OT: Corona virus

[Canoerebel]

There are so many questions, though. Many of the poorer countries are in warmer climates. He discusses that in the paper, though not at length.

We've noted the issues about testing/reporting. Many prefer to use mortality figures as a better/truer indicator. That should be more reliable, though there may be countries that under report there, too (one person yesterday offered thoughts about India, in that regard).

Mortality numbers are a big concern in Italy and Spain now, but Germany, other central European countries, UK and USA remain pretty low, at least for now.

Yesterday, a US healthcare leader (the top person in New Jersey IIRC) predicted about 21 days until the US reaches the top of the curve. That's an intriguing number but may or may not be reliable or useful. First, let's hope it turns out to be less than that. If not, that doesn't seem like an apocalyptic scenario (doubling every three days, for instance, means seven doublings of mortality or cases, if applicable). But her comments might have been flippant or otherwise too general to permit useful extrapolation.

[Canoerebel]

Thoughts on some things at noon eastern (US), while waiting for the numbers to come in from Italy.

[Chickenboy]

ORIGINAL: Canoerebel
What're you thinking, these days?

I'm thinking about the vaccine development.

A comment by Erik Rutkins a couple weeks ago (I tried to find it, but got tired of reading through the political screed of some, so I stopped trying to find it) got me thinking. His comment was to the effect that 'we have no track record with producing a successful vaccine against coronavirus' or something very much along those lines.

While that's probably true for humans, I find myself lamenting the lack of advancement in human vaccine development. Animals, particularly poultry, have had coronavirus infections of importance for many years. In poultry, the disease is "Infectious Bronchitis", caused by the-wait for it-Infectious Bronchitis Virus (IBV). A coronavirus. Poultry are susceptible to respiratory disease that it inflicts.

Morbidity and mortality vary-usually with underlying management or immunosuppressive disorders. High levels of 'stocking density' or problems with in-house waterers lead to litter moisture problems and ammonia production. Ammonia reduces the bronchociliary escalator's effectiveness, thereby reducing the trachea's ability to clear exogenous debris from the trachea. And it also denudes normal bronchiolar cilia as a primary effect-a double whammy for the respiratory tract. Secondary bacterial pneumonia or airsacculitis is a common sequelae.

For many years, standard vaccination protocols for meat-type broilers involves (usually) day-of-age coarse droplet sprays in the hatchery of infectious bronchitis vaccine. Sometimes these efforts are supplemented in the field by a sort of backpack sprayer. Attenuated modified live virus is sprayed directly onto the chicks. Chicks innoculate themselves by getting the MLV into their eyes or nares or ingesting droplets from grooming their neighbors.

Not all viral vaccine subtypes are equally efficacious against given 'field challenge'. There are a number of different IBV vaccine subtypes out there. Old stalwarts are named after the state where they were developed and used originally. The most common IBV vaccinal subtypes are MASS and CONN or MASS/CONN in the vernacular. These have broad, albeit incomplete, coverage. From time to time, other subtype vaccines are rolled out to include more regional strains of importance: DEL-072, GA-98, DPI (DEL/MAR/VA), ARK and ARK-99, etc.

[mind_messing]

ORIGINAL: Canoerebel

There are so many questions, though. Many of the poorer countries are in warmer climates. He discusses that in the paper, though not at length.

We've noted the issues about testing/reporting. Many prefer to use mortality figures as a better/truer indicator. That should be more reliable, though there may be countries that under report there, too (one person yesterday offered thoughts about India, in that regard).

Mortality numbers are a big concern in Italy and Spain now, but Germany, other central European countries, UK and USA remain pretty low, at least for now.

Yesterday, a US healthcare leader (the top person in New Jersey IIRC) predicted about 21 days until the US reaches the top of the curve. That's an intriguing number but may or may not be reliable or useful. First, let's hope it turns out to be less than that. If not, that doesn't seem like an apocalyptic scenario. But her comments might have been flippant or otherwise to general to permit useful extrapolation.

Climate won't help much, in my view. There's already a broad spread of climates with large numbers of total cases.

If it's already spread to Singapore, it's already a hop to Indonesia

Watch Brazil. I suspect cases there may really pick up in the coming weeks.

[BBfanboy]

ORIGINAL: Chickenboy

ORIGINAL: Kull

ORIGINAL: Chickenboy

A drive by posting from me.

I noticed that the John Hopkins COVID-19 chart has changed significantly today. It appears as though they have county by county information from the US now, instead of the less granular state by state data. It really conveys a sense of where the problem areas are. Also, the lower right corner of the screen graph has changed to reflect daily case counts for a given country. This makes (sorry, Kull) individual spreadsheet tracking superfluous at this point.

Yeah, but it doesn't give per-province numbers, nor the ability to make comparisons over time. The granularity is where the real information lies!

Per 'province'? If you're referring to Canada, yes-I noticed that their reporting mechanism doesn't seem to have changed.

But the granularity in the United States is useful to spot where the big hot spots are. Right now, about half of the US cases are in and around New York City. Other top 10 city populations (Los Angeles, Houston, Chicago, San Antonio, Dallas, etc.) are a small fraction of the New York distribution. That's helpful information, IMO.

One of the charts Kull posts shows info per province in Canada, so the info is available. Not our fault if Johns Hopkins chooses to only use the total for the country.
I think Kull was referring to Italian Provinces which he has been following quite closely.

[Kull]

ORIGINAL: Chickenboy

ORIGINAL: Kull

ORIGINAL: Chickenboy

A drive by posting from me.

I noticed that the John Hopkins COVID-19 chart has changed significantly today. It appears as though they have county by county information from the US now, instead of the less granular state by state data. It really conveys a sense of where the problem areas are. Also, the lower right corner of the screen graph has changed to reflect daily case counts for a given country. This makes (sorry, Kull) individual spreadsheet tracking superfluous at this point.

Yeah, but it doesn't give per-province numbers, nor the ability to make comparisons over time. The granularity is where the real information lies!

Per 'province'? If you're referring to Canada, yes-I noticed that their reporting mechanism doesn't seem to have changed.

But the granularity in the United States is useful to spot where the big hot spots are. Right now, about half of the US cases are in and around New York City. Other top 10 city populations (Los Angeles, Houston, Chicago, San Antonio, Dallas, etc.) are a small fraction of the New York distribution. That's helpful information, IMO.

Right now I'm more concerned with Italy, simply because they are further along what appears to be the worst case scenario curve. It's Day 14 of the lockdown, and only now are we seeing a reduction in case growth, although I can't say for sure if that's an anomaly or the start of a trend. There may eventually be an NYC-Lombardy parallel in the US, but it's too early to know. Nevertheless, having the granularity of Italian data will give me some ideas on how to look at the US. As you note, regional numbers DO matter.

[BBfanboy]

ORIGINAL: Canoerebel

There are so many questions, though. Many of the poorer countries are in warmer climates. He discusses that in the paper, though not at length.

We've noted the issues about testing/reporting. Many prefer to use mortality figures as a better/truer indicator. That should be more reliable, though there may be countries that under report there, too (one person yesterday offered thoughts about India, in that regard).

Mortality numbers are a big concern in Italy and Spain now, but Germany, other central European countries, UK and USA remain pretty low, at least for now.

Yesterday, a US healthcare leader (the top person in New Jersey IIRC) predicted about 21 days until the US reaches the top of the curve. That's an intriguing number but may or may not be reliable or useful. First, let's hope it turns out to be less than that. If not, that doesn't seem like an apocalyptic scenario (doubling every three days, for instance, means seven doublings of mortality or cases, if applicable). But her comments might have been flippant or otherwise too general to permit useful extrapolation.

The prediction of a US peak in 21 days is too generic. The various regions have started being affected at different points in time and have started their countermeasures at various points in time. It will look more like a series of peaks rippling through the country. MAYBE the median date for peaks is 21 days off, but if states are learning from each other I expect the peaks will on average come sooner than 21 days so it will be a skewed distribution with a long tail on the distant end.

[Chickenboy]

(Broke this post up to ensure that it didn't get eaten by the server)

In the case of a novel 'field strain', it may not respond to vaccination with stalwart MASS/CONN vaccines. We experienced this in Pennsylvania in the late 1990s with an unusual IBV that caused comparatively rare primary renal (Kidney) lesions-nephropathogenic IBV. Chickens affected with this field strain of IBV did not have much of a respiratory component, but it wiped out their renal tubular epithelium, leaving them with an inability to resorb fluid from normal kidney function. They 'flushed' and died en masse from dehydration.

Industry was desperate for a vaccine to forestall this mortality. It was unlikely that a commercial vaccine manufacturer would assume the mantle of producing a novel vaccine de novo in a timely fashion. So several research groups at my University and another worked on controlled field and laboratory testing what vaccines we *did* have available to see if some combination of them was more effective than others in a combination regimen. I described the pathology in a diagnostic case report. This is the vaccine protection study that followed that I co-authored:

https://www.semanticscholar.org/paper/P ... 4e6fe07f54

Upshot: there was greater protective efficacy in different vaccine regimens from different combinations of off-the-shelf vaccines. None protected as well as an autogenous (e.g., self-made vaccine directly from the field strain), but some combinations did reduce the mortality versus 'standard' MASS/CONN vaccine combinations.

So what? Who cares?

With a virus as liable to change and morph as Coronaviruses are wont to do, one needs to think about vaccine development to cover things 'down the line'. Existing vaccine serotype / subtype vaccines may not work well against future 'wild type' viral challenges. But combinations of live attenuated vaccines and killed vaccines may forestall mortality, even if it's not an identical match to the strain du jour.

So, I can't help but wondering why a SARS/MERS vaccine wasn't developed at all. And if it may not provide at least partial protection against novel coronaviruses (COVID-19) if it had been. I wonder if some combination of MLV (Modified Live) vaccine and a killed vaccine (e.g., injectable-think 'annual flu shot') may not provide some degree of protection.

So when I hear comments about "we haven't been able to make coronavirus vaccines that are protective", I need to remind the speaker that perhaps that's only true in humans. Animal vaccines for this have been around for a long time and we've known how to deal with the respiratory disease caused by coronavirus in animal populations for a long time. There is hope that there may be some partial protection from existing vaccines and [biased comment follows] human physicians can learn a good deal about mass application of vaccines in an outbreak from their veterinary colleagues.

This is on my mind.

[BBfanboy]

ORIGINAL: Chickenboy


Chicks innoculate themselves by getting the MLV into their eyes or nares or ingesting droplets from grooming their neighbors.

So you're saying Belgium's banning of orgies and gangbangs is a mistake? Good to hear! [8|]

[alanschu]

A friend of mine shared that she may have had COVID-19 in Florida in January. She had some flu-like illness that wasn't the flu with several days of fever that ibuprofen didn't do much for, and intense shortness of breath and was out for about 10 days.

Of course it's just speculation as she was never tested for the disease (it wasn't really on most of our radar in January), but I could see it being present around that time.

[Lokasenna]

ORIGINAL: BBfanboy

ORIGINAL: Canoerebel

There are so many questions, though. Many of the poorer countries are in warmer climates. He discusses that in the paper, though not at length.

We've noted the issues about testing/reporting. Many prefer to use mortality figures as a better/truer indicator. That should be more reliable, though there may be countries that under report there, too (one person yesterday offered thoughts about India, in that regard).

Mortality numbers are a big concern in Italy and Spain now, but Germany, other central European countries, UK and USA remain pretty low, at least for now.

Yesterday, a US healthcare leader (the top person in New Jersey IIRC) predicted about 21 days until the US reaches the top of the curve. That's an intriguing number but may or may not be reliable or useful. First, let's hope it turns out to be less than that. If not, that doesn't seem like an apocalyptic scenario (doubling every three days, for instance, means seven doublings of mortality or cases, if applicable). But her comments might have been flippant or otherwise too general to permit useful extrapolation.

The prediction of a US peak in 21 days is too generic. The various regions have started being affected at different points in time and have started their countermeasures at various points in time. It will look more like a series of peaks rippling through the country. MAYBE the median date for peaks is 21 days off, but if states are learning from each other I expect the peaks will on average come sooner than 21 days so it will be a skewed distribution with a long tail on the distant end.

Yep - different areas are getting hit at different rates and a "comet tail" is exactly what I would expect.

The county-level data is good, but US counties are by no means homogeneous. Some states (like Iowa and Georgia) have large numbers of smaller counties that are broken up mostly along regular geographic boundaries (mostly rectangles). Other states (like Maryland and Virginia) have a smaller number of larger counties that are delineated by arbitrary bounds. Still, it's better than state-level data.

[Lokasenna]

ORIGINAL: alanschu

A friend of mine shared that she may have had COVID-19 in Florida in January. She had some flu-like illness that wasn't the flu with several days of fever that ibuprofen didn't do much for, and intense shortness of breath and was out for about 10 days.

Of course it's just speculation as she was never tested for the disease (it wasn't really on most of our radar in January), but I could see it being present around that time.

Indeed just speculation, although theoretically possible. Blow her case up to the rest of the population and it becomes obvious why being able to test for antibodies is going to be critical to our understanding. We aren't able to do so yet.


Worth noting that there was a particularly nasty strain of seasonal cold or flu going around in December/January. Both people in my household had it, as did just about my entire office. It started making the rounds in the first week or so of December, which was before this coronavirus really appeared.

[Chickenboy]

ORIGINAL: BBfanboy

ORIGINAL: Canoerebel

There are so many questions, though. Many of the poorer countries are in warmer climates. He discusses that in the paper, though not at length.

We've noted the issues about testing/reporting. Many prefer to use mortality figures as a better/truer indicator. That should be more reliable, though there may be countries that under report there, too (one person yesterday offered thoughts about India, in that regard).

Mortality numbers are a big concern in Italy and Spain now, but Germany, other central European countries, UK and USA remain pretty low, at least for now.

Yesterday, a US healthcare leader (the top person in New Jersey IIRC) predicted about 21 days until the US reaches the top of the curve. That's an intriguing number but may or may not be reliable or useful. First, let's hope it turns out to be less than that. If not, that doesn't seem like an apocalyptic scenario (doubling every three days, for instance, means seven doublings of mortality or cases, if applicable). But her comments might have been flippant or otherwise too general to permit useful extrapolation.

The prediction of a US peak in 21 days is too generic. The various regions have started being affected at different points in time and have started their countermeasures at various points in time. It will look more like a series of peaks rippling through the country. MAYBE the median date for peaks is 21 days off, but if states are learning from each other I expect the peaks will on average come sooner than 21 days so it will be a skewed distribution with a long tail on the distant end.

I agree. Predictions of a US peak in 21 days are inherently too generic. Maybe NYC / New Jersey hotspot will peak then, but I wouldn't put any credence on that broader applicability for the nation. It may peak nationally in 21 days when NYC starts tailing off and no other city rises to the case count. It may peak in NYC in 21 days and then Chicago in 35 days, Los Angeles in 45 days, or whatever.

[BBfanboy]

ORIGINAL: alanschu

A friend of mine shared that she may have had COVID-19 in Florida in January. She had some flu-like illness that wasn't the flu with several days of fever that ibuprofen didn't do much for, and intense shortness of breath and was out for about 10 days.

Of course it's just speculation as she was never tested for the disease (it wasn't really on most of our radar in January), but I could see it being present around that time.

If possible, she should get tested for antibodies so that (if positive) her blood plasma could be used to help critically ill patients. China started doing that near the end of its efforts at containment and reported that it helped significantly. I don't know if the US has accepted that as a treatment yet, but with everyone grasping at straws right now I can't see why they wouldn't try it.

[USSAmerica]

My lingering doubt about China being on the road to recovery and their economy getting "back to business" makes reports like this one catch my eye. Still a small sample, but...

https://www.cnn.com/2020/03/23/asia/hon ... index.html

[Chickenboy]

ORIGINAL: Lokasenna
being able to test for antibodies is going to be critical to our understanding. We aren't able to do so yet.

Antibody studies (presumably from blood samples) are a poor way of tracking a fulminant outbreak. Serologic antibody screening is useful for determining historical exposure, but antibody production takes several weeks post-exposure to develop sufficient to detect. It's a 'rear view mirror' sort of diagnostic approach.

Viral detection, whether its RT-PCR, antigen kit detection or virus isolation is the best methodology to detect an outbreak as it is occurring. Serosurveillance will be interesting down the road to look at how many people were affected from a historical perspective.

[Chickenboy]

ORIGINAL: USSAmerica

My lingering doubt about China being on the road to recovery and their economy getting "back to business" makes reports like this one catch my eye. Still a small sample, but...

https://www.cnn.com/2020/03/23/asia/hon ... index.html

Agreed. I'm still skeptical about the verity of their reports in mainland China or their case numbers.

[Lokasenna]

ORIGINAL: Chickenboy

ORIGINAL: Lokasenna
being able to test for antibodies is going to be critical to our understanding. We aren't able to do so yet.

Antibody studies (presumably from blood samples) are a poor way of tracking a fulminant outbreak. Serologic antibody screening is useful for determining historical exposure, but antibody production takes several weeks post-exposure to develop sufficient to detect. It's a 'rear view mirror' sort of diagnostic approach.

Viral detection, whether its RT-PCR, antigen kit detection or virus isolation is the best methodology to detect an outbreak as it is occurring. Serosurveillance will be interesting down the road to look at how many people were affected from a historical perspective.

Right, that's what I meant. It's important to help us learn about what to expect, and if we had a way to test for antibodies for this one in NYC on a widespread basis (for example), it would be helpful knowledge as infections spread to other areas. Correct? If nothing else, it would really help nail down the R0, right?

[BBfanboy]

ORIGINAL: Lokasenna

ORIGINAL: Chickenboy

ORIGINAL: Lokasenna
being able to test for antibodies is going to be critical to our understanding. We aren't able to do so yet.

Antibody studies (presumably from blood samples) are a poor way of tracking a fulminant outbreak. Serologic antibody screening is useful for determining historical exposure, but antibody production takes several weeks post-exposure to develop sufficient to detect. It's a 'rear view mirror' sort of diagnostic approach.

Viral detection, whether its RT-PCR, antigen kit detection or virus isolation is the best methodology to detect an outbreak as it is occurring. Serosurveillance will be interesting down the road to look at how many people were affected from a historical perspective.

Right, that's what I meant. It's important to help us learn about what to expect, and if we had a way to test for antibodies for this one in NYC on a widespread basis (for example), it would be helpful knowledge as infections spread to other areas. Correct? If nothing else, it would really help nail down the R0, right?

I think some people have already decided the virus will fade away after we beat the initial onslaught. I think there is no guarantee of that and it is something we will have to live with for some time. Getting a handle on what happened during the onslaught when we could not test everyone would be important on modelling what happens when we come out of isolation and start doing business again. We need to be able to test randomly to detect resurgence of the virus early and then contact trace to contain the spread. We probably have a year of this "holding down the recurrence" situation before herd immunity or virus mutation renders it unnecessary.
If summer weather kills the infection, that will be great but it will still exist in parts of the world not experiencing summer at the same time. It will find its way back.

[alanschu]

ORIGINAL: Lokasenna

Indeed just speculation, although theoretically possible. Blow her case up to the rest of the population and it becomes obvious why being able to test for antibodies is going to be critical to our understanding. We aren't able to do so yet.


Worth noting that there was a particularly nasty strain of seasonal cold or flu going around in December/January. Both people in my household had it, as did just about my entire office. It started making the rounds in the first week or so of December, which was before this coronavirus really appeared.

Very possible, especially with the mind games the illness can play on people (myself definitely included).


EDIT:

If possible, she should get tested for antibodies so that (if positive) her blood plasma could be used to help critically ill patients. China started doing that near the end of its efforts at containment and reported that it helped significantly. I don't know if the US has accepted that as a treatment yet, but with everyone grasping at straws right now I can't see why they wouldn't try it.

I have passed this along. Thank you!