COVID COVID-19 Coronavirus Containment Efforts

[morrobay]

[

My wife also informed that the grandson of an acquaintance has lost two friends (in their 20s) from COVID-19. So just because one is young, 20-49, one should not consider oneself invincible/invulnerable to COVID-19. We don't who is vulnerable a priori.

Why are some vulnerable to infection/ degree of Covid19 symptoms. Most likely in the initial infection and virus loading between the virus protein receptor binding subunit to the host ACE2. Any genetic variation in ACE2 structure could effect the virus protein host ACE2 adhesion prier to virus entry into host cells. The mechanism for the virus binding hotspots are protein salt bridges ( carboxylate RCOO- on one amino acid and Ammonium RN(H)3 + on the other amino acid by ionic or hydrogen bonding.

 

[mfb]

I just heard Willam Haseltine (President and Chair, ACCESS Health International, former professor, Harvard Medical School) say that the virus outer surface has changed so that it is 10x more infectious than it was in January/February. A lot of folks are experiencing permanent lung damage, even if they recover.

They found a mutation that seems to outperform other strains, both in terms of infected people and in the lab.

Preprint: https://www.scripps.edu/news-and-ev...611-choe-farzan-sars-cov-2-spike-protein.html
News: https://www.cnbc.com/2020/07/02/the...me-more-infectious-dr-anthony-fauci-says.html

 

[Vanadium 50]

My wife also informed that the grandson of an acquaintance has lost two friends (in their 20s) from COVID-19. So just because one is young, 20-49, one should not consider oneself invincible/invulnerable to COVID-19. We don't who is vulnerable a priori.

While that is true, it also shouldn't be used to conclude risks are independent of age. ("We're all in this together, taken to extremes") The mortality rate for 20-29 is two orders of magnitude smaller than for 80+.

It especially shouldn't be taken as a reason not to focus on those most at risk. Massachusetts has the 4th highest mortality rate per 100,000. If they were able to keep their nursing homes uninfected they would be #13, just above Indiana.

 

[Vanadium 50]

he virus outer surface has changed so that it is 10x more infectious than it was in January/February

I'm not sure how to interpret this. If it means the new strain has R0 above 10 (and probably above 15 or 20) it makes this the most infectious disease ever (well above measles) and the public health aspects are clear. End the lockdown now because we're all going to get infected, sooner rather than later.

If he means that R0 was 0.15 or so in February, why did it spread so rapidly?

 

[chemisttree]

I'm not sure how to interpret this. If it means the new strain has R0 above 10 (and probably above 15 or 20) it makes this the most infectious disease ever (well above measles) and the public health aspects are clear. End the lockdown now because we're all going to get infected, sooner rather than later.

If he means that R0 was 0.15 or so in February, why did it spread so rapidly?

While I agree with your point that we will all get this eventually, I don’t believe that ending the “lockdown,” such as it is, is a good idea. At this point the lockdown is more about titrating limited healthcare resources than ending the pandemic. Personally, I want to put off the day that I’m infected as long as possible and hope for a vaccine or the best treatment possible.

Wearing a mask everywhere and avoiding crowds isn’t really much of a lockdown after work. And reopening businesses at some level must occur pretty soon, IMO. Had enough of shopping at half-stocked grocers. It’s stressful sensing the precarious nature of our food supply every time I go out.

I’m getting tired of working from home! I started a new job in late April. Really weird, right? I reported to work my first day... at my dining room table! I’ve been there ever since. I’ve had colleagues leave for other opportunities that I’ve never met in person. I sing happy birthday to people I’ve never met. Is this real or the matrix?

These times are so scary-weird!

 

[Vanadium 50]

While I agree with your point that we will all get this eventually, I don’t believe that ending the “lockdown,” such as it is, is a good idea. At this point the lockdown is more about titrating limited healthcare resources than ending the pandemic.

My point isn't that we should end the lockdown immediately no matter what. My point is that if R0 has in fact jumped up from around 2 to around 20 (which would make Covid the most contagious widepread disease in history) lockdown policies intended to bring R0 down from 2-ish to under 1 will be ineffective. Indeed, if R0 is really 20, it's too late. We're all infected. 20 is huge.

As far as "titrating limited healthcare resources", that's back to "flatten the curve". We seem to have moved beyond that, but in any event, if R0 is 20 you aren't going to be able to flatten that.

Because of the exponential nature, a factor 10 more contagious will have enormous impact.

 

[Astronuc]

I'm not sure how to interpret this. If it means the new strain has R0 above 10 (and probably above 15 or 20) it makes this the most infectious disease ever (well above measles) and the public health aspects are clear. End the lockdown now because we're all going to get infected, sooner rather than later.

If he means that R0 was 0.15 or so in February, why did it spread so rapidly?

Good points. I think the 10x seems to be a ballpark or order of magnitude estimate. I'd like to know how that number is determined, and how it relates to R_o. R_o is an epidemiological number, and from I can see from super-spreading events, it seems largely circumstantial.

Complexity of the Basic Reproduction Number (R_o)
https://wwwnc.cdc.gov/eid/article/25/1/17-1901_article

With respect to the infectiousness of SARS-CoV-2, and its R_o, I recently participated in a video-conference from a member of a team studying the virus and its spread, and a comment was made that the team has determined that the virus is relatively fragile outside the human body. They know this because they have measured it on various surfaces, and have measured the virus exposed to various environments, and apparently it doesn't survive very well in the natural environment outside of the human body.

 

[gleem]

I do not know if this article has been reference before in this thread but I will post it anyway.

Complexity of the Basic Reproduction Number (R0)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302597/

Abstract
The basic reproduction number (R0), also called the basic reproduction ratio or rate or the basic reproductive rate, is an epidemiologic metric used to describe the contagiousness or transmissibility of infectious agents. R0 is affected by numerous biological, sociobehavioral, and environmental factors that govern pathogen transmission and, therefore, is usually estimated with various types of complex mathematical models, which make R0 easily misrepresented, misinterpreted, and misapplied. R0 is not a biological constant for a pathogen, a rate over time, or a measure of disease severity, and R0 cannot be modified through vaccination campaigns. R0 is rarely measured directly, and modeled R0 values are dependent on model structures and assumptions. Some R0 values reported in the scientific literature are likely obsolete. R0 must be estimated, reported, and applied with great caution because this basic metric is far from simple.

 

[Jarvis323]

Remember that R0 isn't really a measure of infectiousness per say; it's a measure of transmission in a population dependent on all of the other factors (e.g. if the lockdown ends, R0 goes up). If I remember (I could be wrong) I thought that the 10X number was regarding how infectious it is in cell cultures. So I don't know what that translates into in terms of affecting R0. Transmission rate in a population involves other things such as how the virus transports from one person to another. Whatever the change does to "infectiousness" however they measured it, it also might not be a linear relationship with R0.

What we know is that the mutation results in the presentation of more functional spike proteins. And we know that this strain is dominating over the others, which suggests that it has a higher R0.

Even if we all get it eventually, as time goes on, treatments are getting better and the death rate is getting lower because of that. I'de rather get it later than sooner.

 

[Astronuc]

Even if we all get it eventually, as time goes on, treatments are getting better and the death rate is getting lower because of that. I'd rather get it later than sooner.

The death rate is lower, but many (I've heard 15% of COVID-19 patients) have long-term adverse health effects, e.g., possible neurological damage, cardiovascular damage, and damage to various organs, even if they do not have permanent lung damage. Based on 2.9 million cases in the US, then more than 400,000 people have long term adverse health effects.

 

[Jarvis323]

The death rate is lower, but many (I've heard 15% of COVID-19 patients) have long-term adverse health effects, e.g., possible neurological damage, cardiovascular damage, and damage to various organs, even if they do not have permanent lung damage. Based on 2.9 million cases in the US, then more than 400,000 people have long term adverse health effects.

That is true. I've even heard of people with very mild cases finding that their lungs have been damaged. It's quite scary considering that we still don't know all of the long term damage it may be causing. And I've heard that many survivors of severe cases end up with severe kidney damage and must go on dialysis.

 

[atyy]

Good points. I think the 10x seems to be a ballpark or order of magnitude estimate. I'd like to know how that number is determined, and how it relates to R_o. R_o is an epidemiological number, and from I can see from super-spreading events, it seems largely circumstantial.

I'd guess it's a ballpark and does not refer to R. I think it refers to lab experiments reported in https://doi.org/10.1016/j.cell.2020.06.043 where they put the variants into other viruses (not coronaviruses), and measure the infectious titer. Referring to Fig 6A-C and the legend on p16, one variant has infectious titers that are 3 to 6 times greater. I don't know how that translates into R.

They state limitations of the study
"Shifts in frequency towards the G614 variant in any given geographic region could in principle result from either founder effects or sampling biases; it was the consistency of this pattern across regions where both forms of the virus were initially co-circulating that led us to suggest that the G614 form might be transmitted more readily due to an intrinsic fitness advantage ...

Infectiousness and transmissibility are not always synonymous, and more studies are needed to determine if the D614G mutation actually led to an increase number of infections, not just higher viral loads during infection."

Related paper
https://www.biorxiv.org/content/10.1101/2020.06.12.148726v1

 

[Astronuc]

An additional thought on the R₀; at work we received travel advisories about the potential to be infected on a plane, for example. A diagram (assuming no one wearing a mask) indicated that folks in the rows ahead and behind could be infected by one sitting in a given row (in a middle seat of 3), and certainly the folks in adjacent seats, indicating at least an R₀ between 2 and 8. A person sitting in an aisle seat could infect others sitting across the aisle, then R₀ could increase to as much as 17 (8+9) in a typical 2x3 seating arrangement. If an infected person traverses the aisle, then it's possible many more (tens/dozens) could be infected.

 

[Zap]

Is the media's claim that the protests and riots did not contribute to the second surge well founded? I find it hard to believe. If I remember correctly, reopening was occurring at around the same time. It might be worth noting that protesting is still occurring.

Anyone else suffering from lack of motivation during this thing? I've been cooped up in my room for months now, and I lost focus a long time ago. I don't know how I can live a productive life anymore.

 

[chemisttree]

Is the media's claim that the protests and riots did not contribute to the second surge well founded? I find it hard to believe. If I remember correctly, reopening was occurring at around the same time. It might be worth noting that protesting is still occurring.

I think that’s right (bolded) but I don’t have any data to back it up. In San Antonio we are seeing a big spike. Something like 1,300 new cases just today. We haven’t had large scale protests that could explain those numbers. Hidalgo county in deep south Texas is on emergency stay inside orders. I’ve not heard of any protests down there that could explain their numbers. McAllen Texas is not a hotbed of BLM protests. There are no free hospital beds in the Valley (Rio Grande Valley) right now.

This spike is about people getting tired of the restrictions on their lives meeting a relaxation of distancing and business closures rules. There is really nothing else we can do in response except flatten the curve. It’s here today and it’s here to stay. We’re going to be wearing masks for some time to come. They’ve told us at work that we are going to be telecommuting at least through August. Two months more... minimum.

 

[chemisttree]

As far as "titrating limited healthcare resources", that's back to "flatten the curve". We seem to have moved beyond that, but in any event, if R0 is 20 you aren't going to be able to flatten that.

Because of the exponential nature, a factor 10 more contagious will have enormous impact.

The D614G mutation is responsible for the increase in infectiveness and that strain has been seen in 70% of cases back in April. It’s likely much more prevalent today. This came into the US from Europe and is responsible for the surge seen in New York most likely. New York flattened the curve so it’s possible. New York is somehow managing to keep the Ro close to 1 so it’s unlikely to currently have an Ro of ~20.

 

[Astronuc]

I was collecting data periodically from https://ncov2019.live/data/unitedstates
Their number disagree with other sites, and with some data from some states, but it's useful in ranking the states (over 3 months: April, May and June, and 3 days into July or about 94 days into July):

Date       31-Mar-20                    3-Jul-20
            Positive                    Positive
TOTAL        181,906     TOTAL         2,890,588
New York      75,795     New York        420,774
New Jersey    18,696     California      252,252
Michigan       7,615     Texas           190,387
California     7,453     Florida         178,594
Florida        6,338     New Jersey      176,455
Massachusetts  5,752     Illinois        146,872
Washington     5,250     Massachusetts   109,628
Louisiana      5,237     Pennsylvania     93,418
Illinois       5,057     Arizona          91,872
Pennsylvania   4,843     Georgia          90,493
Georgia        3,817     Michigan         72,175
Texas          3,186     North Carolina   70,562
Colorado       2,627     Maryland         68,961
Connecticut    2,571     Virginia         64,393
Ohio           2,199     Louisiana        63,289
Indiana        2,159     Ohio             55,763
Tennessee      2,026     Tennessee        48,712
Maryland       1,660     Indiana          46,915
North Carolina 1,498     Connecticut      46,717
Wisconsin      1,351     Alabama          41,865
Missouri       1,327     South Carolina   41,532
Arizona        1,289     Minnesota        37,624
Virginia       1,250     Washington       35,641
Nevada         1,113     Colorado         33,612
Alabama          974     Iowa             30,463
Mississippi      937     Wisconsin        30,317
South Carolina   925     Mississippi      29,684
Utah             887     Utah             23,866
Minnesota        629     Missouri         23,717
Oregon           606     Arkansas         22,622
Oklahoma         565     Nevada           20,718
Arkansas         508     Nebraska         19,660
Iowa             497     Rhode Island     16,991
Dist of Columbia 495     Kentucky         16,376
Kentucky         480     Kansas           16,005
Idaho            476     Oklahoma         15,069
Kansas           428     New Mexico       12,776
Rhode Island     408     Delaware         11,923
New Hampshire    314     Dist of Columbia 10,435
Maine            303     Oregon            9,636
Vermont          293     Puerto Rico       7,683
New Mexico       281     Idaho             6,994
Delaware         264     South Dakota      6,978
Puerto Rico      239     New Hampshire     5,857
Hawaii           204     North Dakota      3,722
Montana          185     Maine             3,373
Nebraska         153     West Virginia     3,126
West Virginia    145     Wyoming           1,582
North Dakota     122     Vermont           1,236
Alaska           119     Montana           1,128
Wyoming          109     Alaska            1,063
South Dakota     101     Hawaii              975

Guam              69     Guam                280
US Virgin Islands 30     US Virgin Islands    98
N. Mariana Islands 2     N. Mariana Islands   31
                    
Total deaths (includes some presumptive deaths)
               3,655                     132,101
data from https://ncov2019.live/data/unitedstates
Not in March 31 data but included in July 3:
                         Veteran Affairs  24,111
                         U.S. Military    18,071
                         Federal Prisons   7,798
                         Navajo Nation     7,613

Covidtracking.com reports
Total positive 199,707 and 4,216 deaths on March 31
Total positive 2,786,059 and 122,158 deaths on July 3
https://covidtracking.com/data
https://covidtracking.com/data/us-daily

Data is constantly updated and corrected by the states.
It is not clear that each website corrects historic data.

 

[morrobay]

The D614G mutation is responsible for the increase in infectiveness and that strain has been seen in 70% of cases back in April. It’s likely much more prevalent today. This came into the US from Europe and is responsible for the surge seen in New York most likely. New York flattened the curve so it’s possible. New York is somehow managing to keep the Ro close to 1 so it’s unlikely to currently have an Ro of ~20.

So if the surge in cases in the U.S. are from strain(s) from Europe. Then what is going so wrong in the U.S. ?
The population combining U.K., Spain, Germany and Russia are apprx that of the U.S. But their cases are apprx 1.5 million and the U.S. cases are apprx 2.5 million. Could it be that the U.S. population is in poorer health in general while taking more medications and higher rates of diabetes , hypertension and obesity ?

 

[PeroK]

So if the surge in cases in the U.S. are from strain(s) from Europe. Then what is going so wrong in the U.S. ?
The population combining U.K., Spain, Germany and Russia are apprx that of the U.S. But their cases are apprx 1.5 million and the U.S. cases are apprx 2.5 million. Could it be that the U.S. population is in poorer health in general while taking more medications and higher rates of diabetes , hypertension and obesity ?

One comparison would be between the USA and the five largest Western European countries: Germany, UK, Italy, France and Spain. The populations are rougly equal. The USA has more than twice as many cases, but a much lower death rate. There have been more deaths in total in those five European countries than in the USA.

The current resurgence of the number of cases in the USA is greater than anything in the first wave across the US and Western Europe, but the death rate remains low.

I posted some figures a few pages back on a comparison of death rates globally.

The death rate in the UK is extraordinarily high (3-4 times as high as the USA), although there's been very little analysis of this by the news media here.

 

[hmmm27]

Is the media's claim that the protests and riots did not contribute to the second surge well founded?

The article that I read cited testing of area residents - not protesters/rioters - IIRC less than two weeks after a protest in that area. Draw your own conclusions.

Maybe society should consider a temporary suspension of civil lefts.

 

[Vanadium 50]

Covidtracking.com reports

Do you understand the single-day spike in deaths in late June?

 

[Astronuc]

Do you understand the single-day spike in deaths in late June?

I believe there was one day when one of the states reported previously unreported deaths, but I don't know the time period. In March, I noticed that some data changed due to corrections/revisions. Different states have different reporting methods, and within states, different health departments may do things differently.

It appears that the bump from June 24 to June 25 has to do with the way NJ reports data, and how the covidtracking site uses (manipulates?) the data. On June 25, NJ began reporting total probable deaths, which on the June 25 was about 1854 and so NJ numbers jumped. California had reported about 100, Florida 46, Texas 47, and other states lesser numbers.https://covidtracking.com/data/state/california#historical
California deaths
Thu Jun 25 2020 5,733
Wed Jun 24 2020 5,632

https://covidtracking.com/data/state/florida#historical
Florida deaths
Thu Jun 25 2020 3,423
Wed Jun 24 2020 3,377

https://covidtracking.com/data/state/new-jersey#historical
New Jersey Deaths
Thu Jun 25 2020 14,872 this is dubious, and that and successive numbers should have a caveat
Wed Jun 24 2020 12,995
https://covidtracking.com/screenshots/NJ/NJ-20200625-184444.png

https://covidtracking.com/data/state/texas#historical
Texas deaths
Thu Jun 25 2020 2,296
Wed Jun 24 2020 2,249

I'm aware that counties and states have had concerns about how to report some deaths with multiple co-morbities, and deaths where a COVID test was not performed by the patients had symptoms or COVID or SARS-like illness.

 

[Vanadium 50]

I'm away that counties and states have had concerns about how to report some deaths with multiple co-morbities,

There was also a change in Medicare coding. Reimbursements for "Disease X with Covid" are different for "Covid with Disease X" and in fact changed. So I would expect the statistics to follow suit.

 

[Vanadium 50]

Covidtracking.com reports

One can make a number of interesting plots, especially if one enters in population (by hand, unfortunately) to normalize. Some have a ready explanation, others are more puzzling.

There is a strong correlation between hospitalizations and deaths, which is what I would have expected. (Note that this is actually "in a hospital today today" vs. "total deaths".) There is also a strong correlation between fraction testing positive and fraction hospitalized. Again, what I expected. The curve looks almost quadratic, i.e. as if the death rate depends on the square of the positive-testing fraction, which I am going to assume is just random noise.

This would suggest that the fraction testing positive would be strongly correlated with the fraction hospitalized. It is correlated, but there's a lot more spread.

Plotting the testing fraction vs. positivity fraction shows that they are largely independent of each other, which is what I would expect. There is a slight positive correlation, which I don't understand and a strong positive correlation at low testing rates (which are also low positivity rates). The states are AK, MT, HI, WV and VT.

 

[mfb]

The current resurgence of the number of cases in the USA is greater than anything in the first wave across the US and Western Europe, but the death rate remains low.

Deaths are always behind new cases. Give it two weeks and I expect new deaths in the US to rise, at least if states report them accurately.

 

[Zap]

Many protesters were from out of state, if I heard correctly. It would be tough to conclude whether they did or did not contribute to the resurgence based on whether a re-surging area had protests or not. It sounds crazy to say that the protests did not lead to spreading the virus, as the media claims.

Brazil is approximately like United States in population. Brazil has been pretending like the virus does not exist this entire time, and still their numbers are not nearly as bad as ours. So, somehow a country that completely ignored the pandemic is doing a better job at containing it than we are.

 

[PeroK]

Brazil is approximately like United States in population. Brazil has been pretending like the virus does not exist this entire time, and still their numbers are not nearly as bad as ours. So, somehow a country that completely ignored the pandemic is doing a better job at containing it than we are.

There's no plausible analysis of the the global data. In my opinion there must be geo-political factors at play. It's not clear what data you can trust.

The death rate in Western Europe (and more recently the UK in particular) is out of all proportion to the rest of the world, with the possible exception of Mexico.

There are, for example, some countries with large numbers where almost no one dies.

 

[mfb]

Brazil is approximately like United States in population. Brazil has been pretending like the virus does not exist this entire time, and still their numbers are not nearly as bad as ours. So, somehow a country that completely ignored the pandemic is doing a better job at containing it than we are.

~45,000 new cases and ~1200 deaths per day in Brazil, if I scale that to the population of the US it would be ~73,000 and ~1900. The actual US numbers are ~55,000 and ~500. Per capita Brazil reports 50% more new cases and 4 times the deaths. And that despite concerns that they miss even more cases and deaths than the US.
New cases are currently going up in both countries, we'll see how the situation evolves.

 

[OmCheeto]

For the life of me, I can't see anything special about Brazil.
Like lots of nations, the disease came later than sooner.
But like all* the nations, sooner or later, they are going to catch up.
My maths predicts that between July 14th and July 23rd, Brazil will reach cumulative deaths/million parity with the USA.

--------
* Maybe not Singapore. Now there's an anomaly. Though I do like the explanation I've seen as to why it's anomalous.

ps. I am no Nate Silverman, so please don't share my graphs with the news.

 

[morrobay]

Now Bloomberg television is showing the Boston Pops 4 July celebration. Indoors with people without masks singing loudly standing next to others on and off stage. This I cannot fathom.