths by a bigger population and water down the finding. 

A key thing to remember is NY accounts for 29% of the deaths in the whole country and 45% of the deaths in the hot zone. I chose the other six states partly to reduce the dominance of NY in the data set, while removing their dynamics from the national data. When you plot the national data you see a peak and decline afterward. But this is misleading. It is an artifact of including NY and a handful of other states in the total. Take those out (i.e. the Hot Zone) and you get the profile in a majority of the country. There was no peak, no "first wave".  It's just a steady progression.  As states open up, the state and local health departments will be working to isolate infected people since we now have MUCH more testing that we did in March. There will probably be no "second wave".  The flat trend may be replaced by a slowly rising trend, but that is a lot less scary.

I would point out that the shape of the hot zone profile is also shown by 4 hot zone state that are not NY. Two are adjacent to NYC (NJ, CT) and so are really part of the NYC outbreak.  Another state (MA) may are may not have its own outbreak. Then there is my state (MI) which likely got its own innoculum from Europe or maybe even Wuhan because of the links between the auto industry and suppliers there. So I consider MI to be a separate outbreak, like the early ones in WA and CA. These outbreaks were crushed by the authorities, keeping these states from becoming part of the hot zone.

LA may have had its own outbreak too, I am not very familiar with their experience.

It's a good graph and method. THere's a difference between the "hot" states and the rest of the country.

I might think of the hot zone as the eastern seaboard from VA to MA, a contiguous territory being a "zone." VA and MD are hot because their # of new cases is frequently among the highest now. I would call that entire area the hot zone.

It has been hot because of its location and its demographic.

I don't think we still do enough testing. With so many infected people and newly infected people out there, a second wave could develop after too much opening up. Trump is pushing for a second wave. But predicting this thing is hard just based on what's happening and the surface stats.

The zone is not intended to be geographical. It is conceptual. It is a comparison of the collective behavior in the largest contributors to US deaths relative to the rest. The definition of "big" has been personal, close to Michigan, my state, which I did not expect to get slammed as hard as it did. So its states with more deaths that us, plus two with just under our numbers who have been gaining, plus CT because it is part of the tristate area and has been in other comparisons I've seen on the media.

[Warren Dew]

(05-26-2020, 04:32 PM)Mikebert Wrote: Are you talking about Massachusetts only?

Yes.  If your 75% reduction was for your whole "hot zone", I'll trust you on that, though I think that's dominated by New York.

I think Illinois is different because cases are actually increasing there; Chicago might be on its way to becoming another New York, perhaps in slow motion.

I do think that R hovering so close to 1.0 in so many states seems strange.  How can it be so easy to cut it down from, say, 2 or 3 to 0.9, but then so difficult to cut it from 0.9 to 0.5 or something?

[Bob Butler 54]

(05-26-2020, 06:03 PM)Warren Dew Wrote:

(05-26-2020, 04:32 PM)Mikebert Wrote: Are you talking about Massachusetts only?

Yes.  If your 75% reduction was for your whole "hot zone", I'll trust you on that, though I think that's dominated by New York.

I think Illinois is different because cases are actually increasing there; Chicago might be on its way to becoming another New York, perhaps in slow motion.

I do think that R hovering so close to 1.0 in so many states seems strange.  How can it be so easy to cut it down from, say, 2 or 3 to 0.9, but then so difficult to cut it from 0.9 to 0.5 or something?

I suspect it is the people's attitudes.  It is bad to overload the health system,  but if the health system is ok then let us party. A lot of people will do just barely enough.  This is an understandable attitude, but it doesn't put the virus in the rear view mirror. It doesn't result in a fully open economy.

[David Horn]

(05-26-2020, 07:38 AM)Bob Butler 54 Wrote: CNN is reporting on the lax attitude of many Americans, that even while cases are going up in some states the attitude is getting easier.  One comment...

Quote:"My family has the same mindset as me and we kind of just agreed that if we get it, we get it. We're going to handle it as a family and get over it," one beachgoer told CNN's Gary Tuchman.

This sort of reflects what I am hearing on the local Facebook group.  Many are not taking this seriously, thus the R value is higher than it could be.

I don't agree completely. These folks that have made the decision to socialize are being serious, but reaching conclusions that logic doesn't support. Most people need to be with other people, and that alone will draw them out to mingle ... hopefully in some rational way.  Then again, I live in an area that doesn't take this all that seriously for tribal and political reasons, so don't count on 'rational'.

[Warren Dew]

(05-26-2020, 06:25 PM)Bob Butler 54 Wrote: I suspect it is the people's attitudes.

That may well be it.  On my weekly grocery run this morning, a lot more people were ignoring the mask wearing rules, with maybe 20% wearing them around their necks or not having one at all.  This would, however, assume that people are good at evaluating the real risk, perhaps subconsciously, and behaving accordingly.

It would also imply that we could reopen fully and count on people to adjust properly.  I'm not sure I'm ready to trust people that far.