OT: Corona virus

[Ian R]

ORIGINAL: Cap Mandrake

ORIGINAL: obvert

ORIGINAL: Ian R

Interesting sounding article in the LA times, but unfortunately behind a paywall, if anyone has access could they post a short summary.

What is really needed is a test that tells you if you already had it and recovered without even noticing.

The UK just bought 3.5 million of those. Anti-body tests. They're going to try to start the testing by the end of the week, according to the Health minister.

The whole idea is trying to see who has had to let those NHS workers and other frontline personnel deal with the most difficult areas, where they're at risk. The larger goal is to see how much herd-immunity has been achieved as there are now some odd outlying studies (like he one I linked from Oxford yesterday) that buck the trend of saying this is just beginning. Some think it's been moving around for a good while undetected as it was among young healthy populations.

EDIT: just listened to the live press conference on this. First go to NHS and critical workers. Then probably other priority personnel. Eventually it'll run out to the public and then will become part of a study to determine how many have had it.

Also said trying to ramp up basic testing still. At 97k as of now.

I think you can deduce from the ramping up of cases in country after country it is just entering the population but a study to look at the prevalence of antibody levels would be very useful. It would tell you about subclinical cases, which are likely substantial.

For example, in the Seattle-area nursing home, it was discovered after the seniors began falling like flies that HALF THE STAFF were already infected and the great majority were still working.

Also, a single Connecticut birthday party gave rise to FIFTY infected individuals, with quite a few just having mild disease. Whoever made the bean dip should have washed their hands better.

Haven't testing numbers also exponentially ramped up in at least some countries recently? Perhaps there is a correlation? I am not sure you can make the deduction that C19 is only just entering the population from that in isolation. I agree that there are quite probably a significant number of subclinical cases, including some recovered cases, that are unknown/unrecorded.

In any event, the sooner the tests that Obvert mentions are able to clear recovered people back to work so as to stave off economic disaster, the better.

[Kull]

Dr. Birx (White House corona virus coordinator) made a few interesting comments the other day:

1) They will soon deploy a "self-test" swab kit for use at the drive through testing facilities (and presumably other places) which individuals will use to take their own swabs. The benefit is that it does not require a person in full PPE to contact the individual, so they don't use up a full set of PPE with every swab. This is not a "home test".

2) The types of mutation (and rate) for the coronavirus make it unlike the flu, in that once a vaccine is developed it should work on all varieties of SARS-CoV-2:

“At this point, the mutation rate of the virus would suggest that the vaccine developed for SARS-CoV-2 would be a single vaccine, rather than a new vaccine every year like the flu vaccine.” Rather, a potential coronavirus vaccine would act more like those for the measles or chicken pox, in which one shot grants immunity for a substantial amount of time.

3) They are working to review and approve a fingertip pri-ck test for Covid-19 antibodies, which would vastly improve the ability to identify those who have had the virus. Such a kit will be deployed in the UK "in days".

(To avoid politicization, all links are to other sources)

[RangerJoe]

What you need to know about Minnesota's 'stay-at-home' order
Minnesota Gov. Tim Walz issued an order for Minnesotans to stay at home unless absolutely necessary.

more

Gov. Tim Walz is asking Minnesotans to stay at home unless absolutely necessary in order to slow the spread of coronavirus in the state.

The “stay-at-home” order is his most dramatic executive action yet, asking Minnesotans to partake in a form of extreme social distancing as the virus spreads to a growing number of people in the state and hospitals prepare for more patients.

But it’s far from a total lockdown of the state.

What does Walz’s new order say?

On Wednesday, the governor issued an executive order that asks Minnesotans to stay home except for essential needs and services starting at 11:59 p.m. on Friday, March 27 until at least April 10, with more limited social distancing plans to follow with a focus on people at greatest risk of COVID-19 complications — mostly people who are elderly or have underlying health conditions.

What are considered essential needs and services?

The order still allows people to leave the house for things like groceries, gas, emergency medical services or supplies, caring for family members, friends or pets and moving between emergency shelters for those who are homeless.

And people who work in “critical sectors” are exempt from the stay at home order, including health care workers, emergency responders, law enforcement, shelters, child care facilities, food production, utilities, the news media and critical manufacturing. Other workplaces are asked to shift to a telework and work from home model under the order.

https://www.startribune.com/stay-at-hom ... 568484941/

Due to a nationwide shortage of COVID-19 testing supplies, MDH announced March 17 that the state's public health lab would restrict testing to health care workers, hospitalized patients and residents of long-term care facilities. As a result, people experiencing milder symptoms will not be tested, and people with respiratory illnesses are asked to remain isolated for at least seven days after symptoms first appear or at least three days after being fever-free, whichever is longer. The state will rely on ongoing influenza surveillance as a proxy for whether the coronavirus is spreading, MDH officials said.

The number of tests conducted reflect those reported by MDH. On March 25, the department reported a large number of tests completed by other laboratories, such as the Mayo Clinic. Previously, MDH did not consistently include outside tests in its totals.

https://www.startribune.com/coronavirus ... 568712601/

[RangerJoe]

From the wayback machine:

Minnesota Disease Expert Says Coronavirus Spread Unlikely But Would Have High Consequence

“Today in the modern world of transportation where millions of people are on airplanes flying on any one moment flying around the world its not at all a surprise it would show up in potentially many different countries,” Dr. Michael Osterholm, the director of the center for infectious disease research and policy at the University of Minnesota, said.

Osterholm says, if Coronavirus is anything like its relatives SARS and MERS, “we can expect to see ongoing transmission by humans to humans and that’s what really concerns us.”

[Cap Mandrake]

Large Chinese study. Time from exposure to symptoms about 2 to 11 days with a mean of 5 days and 95% will become symptomatic by 11 days (this is where they got the 14 day quarantine figure)

Then there is another lag until patients develop more severe illness.

Amazing and utterly convincing map of the transmission of Covid-19 based on the amazing 111 genotypes identified so far. I saw this same damn thing in "Contagion" in December on Netflix. It is absolutely prescient.

https://nextstrain.org/ncov

[Cap Mandrake]

The first human-derived isolate is from Dec 3, 2019

This does NOT mean the first human infection was from that date. It took some time for the infection to amplify and come to the attention of doctors in Wuhan. It takes 1 or 2 or 3 doctors talking to each other over lunch. "Man that guy could not take a joke! His O2 sat is 95% and then 8 hrs later he is dead!"

I know it sounds cynical but that's how it is....then the second guys says...."Shit, that sounds like SARS!" because he is a bit older and remembers SARS...and then they all leave their food on the table.

[Chickenboy]

ORIGINAL: Kull
3) They are working to review and approve a fingertip pri-ck test for Covid-19 antibodies, which would vastly improve the ability to identify those who have had the virus. Such a kit will be deployed in the UK "in days".

I guess that's my point. Little is known about typical 'clearance' of the virus relative to production of detectable antibodies. Is it possible that someone that is seropositive has a titer that is insufficient to protect against future challenges? Yes. Is it possible that someone that thinks they're antibody negative has only started with the disease and therefore hasn't had time to produce a detectable serologic response (this takes several days)? Yes. Is it possible that someone that is antibody positive could be shedding virus? Yes.

*Maybe* paired samples-RT-PCR and simultaneous antibody screening could provide a more useful picture. Antibody positive and simultaneous virus negative is a greater margin of safety IMO.

We run into this from time to time with animal disease outbreaks. Serosurveillance is nice for planned, routine screens of a population for diseases that one should not find antibody (or to quality check vaccination strategies when a titer *is* expected). But there is an inherent delay between the introduction of a pathogen (e.g., avian influenza) and production of detectable antibodies. Depending on the test and the disease, this could be 48-96 hours or more.

Performing antibody serosurveillance as a quasi-realtime diagnostic tool in a rapidly evolving disease outbreak is usually selecting the wrong tool for the task. Unless there was considerable (2+ days) delay in getting antigen testing results back, there are better choices.

Rapid antigen (read: virus) detection kits can be used as a proxy for virus isolation or PCR in a pinch. But antibody detection tests require too many assumptions about temporal exposure to be proactive in a timely fashion, IMO.

Lots of folks / companies trying to dump test kits or treatments or cures on a panicked public. I question the rationale of this antibody detection implementation without deeper thought about whether some better choices may exist.

[Cap Mandrake]

The Covid 19 genotype maps to bat and pangolin hybridization of the species-specific Cornavirus viral genome.

Somebody in Wuhan thought it was a good idea to eat one of these.

[Cap Mandrake]

Yummy! Maybe about 6 hrs of smoking after a nice rub!

Thanks Wuhan!

Now, in fairness, it might be that a pangolin shat on a fruit that that bat ate and then someone in Wuhan had some delicious bat cioppino but I favor the former.

This is interactive.

click on the vertical red dots in the middle to view the Covid-19 phylogeny

https://nextstrain.org/groups/blab/sars-like-cov?c=host

[MakeeLearn]

EVERYTHING in China is on the menu.

[RangerJoe]

ORIGINAL: Cap Mandrake

The Covid 19 genotype maps to bat and pangolin hybridization of the species-specific Cornavirus viral genome.

Somebody in Wuhan thought it was a good idea to eat one of these.

Maybe they will finally get serious on banning the trade of these cuddly creatures.

[Kull]

ORIGINAL: Chickenboy

ORIGINAL: Kull
3) They are working to review and approve a fingertip pri-ck test for Covid-19 antibodies, which would vastly improve the ability to identify those who have had the virus. Such a kit will be deployed in the UK "in days".

I guess that's my point. Little is known about typical 'clearance' of the virus relative to production of detectable antibodies. Is it possible that someone that is seropositive has a titer that is insufficient to protect against future challenges? Yes. Is it possible that someone that thinks they're antibody negative has only started with the disease and therefore hasn't had time to produce a detectable serologic response (this takes several days)? Yes. Is it possible that someone that is antibody positive could be shedding virus? Yes.

*Maybe* paired samples-RT-PCR and simultaneous antibody screening could provide a more useful picture. Antibody positive and simultaneous virus negative is a greater margin of safety IMO.

We run into this from time to time with animal disease outbreaks. Serosurveillance is nice for planned, routine screens of a population for diseases that one should not find antibody (or to quality check vaccination strategies when a titer *is* expected). But there is an inherent delay between the introduction of a pathogen (e.g., avian influenza) and production of detectable antibodies. Depending on the test and the disease, this could be 48-96 hours or more.

Performing antibody serosurveillance as a quasi-realtime diagnostic tool in a rapidly evolving disease outbreak is usually selecting the wrong tool for the task. Unless there was considerable (2+ days) delay in getting antigen testing results back, there are better choices.

Rapid antigen (read: virus) detection kits can be used as a proxy for virus isolation or PCR in a pinch. But antibody detection tests require too many assumptions about temporal exposure to be proactive in a timely fashion, IMO.

Lots of folks / companies trying to dump test kits or treatments or cures on a panicked public. I question the rationale of this antibody detection implementation without deeper thought about whether some better choices may exist.

My impression was the CDC is not looking at home use (although undoubtedly that will happen too), but using these as part of a contact tracing regimen, along with randomized regional checks to ascertain how much infection really has occurred (i.e. all the asymptomatic/minor symptom folks who currently aren't on the radar). Also, apparently their current system requires drawing venous blood, which once again uses one set of PPE for every test, and requires a lab to run the test.

[Cap Mandrake]

ORIGINAL: RangerJoe

ORIGINAL: Cap Mandrake

The Covid 19 genotype maps to bat and pangolin hybridization of the species-specific Cornavirus viral genome.

Somebody in Wuhan thought it was a good idea to eat one of these.

Maybe they will finally get serious on banning the trade of these cuddly creatures.

Yes! Hop up here scaly-boy! That's a good pangolin!

You see something like that in Louisiana or East Texas you TRY to run over it. Am I right? You certainly don't EAT it

[MakeeLearn]

ORIGINAL: Cap Mandrake

Yummy! Maybe about 6 hrs of smoking after a nice rub!

Thanks Wuhan!

Now, in fairness, it might be that a pangolin shat on a fruit that that bat ate and then someone in Wuhan had some delicious bat cioppino but I favor the former.

This is interactive.

click on the vertical red dots in the middle to view the Covid-19 phylogeny

https://nextstrain.org/groups/blab/sars-like-cov?c=host

What's a little Transfer of RNA among friends.

[RangerJoe]

ORIGINAL: Cap Mandrake

ORIGINAL: RangerJoe

ORIGINAL: Cap Mandrake

The Covid 19 genotype maps to bat and pangolin hybridization of the species-specific Cornavirus viral genome.

Somebody in Wuhan thought it was a good idea to eat one of these.

Maybe they will finally get serious on banning the trade of these cuddly creatures.

Yes! Hop up here scaly-boy! That's a good pangolin!

You see something like that in Louisiana or East Texas you TRY to run over it. Am I right? You certainly don't EAT it

Some people eat them. But they can carry the bacteria for Hansen's disease:

https://www.smithsonianmag.com/smart-ne ... 180954440/

https://www.cdc.gov/leprosy/transmission/index.html

[Chickenboy]

ORIGINAL: Cap Mandrake

You see something like that in Louisiana or East Texas you TRY to run over it. Am I right? You certainly don't EAT it

No FFS! They don't need help gittin' run over. They kind of do it by themselves. Plus, who wants all that gristle and goop on your (truck) front grill.

Talking with some of the USDA folks about the prevalence of Brucellosis in feral hogs around these here parts. About 50%. 50%? That's shoot 'em and leave 'em numbers, not eatin' numbers.

[BBfanboy]

ORIGINAL: Cap Mandrake

ORIGINAL: obvert

ORIGINAL: Ian R

Interesting sounding article in the LA times, but unfortunately behind a paywall, if anyone has access could they post a short summary.

What is really needed is a test that tells you if you already had it and recovered without even noticing.

The UK just bought 3.5 million of those. Anti-body tests. They're going to try to start the testing by the end of the week, according to the Health minister.

The whole idea is trying to see who has had to let those NHS workers and other frontline personnel deal with the most difficult areas, where they're at risk. The larger goal is to see how much herd-immunity has been achieved as there are now some odd outlying studies (like he one I linked from Oxford yesterday) that buck the trend of saying this is just beginning. Some think it's been moving around for a good while undetected as it was among young healthy populations.

EDIT: just listened to the live press conference on this. First go to NHS and critical workers. Then probably other priority personnel. Eventually it'll run out to the public and then will become part of a study to determine how many have had it.

Also said trying to ramp up basic testing still. At 97k as of now.

I think you can deduce from the ramping up of cases in country after country it is just entering the population but a study to look at the prevalence of antibody levels would be very useful. It would tell you about subclinical cases, which are likely substantial.

For example, in the Seattle-area nursing home, it was discovered after the seniors began falling like flies that HALF THE STAFF were already infected and the great majority were still working.

Also, a single Connecticut birthday party gave rise to FIFTY infected individuals, with quite a few just having mild disease. Whoever made the bean dip should have washed their hands better.

TV News tonight said that a Biotech company in Colorado has offered to do 100% blood sample antibody tests on the residents of the county it is in. County officials have agreed and as soon as it can be arranged, they will do the tests (door-to-door presumably) and another set 14 days later. As Chickenboy pointed out, it takes time to develop the antibodies and the amount of antibody will help establish a timeline for when the positive test people got the virus.

The epidemiologists are excited about being able to use the data to get a handle on the real number of cases (including the no-symptom ones). It could also show who has some immunity to the disease and can begin working in public again. This will be especially useful for medical staff. (No mask for you, antibody man!)

EDIT to add: The Biotech company is doing the tests for free. Their motivation must be to develop creds for their test and data analysis methods afterward. The test is said to be much cheaper than the ones being done to determine infection at the time of infection and results much faster to produce.

[BBfanboy]

ORIGINAL: Cap Mandrake

The first human-derived isolate is from Dec 3, 2019

This does NOT mean the first human infection was from that date. It took some time for the infection to amplify and come to the attention of doctors in Wuhan. It takes 1 or 2 or 3 doctors talking to each other over lunch. "Man that guy could not take a joke! His O2 sat is 95% and then 8 hrs later he is dead!"

I know it sounds cynical but that's how it is....then the second guys says...."Shit, that sounds like SARS!" because he is a bit older and remembers SARS...and then they all leave their food on the table.

Medical humour! I was married to a nurse so I heard a bit of it ...[X(]

[obvert]

One reason why Italy got so bad so fast.

https://sports.yahoo.com/italian-mayor- ... 18347.html

[obvert]

ORIGINAL: Cap Mandrake

The first human-derived isolate is from Dec 3, 2019

This does NOT mean the first human infection was from that date. It took some time for the infection to amplify and come to the attention of doctors in Wuhan. It takes 1 or 2 or 3 doctors talking to each other over lunch. "Man that guy could not take a joke! His O2 sat is 95% and then 8 hrs later he is dead!"

I know it sounds cynical but that's how it is....then the second guys says...."Shit, that sounds like SARS!" because he is a bit older and remembers SARS...and then they all leave their food on the table.

They traced case zero to Nov 17. The first case who presented in a hospital which they diagnosed retroactively. I remember distinctly as that is the day my wife returned from a trip to China. However a geneological study on the virus went back to mid-late-October for its origin.

This was some of what fed the hype of it being a military developed virus, as there was a military games in Wuhan in mid-October. Since also disproven.