Coronavirus

[DrGriz]

This article in 'Science' has some information that others don't, regarding the whole situation:

Science | AAAS

www.science.org

"Unearthed genetic sequences from China market may point to animal origin of COVID-19
French scientist finds previously undisclosed data from Chinese research team"

Since Débarre spotted the sequences, GISAID has removed them, noting that this was at the request of the submitter.

Gao’s team used swabs to collect environmental samples from many of the stalls of the Huanan market between 1 January 2020, the day it was shut down, and 2 March 2020. The group reported last year that some of the samples that tested positive for SARS-CoV-2 also had human genetic material, but no DNA from other animals.

The group says it reached out to Gao and colleagues to collaborate on analyzing the unearthed market sequences, and soon after that, the data disappeared from GISAID. When Science asked Gao why GISAID removed the sequence data, he did not reply, but he indicated that the data did not resolve the question of SARS-CoV-2’s origin, which he said is “still scientific and open.”

Nothing to see here. 🤷‍♂️

 

[Norbert]

Nothing to see here. 🤷‍♂️

It sounds a bit like the data may be in the process of getting updated, like the chinese research article (that it apparently will be used for) "is in the process of being re-submitted":

SAGO statement on newly released SARS-CoV-2 metagenomics data from China CDC on GISAID

On 12 March 2023, WHO was made aware of new SARS-CoV-2 sequences and metagenomics data associated with samples collected in the Huanan Seafood Wholesale Market, Wuhan, China, from January 2020, that became available on GISAID for a short period of time.

www.who.int

 

[dhanson865]

Deaths dropping but no where near summer levels (chart ends at Jan 31)

View attachment 908597

Updated chart ends on Mar 01 2023 at 299 still above the summer lows but lower than the month before.

most recent Peak was at 592 on Jan 14th

Still waiting for it to someday drop below 200 (which we haven't seen since Mar 25th 2020 (in the earliest days of the pandemic)).

 

[bkp_duke]

I don’t!

I was surprised at how little the CFR has changed actually. It is pretty sad given the existence of effective vaccines. I would guess half of the deaths were probably avoidable.

And H1N1 was no joke, and there were a lot of people upset at the response to it, claiming not enough was done.

Undoubtedly not. Unclear which way things would go, of course. There would be significantly less health-care seeking with H1N1 presumably. Diagnostics were scarce. Etc. I’m not sure about the estimates for number infected. Has been discussed here before.

No idea how IFRs compare. I would guess COVID probably quite a bit higher given the much higher mortality.

In any case, unusually high mortality in both cases and undoubtedly a swine flu vaccine early on would have been very helpful and strongly advised.

Well, here's the problem.

IF your CFR is right (and I don't think it is, see below) - then that would be damning evidence for a really piss-poor efficacy on the vaccine. It's primary design goal - reduction of death - would have been a failure.

What I think is going on is that the data, particularly that over the last 18 months, is inaccurate. The cases reported is low, too low, because previously when people tested at home and had a positive they called their doc and/or went to the ER and that was a "reportable case", in addition to those tests found positive by labs, Dr. offices, and hospitals. Now? People aren't reporting it. My dad (3 shots) tested positive at home on a rapid test this week with COVID. He's 79, has URI symptoms and some malaise, but is otherwise improving (with strict instructions from his physician son to call 911 if he has any difficulty breathing). He didn't notify his doc or anything else. But he's also an ox and will probably die at about 99-105 (per the norm of his family)

So, your cases number is low, that is cutting the denominator, and thereby increasing the calculated rate.

It's some grey zone between CFR and IFR, in reality.



But - your own data, albeit somewhat incomplete (per above), shows that efficacy of the vaccine against generalized illness leaves something to be desired.

 

[DrGriz]

It sounds a bit like the data may be in the process of getting updated, like the chinese research article (that it apparently will be used for) "is in the process of being re-submitted":

SAGO statement on newly released SARS-CoV-2 metagenomics data from China CDC on GISAID

On 12 March 2023, WHO was made aware of new SARS-CoV-2 sequences and metagenomics data associated with samples collected in the Huanan Seafood Wholesale Market, Wuhan, China, from January 2020, that became available on GISAID for a short period of time.

www.who.int

This is helpful. Thank you for posting it.

Although this does not provide conclusive evidence as to the intermediate host or origins of the virus, the data provide further evidence of the presence of susceptible animals at the market that may have been a source of human infections.

This is so circumstantial it can hardly be considered evidence. Although I agree that in all likelihood there was an animal source, the language used makes it feel like they have a hypothesis and are bending over backwards to reinforce it. It's along the lines of "we think he might have walked along the street the house is on the night of the murder, therefore he did it." Maybe there will be more, but so far it's not there.

 

[AlanSubie4Life]

What I think is going on is that the data, particularly that over the last 18 months, is inaccurate. The cases reported is low, too low, because previously when people tested at home and had a positive they called their doc and/or went to the ER and that was a "reportable case",

It is like you did not read my post! Where I specifically and clearly addressed this. CFR is CFR btw; there is no such thing as cases being too low!

What is the lower limit for IFR in this case?

You said yourself 10% or whatever are getting the vaccine. Uptake in the young has been awful!

Why would you expect with that uptake and the difference in ascertainment that the CFR would budge?

You were the one making the claim that CFR was going to be much better with this “mild” virus and with infection-acquired immunity.

Unsurprisingly (now that I have thought about the factors), it is not.

And IFR is awful too. What % of children have been infected? I would guess between 70-85% or so. (Some not exposed, and some who will be extremely resistant and will take years to be infected, due to vaccination and strong immune systems that prevent infection.)

Roughly 70-75 million under 18 FYI for your calculations.

What would be interesting with above captures and going to current data for other groups is to look at CFR for other age groups. I bet that has gone down a bit! I will do that later. Since few others here will engage with actual data and instead just make rash evidence-free statements. All the data is available using above captures and current CDC data for anyone who wants to do it. EDIT: (Actually I need to find a post of mine which captures all the age groups data, which does exist, at some point in time...we'll see what I can find.) This is easy math!

 

[bkp_duke]

It is like you did not read my post!

What is the lower limit for IFR in this case?

You said yourself 10% or whatever are getting the vaccine. Uptake in the young has been awful?

Why would you expect with that uptake and the difference in ascertainment that the CFR would budge?

You were the one making the claim that CFR was going to be much better with this “mild” virus and with infection-acquired immunity.

Unsurprisingly (now that I have thought about the factors), it is not.

And IFR is awful too. What % of children have been infected? I would guess between 70-85% or so. (Some not exposed, and some who will be extremely resistant and will take years to be infected, due to vaccination and strong immune systems that prevent infection.)

Roughly 70 million under 18 FYI for your calculations.

I read your post. The CFR is not remotely what you are calculating. It doesn't pass the "sniff" test, and here is why:

If the CFR was unchanged from 2020/21 then the hospitals and ICUs would be packed (you reported cases are still up), and that just isn't the case. The lethality of the current strains is MUCH lower, and the clear evidence for a lower CFR is lower hospitalization rates and ICU utilization. I don't know what is happening in the "ivory castle" of the CDC and how they got these numbers (politics aside, they don't make sense on fatalities, and other sources like Worldometer don't correlate with them), but from the "boots on the ground" I'm sure @madodel's wife, @PACEMD, and @DrGriz will confirm that:
1) hospitalizations of COVID have dropped hard and ICU utilization is down along with that
2) the "clinical presentation" of someone with COVID now is not remotely the same as in 2020/2021. The typical presentation is far milder than it was.

Are their still sick people? Yes. But it's not as typical.

My argument stands:
1) The vaccines are far less effective than they were against the earlier variants.
2) The IFR/CFR of COVID has dropped (as expected with a pandemic to epidemic progression).

 

[AlanSubie4Life]

The CFR is not remotely what you are calculating.

The CFR is what I calculated. It’s not a complicated metric. You count deaths, and you count confirmed cases per the definition of a case. It’s not IFR!

If the CFR was unchanged from 2020/21 then the hospitals and ICUs would be packed (you reported cases are still up),

Look at the case charts! The cases are WAY down from prior peaks. They are extremely low.

Furthermore, we are talking about CFR in a group which has no appreciable impact on hospital loading!!!

So we’re not even looking at a metric which would be relevant for that, so not sure why you are bringing that up as a counter argument to the CFR data provided.

If someone would actually do the calculations, I bet the relevant CFR is down, and also the cases (and actual infections) are of course substantially lower than those bad days. Because the vaccine works, and prior infection works. (And also Omicron is somewhat less severe than the prior virus - probably by about a factor of 1.5 or 2.)

1) hospitalizations of COVID have dropped hard and ICU utilization is down along with that
2) the "clinical presentation" of someone with COVID now is not remotely the same as in 2020/2021. The typical presentation is far milder than it was.

Yes of course, why would this not be true??? Why are we discussing that? Since it is not relevant to this discussion for the most part?

 

[PACEMD]

It's along the lines of "we think he might have walked along the street the house is on the night of the murder, therefore he did it." Maybe there will be more, but so far it's not there.

I know in my heart of hearts that he did it! I saw that house walking down the street when suddenly it hit me!

 

[PACEMD]

People, but particularly them younger peolpes, ain't gettin' immunizations or boosters recently because covid ain't really a thing just now. No one is scared or cares enough recently to jam their arms. Our corporate multi-state sh*t ton of hospitals system just officially policy stated......."Mask? Eh, who needs 'em?" I suspect Juk hacked the software..........

 

[DrGriz]

I read your post. The CFR is not remotely what you are calculating. It doesn't pass the "sniff" test, and here is why:

If the CFR was unchanged from 2020/21 then the hospitals and ICUs would be packed (you reported cases are still up), and that just isn't the case. The lethality of the current strains is MUCH lower, and the clear evidence for a lower CFR is lower hospitalization rates and ICU utilization. I don't know what is happening in the "ivory castle" of the CDC and how they got these numbers (politics aside, they don't make sense on fatalities, and other sources like Worldometer don't correlate with them), but from the "boots on the ground" I'm sure @madodel's wife, @PACEMD, and @DrGriz will confirm that:
1) hospitalizations of COVID have dropped hard and ICU utilization is down along with that
2) the "clinical presentation" of someone with COVID now is not remotely the same as in 2020/2021. The typical presentation is far milder than it was.

Are their still sick people? Yes. But it's not as typical.

My argument stands:
1) The vaccines are far less effective than they were against the earlier variants.
2) The IFR/CFR of COVID has dropped (as expected with a pandemic to epidemic progression).

Was talking last night about the hospitalization rates with a nurse who was, when it was a big thing, a covid ward nurse in one of the major hospitals in Boise, and she has been stood down as far as that goes. There might be 8 or 10 patients at any given time now, but not full wards and ICU overflow.

And it is hard to get a handle on the number of cases. We had a mini epidemic go through our nursing home a few weeks ago, and one person died (which is significant as the county totals for the entire 3 years is still under 20 officially). There have been plenty of cases despite the CDC reports (we actually were "high" for two weeks last month but have been "low" for the last 3). But many cases are someone gets exposed and home tests positive. A doc I know was exposed by a patient in clinic a couple of weeks ago. She's vaccinated and had slight symptoms so she home tested. Her vaccinated family members, including young kids, never did get it from her despite a lot of testing.

Many people I know who had not gotten infected finally have been this year. I think that's because many have let their guard down. We'll continue to see some significant cases as long as there are people who are susceptible.

We have a relatively high unvaccinated population here and I think they are spreading it around, but there's just not the level of sickness we saw with delta.

I think the vaccines are still effective for severe disease, and maybe even keep the mild disease relatively at bay. I would not say they don't work. Simply that they don't prevent transmission as much as we would like. That's a different animal.

 

[bkp_duke]

The CFR is what I calculated.

Look at the case charts! The cases are WAY down from prior peaks. They are extremely low.

Furthermore, we are talking about CFR in a group which has no appreciable impact on hospital loading!!!

So we’re not even looking at a metric which would be relevant for that, so not sure why you are bringing that up as a counter argument to the CFR data provided.

If someone would actually do the calculations, I bet the relevant CFR is down, and also the cases (and actual infections) are of course substantially lower than those bad days. Because the vaccine works, and prior infection works.


Yes of course, why would this not be true??? Why are we discussing that? Since it is not relevant to this discussion for the most part?

Then I'm missing the point you are trying to make. Please restate. Perhaps it's the fog of a 17h drive yesterday still hanging over.

I'm seeing the aggregate CDC data for COVID deaths from 2020-2023 (Mar 15) in the 0-17 age group is 1,529. That's over 3.2 years. ~478/yr average.
Reference:

COVID-19 Provisional Counts - Weekly Updates by Select Demographic and Geographic Characteristics

Tabulated data on provisional COVID-19 deaths by age, sex, race and Hispanic origin, and comorbidities. Also includes an index of state-level and county-level mortality data available for download.

www.cdc.gov

Non-pandemic influenza deaths in the 2018-2019 flu season (which was a pretty mild one - not pandemic levels) was 372.

Estimated Flu-Related Illnesses, Medical visits, Hospitalizations, and Deaths in the United States — 2018–2019 Flu Season | CDC

CDC calculates estimates of disease burden in the United States using surveillance data and modeling to adjust for sources of under-detection. Burden estimates for the 2018-2019 season found here.

www.cdc.gov

This was far milder than H1N1 in the pediatric population.

The CDC lists the influenza mortality rate in that aggregate group as about ~0.7% (1.1% for 0-4 yrs and 0.3% for 5-17 yrs).


What am I missing?

 

[AlanSubie4Life]

Then I'm missing the point you are trying to make.

That this is a serious disease with significant mortality in children, so it is highly advisable to have your child (especially the 6mo to 4 age group!) vaccinated for it.

I think you've made that point - thank you for that. The data make it very clear.

As we all know, we have flu vaccines in children for a reason!!!

I'm seeing the aggregate CDC data for COVID deaths from 2020-2023 (Mar 15) in the 0-17 age group is 1,529

There are a couple of different counts for this. There's also CDC data which suggests closer to 2k (posted above). Anyway they aren't that different so it doesn't really matter.

 

[DrGriz]

That this is a serious disease with significant mortality in children, so it is highly advisable to have your child (especially the 6mo to 4 age group!) vaccinated for it.

I think you've made that point - thank you for that. The data make it very clear.

As we all know, we have flu vaccines in children for a reason!!!


There are a couple of different counts for this. There's also CDC data which suggests closer to 2k (posted above). Anyway they aren't that different so it doesn't really matter.

Looks like from the graph @bkp_duke posted there was roughly 4x mortality from Covid vs Flu in the pediatric group overall for the last 4 years.

Those raw numbers tell more than case rates at this point.

 

[bkp_duke]

That this is a serious disease with significant mortality in children, so it is highly advisable to have your child (especially the 6mo to 4 age group!) vaccinated for it.

I think you've made that point - thank you for that. The data make it very clear.

As we all know, we have flu vaccines in children for a reason!!!


There are a couple of different counts for this. There's also CDC data which suggests closer to 2k (posted above). Anyway they aren't that different so it doesn't really matter.

Then it is the interpretation of that point we don't agree upon. And that's fine to agree to disagree.

I would be behind a booster for kids IF (and ONLY IF) it was more efficacious than what they have had to date. Perhaps the new bivalent booster will be better and have specific coverage for the new variants. But we are so far removed from the initial viral genome that effectiveness is . . . marginal. The antigenic coverage of the current boosters (S-protein) is poor and indicates marked immune escape by the virus (i.e. the boosters are "boosting" the non-neutralizing antibodies).

Should kids get the first series? Vaccine + booster? Yes.
Should they get 2nd and 3rd boosters? No, not till the booster is re-sequenced for the current viral variants. Both our kids were boosted in Dec. Both got COVID in Jan/Feb, very mild.

TL;DR - we need a new booster with better coverage before pediatricians will push it on their patients.

 

[bkp_duke]

Looks like from the graph @bkp_duke posted there was roughly 4x mortality from Covid vs Flu in the pediatric group overall for the last 4 years.

Those raw numbers tell more than case rates at this point.

4X the total numbers, but remember we don't 100mil kids per year in the USA get influenza. The fatality rates are remarkably similar (and a little lower for COVID), once adjusted for total numbers of infected with COVID being like 7X what we see annually with influenza.

 

[AlanSubie4Life]

Then it is the interpretation of that point we don't agree upon. And that's fine to agree to disagree.

I would be behind a booster for kids IF (and ONLY IF) it was more efficacious than what they have had to date. Perhaps the new bivalent booster will be better and have specific coverage for the new variants. But we are so far removed from the initial viral genome that effectiveness is . . . marginal. The antigenic coverage of the current boosters (S-protein) is poor and indicates marked immune escape by the virus (i.e. the boosters are "boosting" the non-neutralizing antibodies).

Should kids get the first series? Vaccine + booster? Yes.
Should they get 2nd and 3rd boosters? No, not till the booster is re-sequenced for the current viral variants. Both our kids were boosted in Dec. Both got COVID in Jan/Feb, very mild.

TL;DR - we need a new booster with better coverage before pediatricians will push it on their patients.

Omicron is omicron. The booster is targeted at that, which is what is circulating!

Omicron is inherently immune evasive so avoiding infection is not really the objective.

The vaccine is likely quite good at improving outcomes since it is targeted at a version of Omicron.

Unfortunately only 16% of the population or something has got it. (I think they is the number I saw on the CDC website anyway.) Of course many have already had Omicron which helps, though of course that is not a desirable path prior to vaccination.

 

[PACEMD]

And that's fine to agree to disagree.

I disagree........

 

[PACEMD]

TL;DR - we need a new booster with better coverage before pediatricians will push it on their patients.

I agree.......

 

[DrGriz]

4X the total numbers, but remember we don't 100mil kids per year in the USA get influenza. The fatality rates are remarkably similar (and a little lower for COVID), once adjusted for total numbers of infected with COVID being like 7X what we see annually with influenza.

While I am all in for better vaccine efficacy, I would still say that the raw numbers are more important than the rates.

Would you rather have 100 kids die or 1000 kids die? I just don't care all that much about ratios.