All things CoronaVirus

[jhu72]

Vaccinated patient reports the progress of her COVID breakthrough case.

Hey JHU72, thought you and your science crew would appreciate this but planning my sons birthday party for later this month and the bowling alley is out (renovations) and asked if he had any ideas of interest and his first thought was “something science” so we found a group that comes to homes and works with kids doing science projects for a couple of hours.

Don’t get me wrong we still played catch (baseball) , soft tag/tackle football and lacrosse (just catching and we have these knock down ground ball “battles with me and my kids I let them get some but don’t make it easy and we all end up dirty) all weekend but he loves reading and science. His career ambition for the new school year he wrote is that he’s going to be a professional bike rider/scientist/linebacker/chef when he grows up...turning 9 on 8/23

Neat!

[CU88]

J. Stacey Klutts
Chief Pathologist at Veterans Affairs Medical Center

It's been a while since I weighed in on anything related to SARS-CoV-2/COVID. I see many posts describing the 'on the ground' impact of the Delta variant with desperate pleas for people to get vaccinated and wear masks. I couldn't agree more with these sentiments, but I will take a bit of a different educational approach. I am in a unique position to report on what is going on with the virus itself and how it interacts with the vaccines. I'm currently the Special Assistant to the National Director of Pathology and Lab Medicine for the entire VA system, with a specific role in advising on elements of COVID testing for the system. As such, I have a front row seat to all of the latest data, as we have to use those data in making our national policy decisions. So, here are a few important points about the Delta variant that may be of acute interest along with some education and salient points about the vaccines. I'll do my best to stitch this all together to where it makes some sense:

1. The Delta variant (lineage B.1.617.2) has a particular collection of mutations in the spike protein (that knob-like projection you see in renderings of the virus) that make it extremely effective in attaching to human cells and gaining entry. If the original CoV-2 strains were covered in syrup, this variant is covered in ultra-fast drying Gorilla Super Glue (industrial strength).

2. There are two recent publications which demonstrate that the viral loads in the back of the throats of infected patients are 1000X higher with Delta variant than with previous variants. I can tell you from data in my own labs, that is absolutely true! We are seeing viral signals we NEVER saw last year using the exact same assays.

3. This much higher load PLUS the ultra-'stickiness' of the Delta strains for adhering to human cells makes it remarkably more infectious than previous strains. You may have heard of R0 (Read: R naught) which is, in a nutshell, the expected number of persons to which an infected person would be expected to transmit the virus. Early versions of the virus had a 2 to 2.5 R0 value. So one infected person would infect two or so people on average. Delta has an R0 of about 8! In the infectious disease world, that's almost unheard of. Chickenpox and Measles are about all we have ever seen that spread that efficiently from human to human. This changes the story line completely from earlier in the pandemic and makes this surge, in many ways, like a completely different pandemic event.

4. There is another recent publication out of Singapore with data that confirms something we suspected. I will explain more about the 'why' on this below when I talk about vaccines, but the gist is this: The viral loads in the throats of vaccinated persons who become infected with Delta (more about that below) rises at identical rates as in unvaccinated persons, but only for the first few days. After 5 days or so, the viral loads in the vaccinated person start to quickly drop whereas those in the unvaccinated person persist. This key set of observations is important for several reasons relating to vaccinated persons serving as vectors for spread (see below).

5. This pandemic, round 2 is primarily being observed in younger patients than in round 1. Our Children's hospitals are even already filling up or full. Because of the Delta viral dynamics, it is much more capable of causing severe disease in a larger swath of the population. You spew enough of any human pathogen on someone without immunity, and it's not going to end well. This sets up very poorly for the beginning of the school year, and it scares me. Check that...it is actually terrifying. I sure hope we have vaccines for the 5-11 year olds soon...

6. Speaking of vaccines...are they working? YES! They are absolutely doing their expected job. We know a lot about vaccines for upper respiratory viruses, as we have been giving the population one every year for decades (influenza). To explain all of this, I need to provide some biological context. When you get a vaccine as a 'shot', the 'antigen' in the vaccine leads to formation of an antibody response. You probably knew that. What's important, though, is that it primarily leads to a specific IgG response. That's the antibody type that circulates around in really high numbers in the blood, is located some in tissues and is more easily detectable by blood tests, etc. What that shot does NOT do is produce an IgA antibody response to the virus at the surface of the throat mucosa. That's the antibody type that could prevent the virus from ever binding in the first place. As such, in a vaccinated person, the virus can still attach like it's about to break into the house, but it doesn't realize that there is an armed homeowner on the other side of the door. When that virus is detected, the IgG beats it up and clears it before the person gets very ill (or ill at all). (Sidebar: Anyone ever had their kid (or themselves) get the 'Flumist' vaccine? Idea there is to introduce the antigens at the surface of the throat mucosa leading to that IgA response that will prevent infection from happening at all. Sounds good and still has a place, but it isn't quite as effective overall as the shot.)

7. The SARS-CoV-2 vaccines are designed to prevent disease/death through that IgG response (though it does also reduce infections somewhat). How good are the vaccines at doing all of this with Delta? CDC released data just this week addressing that very question. Punchline: They're remarkably good! The vaccine shows an 8-fold reduction in the development of any symptomatic disease secondary to Delta. For hospitalization, it is a 25-fold reduction. That's 25X! Remarkable. For death, it is also 25X! This is a very effective pharmaceutical class when looking at overall efficacy toward the intended/expected purpose. When looking at the very tiny side effect profile, I'd personally consider it one of the best overall pharmaceuticals on the market in any class of drugs.

8. So, you're vaccinated? First of all, a sincere, heart-felt thank you! But you may now ask, so why do I again need to wear a mask? We talked about disease, hospitalizations and death in 7. above, but what about infections themselves? Vaccine is now estimated to provide a 3X reduction in infection. For reasons that I tried to make clear above, it isn't surprising that the vaccine is less effective at preventing infection vs preventing disease. We are indeed seeing detectable virus, at high levels, in asymptomatic, vaccinated persons when we test them prior to procedures, etc. We have a few that are mildly symptomatic, too. While we now understand that the virus fades from the back of the throat pretty quickly in a vaccinated person, we also know that an infected, vaccinated person can transmit this very infectious virus to others for at least a couple of days. So, as before, you are being asked to wear a mask to primarily protect others. We need you again to interrupt the transmission cycle of the virus, as you don't know when you might be infectious. The vaccine alone cannot interrupt this cycle when there is a lot of virus in the community within unprotected persons.

9. What's next? Living in Iowa, I see the tsunami wave on the horizon. It's typical for respiratory viruses to begin in the southern US (where it is hot and everyone goes indoors to escape the heat) and then creep north to affect those areas when it gets colder (and people go inside because it's getting colder). It's definitely coming to Iowa and areas in the northern half of the US. If you live in those northern areas and are not vaccinated, it is not too late, but it's getting damn close. It's also time to start wearing masks in public again (ugh...I hate it, too). For areas like AR, MO, LA, FL, etc, the tsunami is already on your shores. If you weren't already off the beach, you might be in trouble. However, if you are there and haven't yet been affected, run like hell to higher ground (get vaccinated, wear a mask). I beg of you, please observe that wave and don't ignore it. I have zero political agenda (hate politics). I'm just a nerdy scientist and physician who loves you all, and I certainly don't want to see a mass of my friends grieving (or dead) because I didn't yell loud enough to get you and your families off that beach. So, Run! (to your pharmacy...driving is allowed). You don't want any part of this thing w/o vaccine on board.

[youthathletics]

Great read...thanks for posting.

[MDlaxfan76]

Great read...thanks for posting.

+1

[Typical Lax Dad]

J. Stacey Klutts
Chief Pathologist at Veterans Affairs Medical Center

It's been a while since I weighed in on anything related to SARS-CoV-2/COVID. I see many posts describing the 'on the ground' impact of the Delta variant with desperate pleas for people to get vaccinated and wear masks. I couldn't agree more with these sentiments, but I will take a bit of a different educational approach. I am in a unique position to report on what is going on with the virus itself and how it interacts with the vaccines. I'm currently the Special Assistant to the National Director of Pathology and Lab Medicine for the entire VA system, with a specific role in advising on elements of COVID testing for the system. As such, I have a front row seat to all of the latest data, as we have to use those data in making our national policy decisions. So, here are a few important points about the Delta variant that may be of acute interest along with some education and salient points about the vaccines. I'll do my best to stitch this all together to where it makes some sense:

1. The Delta variant (lineage B.1.617.2) has a particular collection of mutations in the spike protein (that knob-like projection you see in renderings of the virus) that make it extremely effective in attaching to human cells and gaining entry. If the original CoV-2 strains were covered in syrup, this variant is covered in ultra-fast drying Gorilla Super Glue (industrial strength).

2. There are two recent publications which demonstrate that the viral loads in the back of the throats of infected patients are 1000X higher with Delta variant than with previous variants. I can tell you from data in my own labs, that is absolutely true! We are seeing viral signals we NEVER saw last year using the exact same assays.

3. This much higher load PLUS the ultra-'stickiness' of the Delta strains for adhering to human cells makes it remarkably more infectious than previous strains. You may have heard of R0 (Read: R naught) which is, in a nutshell, the expected number of persons to which an infected person would be expected to transmit the virus. Early versions of the virus had a 2 to 2.5 R0 value. So one infected person would infect two or so people on average. Delta has an R0 of about 8! In the infectious disease world, that's almost unheard of. Chickenpox and Measles are about all we have ever seen that spread that efficiently from human to human. This changes the story line completely from earlier in the pandemic and makes this surge, in many ways, like a completely different pandemic event.

4. There is another recent publication out of Singapore with data that confirms something we suspected. I will explain more about the 'why' on this below when I talk about vaccines, but the gist is this: The viral loads in the throats of vaccinated persons who become infected with Delta (more about that below) rises at identical rates as in unvaccinated persons, but only for the first few days. After 5 days or so, the viral loads in the vaccinated person start to quickly drop whereas those in the unvaccinated person persist. This key set of observations is important for several reasons relating to vaccinated persons serving as vectors for spread (see below).

5. This pandemic, round 2 is primarily being observed in younger patients than in round 1. Our Children's hospitals are even already filling up or full. Because of the Delta viral dynamics, it is much more capable of causing severe disease in a larger swath of the population. You spew enough of any human pathogen on someone without immunity, and it's not going to end well. This sets up very poorly for the beginning of the school year, and it scares me. Check that...it is actually terrifying. I sure hope we have vaccines for the 5-11 year olds soon...

6. Speaking of vaccines...are they working? YES! They are absolutely doing their expected job. We know a lot about vaccines for upper respiratory viruses, as we have been giving the population one every year for decades (influenza). To explain all of this, I need to provide some biological context. When you get a vaccine as a 'shot', the 'antigen' in the vaccine leads to formation of an antibody response. You probably knew that. What's important, though, is that it primarily leads to a specific IgG response. That's the antibody type that circulates around in really high numbers in the blood, is located some in tissues and is more easily detectable by blood tests, etc. What that shot does NOT do is produce an IgA antibody response to the virus at the surface of the throat mucosa. That's the antibody type that could prevent the virus from ever binding in the first place. As such, in a vaccinated person, the virus can still attach like it's about to break into the house, but it doesn't realize that there is an armed homeowner on the other side of the door. When that virus is detected, the IgG beats it up and clears it before the person gets very ill (or ill at all). (Sidebar: Anyone ever had their kid (or themselves) get the 'Flumist' vaccine? Idea there is to introduce the antigens at the surface of the throat mucosa leading to that IgA response that will prevent infection from happening at all. Sounds good and still has a place, but it isn't quite as effective overall as the shot.)

7. The SARS-CoV-2 vaccines are designed to prevent disease/death through that IgG response (though it does also reduce infections somewhat). How good are the vaccines at doing all of this with Delta? CDC released data just this week addressing that very question. Punchline: They're remarkably good! The vaccine shows an 8-fold reduction in the development of any symptomatic disease secondary to Delta. For hospitalization, it is a 25-fold reduction. That's 25X! Remarkable. For death, it is also 25X! This is a very effective pharmaceutical class when looking at overall efficacy toward the intended/expected purpose. When looking at the very tiny side effect profile, I'd personally consider it one of the best overall pharmaceuticals on the market in any class of drugs.

8. So, you're vaccinated? First of all, a sincere, heart-felt thank you! But you may now ask, so why do I again need to wear a mask? We talked about disease, hospitalizations and death in 7. above, but what about infections themselves? Vaccine is now estimated to provide a 3X reduction in infection. For reasons that I tried to make clear above, it isn't surprising that the vaccine is less effective at preventing infection vs preventing disease. We are indeed seeing detectable virus, at high levels, in asymptomatic, vaccinated persons when we test them prior to procedures, etc. We have a few that are mildly symptomatic, too. While we now understand that the virus fades from the back of the throat pretty quickly in a vaccinated person, we also know that an infected, vaccinated person can transmit this very infectious virus to others for at least a couple of days. So, as before, you are being asked to wear a mask to primarily protect others. We need you again to interrupt the transmission cycle of the virus, as you don't know when you might be infectious. The vaccine alone cannot interrupt this cycle when there is a lot of virus in the community within unprotected persons.

9. What's next? Living in Iowa, I see the tsunami wave on the horizon. It's typical for respiratory viruses to begin in the southern US (where it is hot and everyone goes indoors to escape the heat) and then creep north to affect those areas when it gets colder (and people go inside because it's getting colder). It's definitely coming to Iowa and areas in the northern half of the US. If you live in those northern areas and are not vaccinated, it is not too late, but it's getting damn close. It's also time to start wearing masks in public again (ugh...I hate it, too). For areas like AR, MO, LA, FL, etc, the tsunami is already on your shores. If you weren't already off the beach, you might be in trouble. However, if you are there and haven't yet been affected, run like hell to higher ground (get vaccinated, wear a mask). I beg of you, please observe that wave and don't ignore it. I have zero political agenda (hate politics). I'm just a nerdy scientist and physician who loves you all, and I certainly don't want to see a mass of my friends grieving (or dead) because I didn't yell loud enough to get you and your families off that beach. So, Run! (to your pharmacy...driving is allowed). You don't want any part of this thing w/o vaccine on board.

That was excellent. Hopefully we get more and more people vaccinated.

[youthathletics]

J. Stacey Klutts
Chief Pathologist at Veterans Affairs Medical Center

It's been a while since I weighed in on anything related to SARS-CoV-2/COVID. ....

I tried searching google for this....do you have a link?

[RedFromMI]

J. Stacey Klutts
Chief Pathologist at Veterans Affairs Medical Center

It's been a while since I weighed in on anything related to SARS-CoV-2/COVID. ....

I tried searching google for this....do you have a link?

https://www.tampabay.com/opinion/2021/0 ... utType=amp

[youthathletics]

J. Stacey Klutts
Chief Pathologist at Veterans Affairs Medical Center

It's been a while since I weighed in on anything related to SARS-CoV-2/COVID. ....

I tried searching google for this....do you have a link?

https://www.tampabay.com/opinion/2021/0 ... utType=amp

TU

[CU88]

J. Stacey Klutts
Chief Pathologist at Veterans Affairs Medical Center

It's been a while since I weighed in on anything related to SARS-CoV-2/COVID. ....

I tried searching google for this....do you have a link?

https://www.tampabay.com/opinion/2021/0 ... utType=amp

Thank for finding and sharing. My niece sent that to me, who did a shared residencey with Dr. Klutts at a VA.

[CU88]

Fingers crossed as we send kids back to schoool.


Pediatric numbers: 3 things to keep an eye on

Katelyn Jetelina

There’s no lack of anecdotal evidence that pediatric hospitals are reaching capacity in many states. This past weekend, Dallas had zero ICU beds for kids.

But, anecdotal evidence can be very different than population-level evidence. So, what are we seeing on a population-level? And, is there anything we should be concerned about?

Epidemiology

In the past week, 121,427 kids tested positive for COVID19, which represented 18% of the weekly reported cases in the United States. This is increasing at an exponential rate, but adult cases are also increasing exponentially.

In 23 states, 1.9% of child COVID-19 cases resulted in hospitalization. Last Saturday, 1,902 kids were hospitalized for COVID19. On a state-level, Texas is in the lead with 509 kids hospitalized for COVID19 today. This equates to more than 8 hospitalized per 100,000 kids in the state of Texas. The CDC has also made MIS-C (serious condition associated with COVID-19) data publicly available. As of July 31, 4,404 kids were diagnosed with MIS-C associated with COVID19 in the United States.

We are very lucky that kids aren’t as high of risk for severe disease as older adults. But, even given this, I’m still concerned about three things…

First, the rate in which hospitalizations are increasing. We are far beyond the January peak, which is particularly apparent in the South (second graph). This could be due to pandemic fatigue (we just don’t care anymore). Or this could be due to Delta being more serious than previous variants. There is preliminary evidence from Scotland and Canada that adult hospitalization is more severe with Delta. We have yet to see kid data, but I don’t have reason to believe that it’s different.

Second, pediatric ICU (PICU) capacity. We desperately need to flatten the pediatric hospital curve. Only ~38% of kids have “natural” immunity and the majority of kids aren’t eligible for vaccines, which means we have an estimated 34 million susceptible children in the United States. If 1.9% of infected children are hospitalized, 33% of the kids go to the PICU, and the average hospital stay is 4 days, that means we need 6,800 PICU beds. The U.S. only has 4,500 PICU beds total. (If you want to check the math, go to this amazing thread by Dr. Denise Dewald).

We could easily overwhelm our pediatric hospitals. And this is just with COVID19. RSV is also at an all time high. Car accidents and drownings, for example, are also still happening in the background. We can’t just put kids in adult hospital beds. Kids aren’t tiny adults, they need special equipment, correct dosages, and trained hospital staff (who are getting more and more difficult to find because they are burned out). We also can’t just systematically fly children from Texas (where hospitals are full) to Maryland (where hospitals aren’t full).

What schools do (or do not do) will impact case growth and, thus, impact how our hospitals fare too. A group of scientists in North Carolina modeled what may happen across schools that implement masks and/or surveillance testing. Without masks or regular testing, up to 90% of susceptible students may become infected by the end of the semester.

Third, kids’ role in the transmission chain. Yesterday, an important study was published in JAMA. Scientists sought out to answer how kids of all ages transit COVID19 in Canadian households from June 1 and December 31, 2020. They studied both the index cases and the rate of transmission in the household.

Out of 89,191 households, 6,280 households had a pediatric index case

The proportion of index cases increased with age. For example, 12% of households had an index case aged 0 to 3 years and 38% had an index case aged 14 to 17 years

Younger index cases had a higher proportion associated with a school/childcare outbreak than older kids

Kids aged 4 to 8 years and 9 to 13 years had higher proportion with no symptoms reported compared with index case individuals aged 14 to 17 years or aged 0 to 3 years

1717 households (27%) experienced secondary transmission (i.e. spread in the house)

Of these households, the index case passed it, on average, to 2 other household members

Younger children (aged 0-3) were more likely to transmit SARS-CoV-2 compared with older children (aged 14-17). This was irrespective of factors such as symptoms, school/childcare reopening, or school/childcare outbreaks.

This study tells us that we will not stop transmission in the community without stopping transmission among kids, especially younger kids. This is not only important for pediatric health, but also for adults’ health and to stop this virus from mutating.

Bottom Line: We aren’t sure if this pediatric case increase is the iceberg or just the tip of the iceberg. Delta may be changing the severity of disease, but we have yet to see the science for children. Children could certainly overwhelm hospitals and play an important role in transmission. The next few months will be critical for our children and our community.


https://yourlocalepidemiologist.substac ... eH_IQqvfEY

[seacoaster]

The United States is now reporting 706 new coronavirus deaths per day, the highest seven-day average since May 4, according to data from
CNN and Johns Hopkins University.

Average US cases/day via CNN:

Right now: 134,390 cases/day
10 days ago: 107,143 cases/day
20 days ago: 61,306 cases/day
30 days ago: 31,447 cases/day
40 days ago: 15,068 cases/day
50 days ago: 11,871 cases/day

Hard not to be pretty concerned given the upcoming school year. I give thanks every day that my children are out of school.

[MDlaxfan76]

Boosters now available on walk-in basis for immunocompromised, only requires self attest.

Very likely to open up to others very shortly as well.

https://www.supermarketnews.com/health- ... aa947fe03b

Also, lots of positive response from consumers to grocery stores and others requiring masks etc again.

https://www.supermarketnews.com/issues- ... aa947fe03b

[Brooklyn]

re boosters, evidently I missed the news last week:


https://www.vox.com/2021/8/14/22624596/ ... ompromised


The Food and Drug Administration (FDA) and the Centers for Disease Control and Prevention (CDC) announced approvals of third booster shots of the Pfizer/BioNTech or Moderna vaccines for people with weakened immune systems. The green light came within 24 hours of the FDA’s recommendation.



8 months would be November for me. Am wondering should I take the seasonal flu shot before? Will see what my doc says.

[MDlaxfan76]

re boosters, evidently I missed the news last week:


https://www.vox.com/2021/8/14/22624596/ ... ompromised


The Food and Drug Administration (FDA) and the Centers for Disease Control and Prevention (CDC) announced approvals of third booster shots of the Pfizer/BioNTech or Moderna vaccines for people with weakened immune systems. The green light came within 24 hours of the FDA’s recommendation.



8 months would be November for me. Am wondering should I take the seasonal flu shot before? Will see what my doc says.

I would think so. Get'er done.
I'm same time frame.

Unless we're significantly at greater risk, probably best for the boosters to go to those who are first.
I want my 84 year old mom to get it as soon as they green light her, maybe sooner!

That said, I'll probably want it as soon as allowed for 60+ year olds with no other complicating factors.

[Farfromgeneva]

The United States is now reporting 706 new coronavirus deaths per day, the highest seven-day average since May 4, according to data from
CNN and Johns Hopkins University.

Average US cases/day via CNN:

Right now: 134,390 cases/day
10 days ago: 107,143 cases/day
20 days ago: 61,306 cases/day
30 days ago: 31,447 cases/day
40 days ago: 15,068 cases/day
50 days ago: 11,871 cases/day

Hard not to be pretty concerned given the upcoming school year. I give thanks every day that my children are out of school.

Schools been on over a week here now. In fact just got a note from the teacher about our daughters mask slipping down today (she’s not a chin diaper person not anyone in our family). Mentioned this elsewhere but having kids learning at home has been a disaster for myself and every middle upper middle class person I know. Ruined marriages (not yet for me but..), kids are messed up parents are messed up. This is why I get hot seeing 3-4 posts every day, some from people I knew growing up and wouldn’t want teaching my kids, on F**kbook from teachers complaining about how unfair and how hard their lives are ignorant to their constituent parents.

[old salt]

Here's who is currently approved for the booster, 6 mos after fully vaxxed.

https://www.cdc.gov/coronavirus/2019-nc ... mmuno.html

[youthathletics]

Here's who is currently approved for the booster, 6 mos after fully vaxxed.

https://www.cdc.gov/coronavirus/2019-nc ... mmuno.html

Interesting....so jnj is sitting on the sidelines, at this point: https://www.cnn.com/2021/08/17/health/j ... index.html

[wgdsr]

Here's who is currently approved for the booster, 6 mos after fully vaxxed.

https://www.cdc.gov/coronavirus/2019-nc ... mmuno.html

Interesting....so jnj is sitting on the sidelines, at this point: https://www.cnn.com/2021/08/17/health/j ... index.html

not sure what all this waiting on data is. boosters work better, that's good enough for me.

[Typical Lax Dad]

Texas Gov. Greg Abbott tests positive for COVID-19

[Farfromgeneva]

Texas Gov. Greg Abbott tests positive for COVID-19

Saw this it’s about expected.