COVID COVID-19 Coronavirus Containment Efforts

[PeroK]

https://www.statnews.com/2021/01/04...accines-upping-the-stakes-for-the-rest-of-us/

What's the opinion of the experts on here? Is this journalistic exaggeration, or are we risking everything by changing the double vaccination schedule?

 

[mfb]

We have seen that a single dose provides good protection - possibly as good as the two-dose protocol, at least for a while. The BioNTech/Pfizer graph is the most striking example of this. Even if it's not as good as two doses: Delaying the second dose means getting more people protected sooner. Two people with 60% protection are better than one with 80%.

Even rolling out the vaccine at all when there is so much transmission occurring is far from ideal, he said, suggesting it would have been safer to beat down the amount of virus in circulation before beginning the vaccine deployment.

That's a nice approach, but as we have seen that doesn't work well.

 

[atyy]

What's the opinion of the experts on here? Is this journalistic exaggeration, or are we risking everything by changing the double vaccination schedule?

The article has comments from a few other people, and there seem to be differing reasonable views, so I think it's not known for sure. There are other experts quoted in the article besides Paul Bieniasz.

BTW, when we go to Iwasaki's Twitter thread, we see she's concerned about the increased transmissibility of the UK variant. But although there is some evidence to support that, I think the increased transmissibility has not yet been solidly established, eg.Trevor Bedford comments "The @PHE_uk secondary attack rate analysis was not done on the matched cohort. There should be more stratification here. I'm sorry for the confusion. I'd take the 15% vs 10% secondary attack rate with a grain of salt for the moment.".

 

[Rive]

...are we risking everything by changing the double vaccination schedule?

The virus itself is known to cause only partial (? weak, maybe?) immunity: sometimes with very low antibody levels. Compared to - guess only! - 20% of the population having 'natural' unreliable immunity; 6% having artificial 60% immunity or 3% having 95% immunity... Well, the difference does not feels really dramatic.

I think the high number of copies (=> high number of mutations) racing to re-infest that 20% is a far more worse problem.

 

[PeroK]

The virus itself is known to cause only partial (? weak, maybe?) immunity: sometimes with very low antibody levels. Compared to - guess only! - 20% of the population having 'natural' unreliable immunity; 6% having artificial 60% immunity or 3% having 95% immunity... Well, the difference does not feels really dramatic.

I think the high number of copies (=> high number of mutations) racing to re-infest that 20% is a far more worse problem.

Sorry, I can't understand what you are saying here.

 

[mfb]

The virus itself is known to cause only partial (? weak, maybe?) immunity: sometimes with very low antibody levels.

It's good enough to protect almost everyone for at least ~9 months, because double infections are still incredibly rare. They do happen, but not at a level where they would be relevant for the pandemic. In particular, the protection from getting the disease itself is far better than 95% over the observable time range.

 

[Rive]

double infections ... do happen, but not at a level where they would be relevant for the pandemic.

Sorry, but you do not know that. There is no widespread random and regular PCR testing amongst the already infected.
The only thing actually known is that reinfections which are bad enough to be tested again are rare.

Sorry, I can't understand what you are saying here.

From the article:

if you wanted to make a vaccine-resistant strain, what you would do is to build a cohort of partially immunized individuals in the teeth of a highly prevalent viral infection

The virus itself known to be unreliable when it's about antibody levels after an infection. Compared to the virus (which is lacking any quality management standards, as it seems) the vaccine is actually far more reliable (again: it's about antibody levels).
So if somebody is worrying about new strains, then he should look for the growing number of already recovered patients first because at this point they are a far more 'beefy' population of interest for the virus (which were left to grew into a 'healthy' gene pool already, ready for some drifting to occur).

The situation is not good, but the vaccine and its usage is just a very minor part of it.

 

[Jarvis323]

Sorry, but you do not know that. There is no widespread random and regular PCR testing amongst the already infected.
The only thing actually known is that reinfections which are bad enough to be tested again are rare.From the article:

The virus itself known to be unreliable when it's about antibody levels after an infection. Compared to the virus (which is lacking any quality management standards, as it seems) the vaccine is actually far more reliable (again: it's about antibody levels).
So if somebody is worrying about new strains, then he should look for the growing number of already recovered patients first because at this point they are a far more 'beefy' population of interest for the virus (which were left to grew into a 'healthy' gene pool already, ready for some drifting to occur).

The situation is not good, but the vaccine and its usage is just a very minor part of it.

When I was studying the research on immunity months ago, it was thought that antibodies might not last long, but T-memory cell immunity was likely to be pretty reliable and long lasting. I haven't kept up on research since then, except that the vaccines were found to also trigger T-cell immunity. Does anyone know the current knowledge about this issue?

 

[atyy]

So if somebody is worrying about new strains, then he should look for the growing number of already recovered patients first because at this point they are a far more 'beefy' population of interest for the virus (which were left to grew into a 'healthy' gene pool already, ready for some drifting to occur).

It's probably on the time scale of a few years, if it's similar to other coronaviruses.

https://www.biorxiv.org/content/10.1101/2020.12.17.423313v1
A human Coronavirus evolves antigenically to escape antibody immunity
Rachel Eguia, Katharine H. D. Crawford, Terry Stevens-Ayers, Laurel Kelnhofer-Millevolte, Alexander L. Greninger, Janet A. Englund, Michael J. Boeckh, Jesse D. Bloom
Twitter summary by the authors

 

[Jarvis323]

I've been reading through this paper, which goes into depth about the issue.

What are the roles of antibodies versus a durable, high quality T-cell response in protective immunity against SARS-CoV-2?

These findings carry a potentially important message for SARS-CoV-2 vaccines. Most current vaccine candidates are focusing on spike protein as the immunizing antigen, but natural infection induces broad epitope coverage in T-cells. It will be essential to understand the relation between breadth, durability and quality of T-cell responses and resulting protective immunity with SARS-CoV-2 vaccines and natural infection.
...
It would be a public health and “trust-in-medicine” nightmare with potential repercussions for years - including a boost to anti-vaccine forces - if immune protection wears off or antibody-dependant enhancement develops and we face recurrent threats from COVID-19 among the immunized. Data correlating clinical outcomes with laboratory markers of cell-mediated immunity, not only with antibody responses, after vaccination or natural infection with SARS-CoV-2 or other betacoronviruses may prove critically valuable, particularly if protective immunity fades or new patterns of disease emerge.

https://www.sciencedirect.com/science/article/pii/S2590136220300231

Since T-cells give long lasting and cross-reactive protection, not dependent on the spike protein, I would guess that a good T-cell response would be important for minimizing risk of a mutation overcoming vaccine protection. We also already have spike protein mutations that occurred after the vaccines had been developed, so we don't know if the levels of antibody protection seen in trials will be the same against the new fast spreading variant. A population with waning antibody resistance primarily targeting the spike protein, but not good T-cell based protection, would probably be a bad recipe for adaptation. I'm not sure what is known about the effectiveness of vaccine induced T-cells immunity at this stage, except that it is triggered to some extent. The paper mentions some ways to measure T-cell effectiveness, and argues that antibody levels are a bad measure to look at. I also wonder how a second dose of the vaccine affects T-cell immunity.

Another issue I wish I understood more is antibody dependent enhancement.

Antibody-based drugs and vaccines against severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) are being expedited through preclinical and clinical development. Data from the study of SARS-CoV and other respiratory viruses suggest that anti-SARS-CoV-2 antibodies could exacerbate COVID-19 through antibody-dependent enhancement (ADE). Previous respiratory syncytial virus and dengue virus vaccine studies revealed human clinical safety risks related to ADE, resulting in failed vaccine trials. Here, we describe key ADE mechanisms and discuss mitigation strategies for SARS-CoV-2 vaccines and therapies in development. We also outline recently published data to evaluate the risks and opportunities for antibody-based protection against SARS-CoV-2.

https://www.nature.com/articles/s41564-020-00789-5

Is this something we've avoided, having successful trials, or something we need to keep worrying about down the line?

 

[mfb]

Sorry, but you do not know that. There is no widespread random and regular PCR testing amongst the already infected.
The only thing actually known is that reinfections which are bad enough to be tested again are rare.

Well, that is protection.
In addition plenty of people get tested as part of their job, so it's not like we wouldn't have any sample.

 

[Rive]

Well, that is protection.

Regarding the worries linked above it's just not good enough. No conclusive information about cold-like reinfections, while the 'no significant amount of reinfections' kind of responses are just too commonplace. That's just very bad kind of guesswork around an important issue.

...T-cells give long lasting and cross-reactive protection...

As far as I know that's around the field of 'colds'. While it does imply that you get - well: just a cold - it will not actually prevent you get that cold. So this kind of 'protection' would likely kind of allow the virus to coexist in the human population.
It would not be exactly a bad result and would mean a really important and rare chance to observe a virus going endemic, but still has some unclear implications, especially if there are worries about the virus 'learning' the immune system.

 

[mfb]

See the comment about people who get tested as part of their job.

We also know that at least the Moderna vaccine reduces both symptomatic and asymptomatic cases - even with their first dose. They studied that by testing people at the time of the second dose. See this earlier discussion.

 

[nsaspook]

The FDA statement on vaccine dosing.

https://www.fda.gov/news-events/pre...authorized-dosing-schedules-covid-19-vaccines

We have been following the discussions and news reports about reducing the number of doses, extending the length of time between doses, changing the dose (half-dose), or mixing and matching vaccines in order to immunize more people against COVID-19. These are all reasonable questions to consider and evaluate in clinical trials. However, at this time, suggesting changes to the FDA-authorized dosing or schedules of these vaccines is premature and not rooted solidly in the available evidence. Without appropriate data supporting such changes in vaccine administration, we run a significant risk of placing public health at risk, undermining the historic vaccination efforts to protect the population from COVID-19.
...
We know that some of these discussions about changing the dosing schedule or dose are based on a belief that changing the dose or dosing schedule can help get more vaccine to the public faster. However, making such changes that are not supported by adequate scientific evidence may ultimately be counterproductive to public health.

We have committed time and time again to make decisions based on data and science. Until vaccine manufacturers have data and science supporting a change, we continue to strongly recommend that health care providers follow the FDA-authorized dosing schedule for each COVID-19 vaccine.

 

[Ygggdrasil]

This is anecdotal evidence, but some food for thought with regard to discussions of re-infection and generating herd immunity to COVID-19 (through either infection or vaccination):

Researchers published a paper in Science, reporting that in the Brazilian city of Manaus, about 76% of the population had been exposed to COVID-19 by October (though some researchers question the methods). Regardless, the region experienced a huge surge of cases in April exposing a large fraction of the population to the virus. However, in recent weeks, hospitalizations in the city have risen surpass the levels than experienced during the April surge.

(source)

There could be a few (non-mutually exclusive) explanations for these observations. One could be that the researchers greatly overestimated prevalence of infection and the recent new surge reflects spread to new, virus-naïve populations. Alternatively, these data could suggest that immunity to the virus could wane quickly. If waning immunity is an issue, how long the immunity from vaccines last is a major issue to consider (and unfortunately we don't have much longer-term data on the vaccines). However, from what we know about immunology, a two dose vaccination regime would be expected to give longer term protection than a single dose regime. Especially when vaccinating high risk individuals, it would seem best to give them the best shot at long lasting immunity.

 

[Rive]

This is anecdotal evidence...

As I recall there was an article about the area of Bergamo (the most heavily affected area of Italy, with high estimated exposure rate at Spring) still having some (!) free beds in hospitals during the Autumn season.

But: with high exposure and the usual set of preventive measures I would expect them having only a few sporadic clusters and cases, but no actual pandemic (to just almost fill their hospitals).

Anyway, my point is not exactly that Covid works this way. My point is, that it has four human-endemic brothers which works this way (with two others unknown // not endemic), and so far there is no sufficient scientific care were shown for this possibility: while denying it is commonplace.

Just not good. We don't know.

 

[david2]

University of Miami leads groundbreaking trial for COVID-19 treatment

https://www.eurekalert.org/pub_releases/2021-01/uomm-uom010421.php

The paper describes findings from 24 patients hospitalized at University of Miami Tower or Jackson Memorial Hospital with COVID-19 who developed severe acute respiratory distress syndrome. Each received two infusions given days apart of either mesenchymal stem cells or placebo.

Researchers found the treatment was safe, with no infusion-related serious adverse events.


Patient survival at one month was 91% in the stem cell treated group versus 42% in the control group. Among patients younger than 85 years old, 100% of those treated with mesenchymal stem cells survived at one month.

 

[Jarvis323]

Another interesting article about vaccine immune response and adaptation.

If live attenuated vaccines are off the table, then how could other types of vaccines achieve long-lasting protection? According to Le Vert, the answer lies in aiming vaccines at antigens within the SARS-CoV-2 virus. His company, Osivax, is developing a vaccine candidate that consists of nanoparticles carrying copies of internal Covid-19 antigens.

“We believe that targeting internal antigens such as the nucleocapsid presents an advantage over surface antigens as they have a much lower mutation rate,” said Le Vert. He added that an immune T-cell response against these internal antigens could protect against both current and future strains of Covid-19.

https://www.labiotech.eu/medical/emergex-covid-19-vaccine/

Apparently, some argue there is still a risk of ADE after spike protein mutation.

“If these mutation trends persist and increase with the worldwide spread of the virus, we believe that the vaccines targeting the spike surface antigen might have limited efficacy.”

Furthermore, Le Vert pointed out that mutations in surface proteins on the SARS-CoV-2 virus could even cause some vaccines to exacerbate the infection. This can happen via a phenomenon known as antibody-dependent enhancement, where certain antibodies stick to the virus incorrectly and make it even better at infecting cells.

In a worst case scenario, the vaccines do more harm than good for people infected with a new variant. I hope that risk is low.

 

[mfb]

Based on the vaccination tracker: In the last week a few countries have vaccinated and reported data at a relatively constant rate. Assuming that rate won't decrease we can set lower bounds on vaccination rates.

* Israel gives 125,000 doses per day. Enough for 20% of the population per month. 16% already got a first dose in the last two weeks. If they can keep this rate they'll achieve herd immunity quickly (at least against everything the vaccine protects against).
* Germany administers 40,000 doses per day. This is enough for 600,000 people per month (with two doses), or ~0.8% of the population. Clearly not enough, this has to ramp up massively.
* The trend in the US isn't that linear but they give ~340,000 doses per day. That's 5 million people per month, or ~1.5% of the population. A factor 2 faster than Germany but still far below the needed rate.
* Canada gives 12,000 doses per day, enough for 0.5% of the population per month. Same here.
* Italy is ramping up vaccinations really quickly. We'll learn more in the next few days.
* Other countries report too infrequently or just started vaccinations, so we don't have a trend yet.

What Israel does cannot be done worldwide - the production capacity is not there. But it demonstrates that Israel has the capacity to get people vaccinated at a fast pace, while other countries still have to demonstrate that.

 

[Jarvis323]

More bad news.

Gottlieb cited experimental evidence from Bloom Lab, and explained 501.V2 does appear to partially escape prior immunity. It means that some of the antibodies people produce when they get infected with Covid, as well as the antibody drugs, may not be quite as effective.

“The new variant has mutated a part of the spike protein that our antibodies bind to, to try to clear the virus itself, so this is concerning,” Gottlieb said. “Now, the vaccine can become a backstop against these variants really getting more of a foothold here in the United States, but we need to quicken the pace of vaccination.”
...
“It really is a race against time trying to get more vaccine into people’s arms before these new variants become more prevalent here in the United States,” said Gottlieb.

https://www.cnbc.com/2021/01/05/sou...te-antibody-drugs-dr-scott-gottlieb-says.html

 

[TeethWhitener]

Re: SARS-CoV-2 immunity longevity, there's a new paper out in Science:
https://science.sciencemag.org/cont...scienceroundup&et_rid=34838822&et_cid=3620063
Science 04 Dec 2020:
Vol. 370, Issue 6521, pp. 1227-1230
Abstract
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has caused a global pandemic with millions infected and more than 1 million fatalities. Questions regarding the robustness, functionality, and longevity of the antibody response to the virus remain unanswered. Here, on the basis of a dataset of 30,082 individuals screened at Mount Sinai Health System in New York City, we report that the vast majority of infected individuals with mild-to-moderate COVID-19 experience robust immunoglobulin G antibody responses against the viral spike protein. We also show that titers are relatively stable for at least a period of about 5 months and that anti-spike binding titers significantly correlate with neutralization of authentic SARS-CoV-2. Our data suggest that more than 90% of seroconverters make detectable neutralizing antibody responses. These titers remain relatively stable for several months after infection.

Edit: actually, Science Immunology has a ton of papers on immunity longevity this month:
https://immunology.sciencemag.org/c...scienceroundup&et_rid=34838822&et_cid=3620063

https://immunology.sciencemag.org/c...scienceroundup&et_rid=34838822&et_cid=3620063

https://immunology.sciencemag.org/c...scienceroundup&et_rid=34838822&et_cid=3620063

The consensus seems to be that about 90% of those known to have been infected with SARS-CoV-2 (even mildly/asymptomatically) show elevated antibody levels and production of B (memory) cells for several months after infection.

 

[Astronuc]

In the NY Times, "California has an oxygen shortage for patients as it sees a surge in Covid cases. Los Angeles County’s EMS agency issued guidelines for emergency workers to use the “minimum amount of oxygen necessary” to keep patients’ oxygen saturation level at or just above 90%."

Apparently, emergency medical technicians (EMTs) have been told not bring suspected COVID-19 patients to the some hospitals because there is no room. I think I heard a statistic that 1 or 4 persons in LA county are infected.

 

[mfb]

Total hospitalizations in the US are still increasing, reaching 130,000 now. The April and June peaks were only at 60,000.
Plot

The US has ~900,000 hospital beds overall (plus whatever was added in 2020), but most of them are filled with other patients, the regional distribution matters, and the number of beds with additional oxygen or other special requirements is much smaller.

 

[PeroK]

In the NY Times, "California has an oxygen shortage for patients as it sees a surge in Covid cases. Los Angeles County’s EMS agency issued guidelines for emergency workers to use the “minimum amount of oxygen necessary” to keep patients’ oxygen saturation level at or just above 90%."

Apparently, emergency medical technicians (EMTs) have been told not bring suspected COVID-19 patients to the some hospitals because there is no room. I think I heard a statistic that 1 or 4 persons in LA county are infected.

Where did it all go wrong, one wonders?

 

[AlexCaledin]

- the virus has waay too many spikes! - and the poor antibodies are supposed to bite all the spikes off... hard job, I should say.

 

[OmCheeto]

Where did it all go wrong, one wonders?

Indeed.
For quite a while I've been focusing on the worst cases, which are invariably, recently, small population locations.
It was quite an eye opener when I changed the filters this morning:

Population > 1 million​

Deaths/Million/Day > 18​

Scotland is included, as I heard the other day that they were going into full shutdown for the rest of the month. Which, from the shape of the graph, still has me confused.

 

[mfb]

Scotland is included, as I heard the other day that they were going into full shutdown for the rest of the month. Which, from the shape of the graph, still has me confused.

They don't want to end up like the other places.

If you only start shutting down things when it's bad then it's bad regularly.

 

[PeroK]

Scotland is included, as I heard the other day that they were going into full shutdown for the rest of the month. Which, from the shape of the graph, still has me confused.

You're from a country where the President would rather pretend that COVID doesn't exist, so I can see how you would be confused by a government that takes pro-active measures based on scientific modelling and epidemiology. I know that might be hard to accept, but it does happen!

 

[jim mcnamara]

Wade Fagen-Ulmschneider at illinois.edu has some very useful tools that facilitate visualizing several Covid-19 datasets (JHU, Worldometer, etc):
https://91-divoc.com/pages/covid-visualization/

I used it on Arizona data. Sigh. They currently lead the world in new cases per 100k population.

The site is worth considering when you want to explore some aspect.
"divoc-19" is "covid-19" reversed order of characters in case you didn't notice. Or care.

 

[Astronuc]

January 8, 2021 - States reported 2.1M tests, a record 310,080 new cases, 131,889 COVID-19 hospitalizations, and 3,777 deaths. The 7-day averages for cases, hospitalizations, and deaths are at record highs. From CovidTracking.com

Yesterday, there were CovidTracking reported 4,081deaths, a record for a single day.

The pandemic is far from over, there is essentially no containment, and folks are not getting proper treatment (as in Regeneron monoclonal antibody cocktail, remdesivir and dexamethasone).

Meanwhile - NY Time reports "False Reports of a New ‘U.S. Variant’ Came from White House Task Force"
https://www.nytimes.com/2021/01/08/health/US-variant-covid-false.html

Reports of a highly contagious new variant, published on Friday by multiple news outlets, were based on speculative statements made by Dr. Deborah Birx.

“Researchers at the Centers for Disease Control and Prevention are monitoring all emerging variants of the coronavirus, including in 5,700 samples collected in November and December,” according to Jason McDonald, a spokesman for the agency. “To date, neither researchers nor analysts at C.D.C. have seen the emergence of a particular variant in the United States,” he said.

Among the variants circulating in the U.S. are B.1.1.7, first identified in Britain and now driving a surge and overwhelming hospitals there. The variant has been spotted in a handful of states, but the C.D.C. estimates that it accounts for less than 0.5 percent of cases in the country so far.

Another variant circulating at low levels in the U.S., known as B 1.346, contains a deletion that may weaken vaccines’ potency. “But I have seen nothing on increased transmission,” said Michael Worobey, an evolutionary biologist at the University of Arizona who discovered that variant.

That variant has been in the United States for three months and also accounts for fewer than 0.5 percent of cases, so it is unlikely to be more contagious than other variants, according to a C.D.C. scientist who spoke on condition of anonymity because he was not authorized to speak about the matter.

All viruses evolve, and the Coronavirus is no different. “Based on scientific understanding of viruses, it is highly likely there are many variants evolving simultaneously across the globe,” Mr. McDonald, of the C.D.C., said. “However, it could take weeks or months to identify if there is a single variant of the virus that causes Covid-19 fueling the surge in the United States similar to the surge in the United Kingdom.”

Carl Zimmer contributed reporting from New Haven and Noah Weiland from Washington D.C.

 

[PeroK]

The figures from the UK show 91,000 excess deaths in 2020. There were 697,000 deaths last year, which is almost exactly 1% of the population. There were about 73,500 Covid deaths recorded by the end of 2020.

https://www.bbc.co.uk/news/uk-55631693

And we've had 8,500 Covid deaths already in the first eleven days of this year.

 

[mfb]

Hospitals find extra Pfizer/BioNTech doses.
The whole story is a bit bizarre. Some hospitals discard them - as if the sixth dose taken from the same bottle would suddenly be worse than the nominal first five. If the hospitals are worried about incorrect bottle contents then the obvious action would be to discard all the doses taken from that bottle.

Where Year Two of the Pandemic Will Take Us
A good (and very long) article about the current state and expectations for 2021.

Reported deaths will reach 2 million by the end of this week.

 

[fresh_42]

Who, who have been breaching the social distancing stand up, please!

https://www.sciencemag.org/news/2021/01/captive-gorillas-test-positive-coronavirus

 

[PeroK]

Lichfield Cathedral used as vaccination centre:

 

[Jarvis323]

 

[morrobay]

R0 question: If one infected person infects two in one infection period and those two infect two and those four infect two then after three infection periods there are 2^3 new infections at third infection period. But the total infections are 14. So is the R0 considered 2. Or: (R0)^3 = 14. And 3(logR0)=log14. Then logR0 = .382 . R0=2.4 ?

 

[bhobba]

R0 question: If one infected person infects two in one infection period and those two infect two and those four infect two then after three infection periods there are 2^3 new infections at third infection period. But the total infections are 14. So is the R0 considered 2. Or: (R0)^3 = 14. And 3(logR0)=log14. Then logR0 = .382 . R0=2.4 ?

R0 is the number one person infects each time period and in simple models is considered constant. Roughly it gives a simple differential equation dy/dt = R0*y, y the number infected. The solution is e^(R0*t). It is rough for a number of reasons eg I took it as linear between each period in deriving the differential equation, I did not take into account that infected people are not in the population that can be infected, and people will modify their behaviour as the number of infected grow. Good models are actually not easy to come up with as Oxford discovered with it's original model:
https://www.theguardian.com/science...xposes-the-problems-and-pitfalls-of-modelling

There are, as mentioned in the link above a lot more issues than what I will mention eg you can only really guess some of the parameters involved, but from my reading here are some of the main ones. As a minimum it should be re-run frequently taking into account the current data - which Oxford evidently did not do. Also, it was reported the code for solving the model on a computer was what programmers call 'spaghetti' code eg it has a lot of goto's which makes a program difficult to change and maintain. No goto's was the mantra from day 1 when I studied computing - in fact IMHO no good language should allow it. I have heard however this is not drummed into computing students like it was in my day. Since then recent models are a LOT better eg:
https://engineering.stanford.edu/ma...e-computer-model-predict-how-covid-19-spreads

Thanks
Bill

 

[morrobay]

R0 is the number one person infects each time period and in simple models is considered constant. Roughly it gives a simple differential equation dy/dt = R0*y, y the number infected. The solution is e^(R0*t). It is rough for a number of reasons eg I took it as linear between each period in deriving the differential equation,

Thanks
Bill

Just looking at the math without all the epidemicall variables . Then the R0 like I stated above and you also , is the number of people one infected person transmits infection to in an infection period . Given 3 infection periods ( 12 days/4 day infection period) So three infection periods .Then starting with #1 two infections, #2 four infections , and those four newly infected infect two each. So 8 new infections or 14 total. How does this correspond to e^R0 t. With three infection periods and the R0 in my example being 2. Then the newly infected would be 2^3 or the total for three periods equaling 14. So plugging in: y = e^2*3 = 403 ?

 

[morrobay]

https://en.m.wikipedia.org/wiki/Basic_reproduction_number See chart with ebola R0 = 2 . Then scroll to simple model: new infections(y) = R0^t/infectious period. So with 12 days /4day infectious period then y(t)= 2^3 . Eight new infections . This is just the math I'm looking for because it seems that there is rabbit hole of epidemic variables.

 

[BillTre]

Here is a NY Times opinion article on how the approach of there Biden administration will differ from that of the Trump administration WRT dealing with the Corona virus.

The person in charge of managing the hell out of the operation is Jeff Zients, who served as chief performance officer under President Barack Obama and led the rescue of HealthCare.gov. In a Saturday briefing with journalists, Zients broke the plan down into four buckets. Loosen the restrictions on who can get vaccinated (and when). Set up many more sites where vaccinations can take place. Mobilize more medical personnel to deliver the vaccinations. And use the might of the federal government to increase the vaccine supply by manufacturing whatever is needed, whenever it is needed, to accelerate the effort. “We’re going to throw the full resources and weight of the federal government behind this emergency,” Zients promised.

Most elements of the plan are surprising only because they are not already happening. Biden’s team members intend to use the Federal Emergency Management Agency to set up thousands of vaccination sites in gyms, sports stadiums and community centers, and to deploy mobile vaccination options to reach those who can’t travel or who live in remote places. They want to mobilize the National Guard to staff the effort and ensure that strapped states don’t have to bear the cost. They want to expand who can deliver the vaccine and call up retired medical personnel to aid the campaign. They want to launch a massive public education blitz, aimed at communities skeptical of the vaccine. They’re evaluating how to eke out more doses from the existing supply — there is, for instance, a particular syringe that will get you six doses out of a given quantity of Pfizer’s vaccine rather than five, and they are looking at whether the Defense Production Act could accelerate production of that particular syringe and other, similarly useful goods.

Looks like an improvement to me.

 

[russ_watters]

Here is a NY Times opinion article on how the approach of there Biden administration will differ from that of the Trump administration WRT dealing with the Corona virus.

Looks like an improvement to me.

Is it? It isn't clear to me that it is or should be better. That article is very heavy on opinion and very light on facts, even mis-matching key facts so that the picture of the current situation isn't clear. I've read a bunch of articles about the current situation and still don't think I've seen a clear reason why the roll-out has been so slow or why the current approach should be failing (and not just in the US -- most Western countries seem to be having trouble). So let's start with that.

The Pfizer vaccine was approved in the US on December 11 and the current administration's goal was 20 million innoculations by the end of the year, or a million a day. Plus, presumably, at least a million a day for the first 20 days of January.

The distribution phases are:
1A: Nursing home residents and frontline healthcare workers
1B: Other healthcare workers, essential workers and everyone else over 75.
1C: Everyone else over 65 and high risk people.
2. Everyone else.

https://www.cdc.gov/coronavirus/2019-ncov/vaccines/index.html

Not all states seem to be following this. For example, my state of PA seems to be front-loading phase 1A in their plan, though in reality (based on people I know) it is running more like the CDC's guidance:
https://www.health.pa.gov/topics/disease/coronavirus/Vaccine/Pages/Vaccine.aspx

For the most part, we're still in Phase 1 or just moving to phase 2. So, some obvious/important questions:
1. How many people are in each phase?
2. How many vaccines are avaialble today? Jan 1? Dec 15?

If anyone has that data I'd appreciate sharing, but I'm having trouble finding info on either. But some of the first numbers are available online:
-There are 1.4 nursing home residents in the US. (1A)
-There are 18 million healthcare workers in the US. (1A, though unsure if all are "frontline")
-There are 1.8 million police and fire fighters in the US (1B)
-There are somewhere around 19 million people aged 75 and older. (1B)
-There are somewhere around 36 million people aged 65-74 and older. (1B)
-I have no idea how many "essential workers" and "high risk" people there are. Presumably tens of millions.

So near as I can tell, Phase 1A included just under 20 million people and should have been completed by the new year.
Phase 1B at least another 20 million.
Phase 1C...a hundred million?

The logistical challenges of the different phases are very different from each other. People in 1A are easy to get to and vaccinate using existing infrastructure, so the failure so far is mystifying to me. To vaccinate hospital workers, you just send hundreds of vaccines to thousands of hospitals and they do it themselves. To vaccinate nursing home residents and staff, you send the vaccines to whatever healthcare partner (often pharmacies) already does their mass-vaccinations. From what I've seen and heard from my friends/family, that's happened. So, why the numbers don't bear-out a larger total is confusing. This article (a week old) implies that it is the states that are having trouble:

However, the distribution of vaccines has gotten off to a slower-than-expected start, with millions of doses distributed to states but sitting unused in freezers.

https://www.healthline.com/health-news/why-the-covid-19-vaccine-rollout-is-so-slow

This says the federal guidelines have been relaxed to open up all of the first three phases and make 250 million people eligible:
https://www.webmd.com/vaccines/covi...dy-to-supply-covid-19-vaccines-to-americans#1

In addition, the 40,000 chain drug stores in the US have the capacity to administer about 3 million a day. Then there's hospitals, urgent care centers, doctors offices.

Back to the original article:

Set up many more sites where vaccinations can take place. Mobilize more medical personnel to deliver the vaccinations.

It's a major pandemic so I favor an all-hands-on-deck apprach and x+1>x, so it is trivial to say that that's "better", but I don't see why it should have been necessary so far to achieve the goal. It looks to me like our existing capacity should already have vastly outperformed the goal.

And use the might of the federal government to increase the vaccine supply by manufacturing whatever is needed, whenever it is needed, to accelerate the effort.

That's pretty vague. How does the government do that and how long does it take?

The new administration's goal is 100 million vaccines in 100 days, or exacly the same as the last one, even with hindsight and 40 days of ramp-up. To me, that's a pretty underwhelming goal. There's two ways to look at that: either the new goal is pessimistic and we should do a lot better or the old goal was overly optimistic and we should have expected it to be as slow as it was (or somewhere in between).

 

[russ_watters]

Is it? It isn't clear to me that it is or should be better. That article is very heavy on opinion and very light on facts, even mis-matching key facts so that the picture of the current situation isn't clear.

Here's the mismatch:

According to data from the Centers for Disease Control and Prevention, of the roughly 31 million doses that have been sent out, about 12 million have been used.

On its own, this doesn't tell us anything at all about any sort of problem because we don't know where the remaining 19 million doses are. If they're expired and in a trash can, that's a failure. If they're in a refrigerator to be administered tomorrow or in shipping a shipping container on a truck, then they're somewhere in the supply chain and there isn't necessarily an issue. And maybe more have been vaccinated if there is a lag in reporting the vaccinations. But the numbers are as of January 15, so we can say that the total shipped is below the roughly 35 million that should have been administered by now. So it would seem that too few have shipped (even fewer if you consider that they couldn't pre-stage the vaccine and only started shipping the day after approval). So, what is causing that bottleneck?

This article discusses bottlenecks at the state, federal and manufacturing level, but doesn't make it clear if those bottlenecks cascade up (e.g. if the state bottleneck caused the federal bottleneck):
https://www.nytimes.com/2020/12/17/health/pfizer-covid-vaccine-doses.html

 

[bhobba]

Then the newly infected would be 2^3 or the total for three periods equaling 14. So plugging in: y = e^2*3 = 403 ?

It's in deriving the differential equation. The time period you used is discreet. To get the differential equation let us say the time period is a day. To get to an infinitesimal time period you assume during that one day it is linear (it isn't really but it is a simplifying assumption). The detail is using a one day R0, the increase over 1 day is R0*y where y is the current number of cases. Making the simplifying assumption it is linear, over half a day it is R0*1/2*y, over an infinitesimal period dt it is R0*dt*y. So you get after an infinitesimal time period of dt the increase, dy, is R0*dt*y. So one gets dy/dt = R0*y. Why it does not give your numbers is in deriving the equation we assume it is linear during that one day period. It isn't really, so you do not get the same numbers as your discreet calculation. You could get the R0 (R0') over an infinitesimal period from solving e^(R0') = 1+R0 or R0' = Ln(1+R0). That would be a more refined model. Ln = Log to base e. It still will not give your discreet values because you are assuming a continuous infection rate instead of a discreet one. It would have been better to express your infection rate in terms of an infinitesimal time period to start with so after dt the new number of infections is y + R0*y*dt. For your 3 days the infinitesimal R0, R0' would be e^(R0'*3) = 1 + R0 or R0' = (ln (1 +RO))/3. This is similar to the concept of force of interest in finance:
https://en.wikipedia.org/wiki/Compound_interest

Thanks
Bill

 

[BillTre]

That article is very heavy on opinion and very light on facts, even mis-matching key facts so that the picture of the current situation isn't clear. I've read a bunch of articles about the current situation and still don't think I've seen a clear reason why the roll-out has been so slow or why the current approach should be failing (and not just in the US -- most Western countries seem to be having trouble). So let's start with that.

Well, it is an opinion article (as I clearly labeled it).

However, I think the main issue is that data stream of US government info on the corona virus has been corrupted and the data are not dependable.
This is likely also true with Florida data.

I expect different numbers to become available a week or two.

 

[russ_watters]

Well, it is an opinion article (as I clearly labeled it).

Yes, I know. Doesn't mean I need to be happy abou/agree with the value of such a low quality source.

However, I think the main issue is that data stream of US government info on the corona virus has been corrupted and the data are not dependable.

This is likely also true with Florida data.

I expect different numbers to become available a week or two.

I don't know what you mean by that. What data are you referring to? That sounds vaguely like conspiracy theory.

More to the point, "different numbers" does not fix the logic problem in the media reporting mismatched statistics.

 

[PeroK]

To change the subject, here's an interesting thing.

1) From last Friday morning, flights from Portugal (in addition to S America) to the UK were halted because of fears of a new variant, originating in Brazil and likely to have spread to Portugal.

2) The Portugese Foreign Minister described it as "absurd".

https://www.reuters.com/article/hea...ortuguese-foreign-minister-says-idUSL8N2JQ2G7

3) Today, Portugal (a country of 10 million people) has reported nearly 15,000 cases and 219 deaths. And, it's been about 10,000 cases a day for about 10 days now.

This shows that some governments are still being wholly unrealistic about the extent to which the virus is hitting their country and the threat to other countries posed by international travel.

 

[BillTre]

I don't know what you mean by that. What data are you referring to? That sounds vaguely like conspiracy theory.

Well, I am trying to avoid going into politics, by not responding directly to your challenge(s),
so I won't cite specific causes (also, making my job easier).
In addition, I will avoid providing long explanations that could be portrayed as a conspiracy theory.

But, I will make predictions:

• the numbers of vaccines produced will be revised down
• estimates of numbers (cases, deaths, hospitalizations) associated with the corona virus, will be changing (but this could (will?) be attributable to changes in calculations)
• the federal vaccine back-up supplies will be shown to have been vastly over-estimated and over-hyped
• weird reasons for not doing obvious things will be revealed (some will involve corruption ($'s))

I expect these things will begin to happen within a couple of weeks. Some maybe faster, some slower.
Check back with that latency.

I have, to a large extent, come to be not be so interested in all the corona virus numbers, because I think there are too many problems with them.
Besides the normal causes of uncertainty and differences between states, there are clear indications of politicians messing (which I am not going to go into here (too political, but you can goggle them up for yourself)) with the numbers, thus corrupting them for predictive purposes.

If the data you are using is not good, then your calculated numbers will not make sense.

 

[nsaspook]

https://www.sfgate.com/coronavirus/...-dining-ban-COVID-19-surge-worse-15882565.php

Late last week, Chicago mayor Lori Lightfoot — typically cautious on COVID-19 policy — raised some eyebrows after calling for restaurants and bars to reopen "as soon as possible."

Her logic: The current COVID-19 surge has been primarily fueled by at-home gatherings and parties, and if people are going to gather regardless of what any stay-at-home order dictates, state and local governments should try to provide spaces where at least some mitigation efforts will be taken.
...
Despite the ban, California has had one of the worst winter COVID-19 surges in the country, which begs the following question: Is it possible that shutting down outdoor dining made the state's surge even worse?Dr. Monica Gandhi, an infectious disease expert at UCSF, believes it's highly likely.

"We won’t be able to know the exact percentage it drove, but I would say closing outdoor dining certainly did not help and likely hindered efforts to avoid a surge," she said. "It shut down in early December, and things did not get better from there; things actually got worse. Restrictions should be about understanding the human condition and keeping places that are safe open. Those of us who argue for a harm reduction approach have the same goal as the lockdownists: We want to reduce transmission, but we understand the human condition and the need to be with people."

Locally there has been a risk mitigation reevaluation of dining rules.

 

[russ_watters]

But, I will make predictions:

• the numbers of vaccines produced will be revised down
• estimates of numbers (cases, deaths, hospitalizations) associated with the corona virus, will be changing (but this could (will?) be attributable to changes in calculations)
• the federal vaccine back-up supplies will be shown to have been vastly over-estimated and over-hyped
• weird reasons for not doing obvious things will be revealed (some will involve corruption ($'s))

I expect these things will begin to happen within a couple of weeks. Some maybe faster, some slower.
Check back with that latency.

I have, to a large extent, come to be not be so interested in all the corona virus numbers, because I think there are too many problems with them.
Besides the normal causes of uncertainty and differences between states...

Well, fair enough, but I thought we were in a narrowly focused discussion of the vaccine roll-out. I'm not real interested in case rates for this discussion either.

As far as I can tell, there are no running tallies of vaccine production. The most detail I've seen is from Pfizer, which 6 weeks ago reduced its 2020 global production target from 100 million to 50 million doses, and I don't even know how many were allocated, much less shipped, to the US:
https://time.com/5917847/pfizer-cut-covid-19-vaccine-targets/
https://www.npr.org/2020/12/18/9480...es-are-ready-but-states-say-shipments-were-cu

There's finger-pointing right now, but because the vaccines direct-ship from the manufacturer to the states or users (not through a federal government distribution center), we don't actually have a window into their production volumes and delivery capabilities. There's no way for us to know if there are millions of doses sitting ready for shipment with no address to send them to or if they are struggling to keep the warehouse stocked for shipping. But the admission that they halved their production target tells me that the largest bottleneck is probably in production, not distribution or innoculation.

But I guess we'll see. About all of that.

 

[morrobay]

It's in deriving the differential equation. The time period you used is discreet. To get the differential equation let us say the time period is a day. To get to an infinitesimal time period you assume during that one day it is linear (it isn't really but it is a simplifying assumption). The detail is using a one day R0, the increase over 1 day is R0*y where y is the current number of cases. Making the simplifying assumption it is linear, over half a day it is R0*1/2*y, over an infinitesimal period dt it is R0*dt*y. So you get after an infinitesimal time period of dt the increase, dy, is R0*dt*y. So one gets dy/dt = R0*y. Why it does not give your numbers is in deriving the equation we assume it is linear during that one day period. It isn't really, so you do not get the same numbers as your discreet calculation. You could get the R0 (R0') over an infinitesimal period from solving e^(R0') = 1+R0 or R0' = Ln(1+R0). That would be a more refined model. Ln = Log to base e. It still will not give your discreet values because you are assuming a continuous infection rate instead of a discreet one. It would have been better to express your infection rate in terms of an infinitesimal time period to start with so after dt the new number of infections is y + R0*y*dt. For your 3 days the infinitesimal R0, R0' would be e^(R0'*3) = 1 + R0 or R0' = (ln (1 +RO))/3. This is similar to the concept of force of interest in finance:
https://en.wikipedia.org/wiki/Compound_interest

Thanks
Bill

Thanks, The compound interest formula, final=initial (1+%)^n is exactly how I am solving for the R0 from initial and final infections: 17(R0)^6 = 231. Then (R0)^6=13.58 and 6(logR0) = log 13.58. therefore log R0 =.1888 so R0 is 1.54 I just am asking if this is valid for solving R0. Note 6 infection periods from 24 days/4 day max.infectious period from initial infection.