Cont: 2019-nCoV / Corona virus Pt 3

[Solitaire]

I’m trying to convince them to simply wait until Abbot’s new ID Now test
(we already use the system for flu, strep and RSV) is widely available in
the next month or so.

Interesting problem.

How many cases of the infection will we have to test in a month?

Thanks to the application of the hammer and the closure of unnecessary
business, the rate of infection has slowed dramatically to a quadrupling
per week.

Starting with 250,000 cases in the United States this Friday, we multiply
four times four times four times four, um...

But a month lasts a bit more than four weeks.

Looks a bit more complicated than I thought. I'll need to write
a bit of econometric modeling software and get back to you on that.

 

[lomiller]

Your claim is that the rapid spreading of COVID may be attributed to lack of immunity. I italicized that statement in your last communication.

I do not automatically accept your claim that immunity is associated/correlated to the rapid spread of a disease so I set out to the www.

The spreadability of a disease is assigned an R0 value. I found this resource from the CDC: R0 cannot be modified through vaccination campaigns. Further reading from that same reference declares that the use of a different metric is required to calculate the impact immunization could have on subsequent infections.

That metric is R Rate (Effective Reproduction Number). The article then states when using this new R Rate metric, "vaccination could potentially end an epidemic, if R can be reduced to a value <1." Potentially..potentially..holy nuances batman! I think part of the difficulty is that people whom are immune can still spread the infection? However, those that are immune may not possess a high enough viral load to successfully spread a specific disease.

For the purposes of answering whether immunity is associated/correlated to the rapid spread of a disease, would you accept that the terms immunity and vaccination similar enough that they would not impact the answer to the question I set out to answer? Any thoughts?

R0 is normalized to a population where everyone is susceptible. The R0 value for Measles is MUCH higher than COVID. The reason we are not getting millions of people infected with measles is because the chances of an infected person coming in contact with someone who has little of no resistance is typically quite low.


While early estimates suggest COVID may have an R0 value a little higher than typical seasonal flu strains, IMO it's a more reasonable explanation for the extremely high number of cases is that there is a lot more contact between carriers and people with no resistance.

 

[angrysoba]

Wow! The US must have really upped its game as far as testing is concerned.it has a quarter of a million confirmed cases which is huge but “only” around 6 or 7 thousand deaths. A big number, but not in the ten percent mortality rate of Otaly, Spain and the UK.

 

[marting]

Your claim is that the rapid spreading of COVID may be attributed to lack of immunity. I italicized that statement in your last communication.

I do not automatically accept your claim that immunity is associated/correlated to the rapid spread of a disease so I set out to the www.

The spreadability of a disease is assigned an R0 value. I found this resource from the CDC: R0 cannot be modified through vaccination campaigns. Further reading from that same reference declares that the use of a different metric is required to calculate the impact immunization could have on subsequent infections.

That metric is R Rate (Effective Reproduction Number). The article then states when using this new R Rate metric, "vaccination could potentially end an epidemic, if R can be reduced to a value <1." Potentially..potentially..holy nuances batman! I think part of the difficulty is that people whom are immune can still spread the infection? However, those that are immune may not possess a high enough viral load to successfully spread a specific disease.

For the purposes of answering whether immunity is associated/correlated to the rapid spread of a disease, would you accept that the terms immunity and vaccination similar enough that they would not impact the answer to the question I set out to answer? Any thoughts?

I don't see much of a difference between R0 and R at this point in time but the link provides some useful background.

R0 is the average number of non immune people infected by an infected person. It's not affected by vaccination rates or recovered people that are consequently immune. With a new outbreak from a novel virus its calculation is based on the assumption of universal susceptibility.

R is the average number of people infected by an infected person. It is initially the same as R0 and decreases as the percentage of the population increases from infection, vaccination or recovery where recovery produces immunity.

Both R and R0 are affected by human and environmental factors. The goal of social distancing, hand washing, etc. is to reduce them.

Currently, only a small percentage of the population is in the immune or infected category. Hence R0 and R are close to the same. Once R drops below 1 the number of new infections will gradually decrease. The lower it is the more rapidly it will decrease and the decrease is exponential just like an increase where R > 1 is exponential. R is the exponent.

An R of .5 will decrease the number of new infections by roughly half for each period of time that is the average time between infection and virus shedding. An R of .25 will decrease the number of newly infected people by a factor of 4 over the same period.

 

[lomiller]

Potential treatment that could help early stage infection. Since they only claim early stage benefits I'm skeptical it could be rushed though testing though.

https://www.cell.com/pb-assets/products/coronavirus/CELL_CELL-D-20-00739.pdf

 

[marting]

The most recent estimate for deaths in the US from the government health authority Fauci was between 100 to 200k in one calendar year.

The model Fauci is referencing to make that statement was from the CDC and it estimates that 160 to 240 million people could become infected in one calendar year. Combining Fauci's statement about the total number of deaths and that same models assumption on how many could become infected:

If 100k die and 160 million were infected, the mortality rate would be 0.125%.
If 200k die and 160 million were infected, the mortality rate would be 0.25%.

If 100k die and 240 million were infected, the mortality rate would be 0.042%.
If 200k die and 240 million were infected, the mortality rate would be 0.083%.

This same model has been used to predict a higher amount of deaths, however, that higher amount of deaths has been dismissed as less likely since social distancing has become more normal. Although, social distancing is not being utilized equally across the entire US, the extent of these social distancing changes are difficult to quantify as precisely as we would hope.

The critical question is what assumptions re degree of social distancing / shutdowns the model incorporates. These numbers seem to me consistent with the Hammer and Dance outlined here and assume no vaccine or treatments become available for 18 months. But it would be nice to have the specifics about what assumptions the model uses.

https://medium.com/@tomaspueyo/coronavirus-the-hammer-and-the-dance-be9337092b56

 

[Arcade22]

What’s with the fixation on China? Even if they are underreporting, there is no reason to think their infection and death rates are radically different from Japan or Hong Kong, which still makes them a relatively minor part of the picture right now.

The bodies don't have to be piling up on street corners for them to be just as heavily affected as Italy or Spain is right now, and nothing they report to the WHO would show that.

 

[lomiller]

The bodies don't have to be piling up on street corners for them to be just as heavily affected as Italy or Spain is right now, and nothing they report to the WHO would show that.

There is no evidence for overloaded ICU’s in China. Just the opposite in fact. Even China isn’t going shut down the temporary facilities it build when regular hospitals are still overloaded. Even if they did, why would it matter to the US? I don’t see anything here but a desire to distract from their own mishandling of the pandemic with “but… but… but… China!!!”

 

[dudalb]

Confirmed? as in "No other cause of death possible? No chance of mal diagnosis?"

50,000 pneumonia deaths per year, is 4,000 per month. Only when Covid passes that can there are doubtless actual covid deaths, not "Deaths attributed to covid".

Or, 2.8m deaths per year from all causes. that is 7,700 per day. What was that latest day's attibutibed to Covid?

This is what is known as "Clutching at straws".

 

[dudalb]

I have a question about the Igg/Igm tests that are seemingly flooding the market now. The FDA requires them to say that they are not diagnostic in and of themselves and that a false positive could occur if someone has had an infection with one of the other human Coronaviruses. In my mind, this renders them nearly useless.

I ask because I’m trying to advise the doctors in our clinic whether or not they should order them. I lean towards “not” because we could end up falsely diagnosing a bunch of patients and missing a punch that should be positive. I’m trying to convince them to simply wait until Abbot’s new ID Now test (we already use the system for flu, strep and RSV) is widely available in the next month or so. Their issue is that the PCR test kits are not easily obtainable from the labs that are doing it and they want to be able to offer something and they think it’s accurate enough according to the literature the test makers are publishing.

There are some smart, scientifically oriented people here: what say you?

I would say be very cautiious. The Snake Oil salesmen are working overtime on phony Covid 19 crap.
I

 

[JeanTate]

The most important things we don't yet know

What are the most important things we don't yet know about COVID-19 or SARS-COV-2?

I wrote down some, and had a go at trying to prioritize or categorize them. Didn't really work. So here are some, in no particular order, with comments. What biggies do you think I missed?

When will an effective vaccine be widely available for deployment?

The sooner the better. For lives not cut short. For the sake of the global economy (and that of all nations etc). So we can go out to dinner again, to weddings (and, sadly, funerals). Etc.

When will effective treatments be widely available?

Of many possible kinds: to allieviate symptoms; to lessen infectiousness (especially asymptomatic cases); to reduce the chance of becoming infected; etc.

How seasonal is it?

If SARS-COV-2 is not driven to extinction by ~June 2020, how much respite can we reasonably expect during the northern summer? Or: maybe it gets worse in hotter, more humid conditions?

How quickly can we learn which underlying medical conditions are bad?

There's a lot wrapped up in this: how much more susceptible are you if you have diabetes (say)? which combo of such conditions is particulary bad? Treatments factor in here too: drug combo X may do nothing for a healthy person, but greatly reduce the severity of cytokine storms for those with COPD, say.

How quickly will SARS-COV-2 mutate?

More pertinently: how likely is it to mutate into strains resistant to the vaccine(s)?

How long does immunity last?

Once you've recovered, are you good for the rest of your life? Just until next year?

How infectious are you once you've recovered?

Not just "on average", but the distribution: what %-age of those who've recovered remain carriers? for how long?

Can an infected mother pass it to a breast-feeding child?

The answer to this may already be known.

 

[Planigale]

Some what depressing is this model from LSHTM on duration and severity of lockdown. On the positive side it would seem to be effective on the negative the duration is long, until September with periodic lockdowns thereafter.
This is the information given to HMG on which they are currently basing their strategy. Obviously new information from e.g. seroprevalence studies or drug trials would influence things.
https://cmmid.github.io/topics/covi...uk_scenario_modelling_preprint_2020_04_01.pdf

 

[The Atheist]

I have seen flu; I have seen people die of flu. This is not flu. Take my word. The people coming in have a new illness. They catastrophically deteriorate from seemingly well to needing to go on a ventilator in an hour, this does not happen with flu. Now just stop with the 'it might be flu' nonsense.

Maybe we should take the people chanting "it's just like 'flu" to an emergency ward.

Sans PPE.

You're a legend.

 

[marting]

Some what depressing is this model from LSHTM on duration and severity of lockdown. On the positive side it would seem to be effective on the negative the duration is long, until September with periodic lockdowns thereafter.
This is the information given to HMG on which they are currently basing their strategy. Obviously new information from e.g. seroprevalence studies or drug trials would influence things.
https://cmmid.github.io/topics/covi...uk_scenario_modelling_preprint_2020_04_01.pdf

Interesting models. However the code in in Fortran! Yuck.

 

[The Atheist]

IMO the “frustration” with China’s is on the part of people more interested in looking for things to accuse China of then actually dealing with the COVID 19 pandemic.

Nailed.

Wow! The US must have really upped its game as far as testing is concerned.it has a quarter of a million confirmed cases which is huge but “only” around 6 or 7 thousand deaths. A big number, but not in the ten percent mortality rate of Otaly, Spain and the UK.

*Ahem*

Since we're talking about whether numbers are reliable, this piece suggests parts of USA might be indulging in a little whitening of the statistics: https://www.nbcnews.com/news/us-new...coronavirus-cases-its-hospitals-tell-n1175291

If they're more cases that day than the total they're showing, you don't think deaths might be a touch understated? If a bloke with Covid-19 dies of a heart attack due to the virus, do we count that as a heart attach or Covid death?

I'm guessing Houston is going With the former.

Some what depressing is this model from LSHTM on duration and severity of lockdown. On the positive side it would seem to be effective on the negative the duration is long, until September with periodic lockdowns thereafter.

I'm beginning to think there might be a way out of the complete lockdown.

1 Make mask use in public and all workplaces mandatory.
2 Give employees additional sick leave and make it a dismissable offence to turn up to work sick, or before a doctor's clearance. That could be paid by central gov't as cheaper than paying everyone's wages.
3 Enforce distancing at workplaces.
4 Enforce bars and restaurants to have distant tables and table service only.
5 Ban gatherings.

There are probably a few more, but I think the disease is manageable in a way that would allow 75% of the workforce to go back to work once the growth is slowed. Basically following what China did.

 

[Darat]

Some what depressing is this model from LSHTM on duration and severity of lockdown. On the positive side it would seem to be effective on the negative the duration is long, until September with periodic lockdowns thereafter.
This is the information given to HMG on which they are currently basing their strategy. Obviously new information from e.g. seroprevalence studies or drug trials would influence things.
https://cmmid.github.io/topics/covi...uk_scenario_modelling_preprint_2020_04_01.pdf

Interesting paper. I can’t comment on the methodology -way over my head - but the results are easily understood.

I think the government at the moment is trying to decide if letting ICU beds being overwhelmed is worth the disruption for the next 12 weeks. If as has been stated a few times (but I don’t know the provenance of the figure) only 20% of those that require IC survive we need to see if we can find a diagnostic that allows us to predict those 20%, because that would mean we would only need 20% of the predicted ICU beds.

I know my mother has already decided she will not, assuming it will even be offered, go into hospital if she gets the disease. And I know two other people in the elderly and at increased risked group who have said the same. The modelling didn’t take that group into account, and I think it will be a significant group.

 

[Darat]

Nailed.

...snip...


I'm beginning to think there might be a way out of the complete lockdown.

1 Make mask use in public and all workplaces mandatory.
2 Give employees additional sick leave and make it a dismissable offence to turn up to work sick, or before a doctor's clearance. That could be paid by central gov't as cheaper than paying everyone's wages.
3 Enforce distancing at workplaces.
4 Enforce bars and restaurants to have distant tables and table service only.
5 Ban gatherings.

There are probably a few more, but I think the disease is manageable in a way that would allow 75% of the workforce to go back to work once the growth is slowed. Basically following what China did.

That paper indicated that gathering at events such as football matches will not significantly increase the infection rate.

 

[Ulf Nereng]

I'm beginning to think there might be a way out of the complete lockdown.

1 Make mask use in public and all workplaces mandatory.
2 Give employees additional sick leave and make it a dismissable offence to turn up to work sick, or before a doctor's clearance. That could be paid by central gov't as cheaper than paying everyone's wages.
3 Enforce distancing at workplaces.
4 Enforce bars and restaurants to have distant tables and table service only.
5 Ban gatherings.

There are probably a few more, but I think the disease is manageable in a way that would allow 75% of the workforce to go back to work once the growth is slowed. Basically following what China did.

Turning nursing homes into veritable fortresses against infection should also be part of the plan.

 

[Belz...]

Confirmed? as in "No other cause of death possible? No chance of mal diagnosis?"

50,000 pneumonia deaths per year, is 4,000 per month. Only when Covid passes that can there are doubtless actual covid deaths, not "Deaths attributed to covid".

Or, 2.8m deaths per year from all causes. that is 7,700 per day. What was that latest day's attibutibed to Covid?

You must be joking.

 

[Ulf Nereng]

You must be joking.

Or simply not getting it. Looks like USA's "score" for today is going to be about 1000 deaths. With doubling every three days they'll have 8000 per day in nine days.