Coronavirus

[DrGriz]

Exactly that has changed:

Some of the new samples do have animal DNA/RNA and the virus in the same single sample:
From the Science article:


Your quotes are related to past papers from the chinese research group around Georg Gao, which is expected to publish new material. I actually thought your comment "Nothing to see here" was sarcasm.

The news that we are discussing now is based on new data that french researchers found in new samples posted by the chinese researchers which those didn't comment on yet. These samples were recently posted and then removed again. However they were examined by a group of western researchers who have not yet published a paper, however some of their findings were already reported by some media.

Yes, and if it bears out, I will accept it. But that information was rescinded. So.

 

[DrGriz]

Yes, and if it bears out, I will accept it. But that information was rescinded. So.

I will quote again the article you kindly linked, @Norbert:

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.”

We shall see, but that doesn't seem to be a slam dunk by any stretch. In fact, it is a strange story taken in whole.

 

[Norbert]

We shall see, but that doesn't seem to be a slam dunk by any stretch. In fact, it is a strange story taken in whole.

Yeah, this better evidence is still circumstantial. There is nothing "strange" about the evidence itself, though. Just about how the story of its discovery unfolds, so late. And yes, at this point it is probably better to just see how this continues as the two papers are published (or at least one of them).

 

[AlanSubie4Life]

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.)

I couldn't find a screen capture which had the age group breakdown snapshot at a given time, but the below, which I wrote from just that type of data, is good enough:

For reference/comparison, there's the same number of people over 65 as there are between 5-17 (54 million). There have been 6 million cases in this group.

1.27 million hospitalizations (2351/100k). 1 in 5 cases hospitalized. 550k deaths. 1 in 11 cases dies.

Any errors, please point them out. I'm actually shocked how high it is for children. (But this is all consistent with about a 3x change in risk per decade.)

So that's a CFR in Jan 2022 of 1 in 11 cases resulting in deaths in age 65 & up. (Vaccines had been widely available for 6-8 months, so this is better than it might have been originally, but I don't have a snapshot before that (say from May 2021...might have looked even worse then)!)

Since then we've added 7 million cases and 173k deaths in that 65+ group.

So that's 1 in 41 or so, incrementally, for CFR, age 65+. Given testing has dropped off for a while, likely the actual improvement is larger than this (more testing reduces CFR as discussed).

Quite an improvement; a combination of less vaccination, infection-acquired immunity, and the alleged ~2x reduction in Omicron virulence. Note that a large number of people chose not to be vaccinated in this period (though the rates weren’t bad in this age group), so if that cross-tab could be broken out, this would probably look even better. No wonder hospitals aren’t as overloaded! (This is not a surprise to anyone of course.)

Note that no such improvement was seen in children over that same time period. Wonder what is different? I think it could be a few things - ascertainment rate (a lot more testing reduction in children than adults - but there are mathematical limits to how much of an effect this can have), lack of vaccination, etc. Any other possibilities?

Apropos of nothing...this is a disgrace....

 

[DrGriz]

Yeah, this better evidence is still circumstantial. There is nothing "strange" about the evidence itself, though. Just about how the story of its discovery unfolds, so late. And yes, at this point it is probably better to just see how this continues as the two papers are published (or at least one of them).

Well, after hiding it in plain sight for over a year, someone discovers it and they pull it down ("nothing to see") and decline to give an explanation. Maybe the collection of those samples was suspect. Maybe they were contaminated/didn't follow protocol. Maybe we should take them at their word when they say it doesn't resolve the question of Covid's origin.

I was just underwhelmed, compared to the enthusiasm with which the "evidence" was greeted by the acolytes.

 

[Norbert]

Well, after hiding it in plain sight for over a year, someone discovers it and they pull it down ("nothing to see") and decline to give an explanation. Maybe the collection of those samples was suspect. Maybe they were contaminated/didn't follow protocol. Maybe we should take them at their word when they say it doesn't resolve the question of Covid's origin.

I was just underwhelmed, compared to the enthusiasm with which the "evidence" was greeted by the acolytes.

Does it say "over a year" somewhere? In the WHO article, it says the data was available on GISAID only for a "short period of time". It was pulled down after they were asked about it.

The literal quote from George Gao is that the question of the origin is “still scientific and open”. And that it has to be, simply because the evidence is still circumstantial. I don't see how to read more into it than that.

Regarding the enthusiasm, data about other samples was previously used by chinese papers (or pre-prints) to point in a different direction, so this is a significant change even if circumstantial. Especially considering that there wasn't any new actual evidence reaching the public for a long time.

EDIT: This again is a link to the WHO article which is more specific on the recent events than the Science article :

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

 

[DrGriz]

Does it say "over a year" somewhere? In the WHO article, it says the data was available on GISAID only for a "short period of time". It was pulled down after they were asked about it.

The literal quote from George Gao is that the question of the origin is “still scientific and open”. And that it has to be, simply because the evidence is still circumstantial. I don't see how to read more into it than that.

Regarding the enthusiasm, data about other samples was previously used by chinese papers (or pre-prints) to point in a different direction, so this is a significant change even if circumstantial. Especially considering that there wasn't any new actual evidence reaching the public for a long time.

EDIT: This again is a link to the WHO article which is more specific on the recent events than the Science article :

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

Regarding the "new" sequences, "[when] contacted by Science, Gao said the sequences are “[n]othing new" according to the Science article.

If you want to quibble over the exact date they "showed up" we can do so. But it really changes nothing. There was excitement over this in February in 2022 and here it is again, but it's still circumstantial at best. The WHO article says the same. Mitochondrial 'coon dog DNA shows that 'coon dogs might have been in the market around the time that SARS CoV 2 showed up. OK. I suppose the human DNA found there proves that they were selling human meat? It's just not that powerful to me.

I mean, again, I am very interested in this. But to me the things that Dr. George Gao has said in regard to all of this make it seem underwhelming. To me. You do you and I will still think highly of you!

 

[Norbert]

Regarding the "new" sequences, "[when] contacted by Science, Gao said the sequences are “[n]othing new" according to the Science article.

If his statement was about the new samples altogether, then I'm afraid that's plainly wrong (as I will show below), and not a very promising sign for the potentially upcoming article of Gao. However it is not obvious from the literal quote what exactly he was referring to in that sentence.

If you want to quibble over the exact date they "showed up" we can do so.

The samples that were posted recently have animal DNA/RNA in the same single sample that is virus-positive. That's the news, as examined by an international team of researchers. There is nothing else that makes this worth talking about, that's the whole point, so better be clear about it. The samples that were posted previously didn't have that. In chinese pre-prints those were more associated with having been in the vicinity of human DNA (see below).

But it really changes nothing. There was excitement over this in February in 2022 and here it is again, but it's still circumstantial at best. The WHO article says the same. Mitochondrial 'coon dog DNA shows that 'coon dogs might have been in the market around the time that SARS CoV 2 showed up. OK. I suppose the human DNA found there proves that they were selling human meat? It's just not that powerful to me.

This is about February 2022, in Science, referring to Gao's team:
"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."

That's a completely different message isn't it? And with completely different conclusions by Gao's team.

For reference, this is a link to the pre-print of their article: Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market

I mean, again, I am very interested in this. But to me the things that Dr. George Gao has said in regard to all of this make it seem underwhelming. To me. You do you and I will still think highly of you!

However the news isn't about what George Gao has said. On the contrary. That is context for the story, the background on which this happened and continues. The Science article however is lot about that context, which is why I posted it. I was using the words "regarding the whole situation".

George Gao himself indeed hasn't said anything so far that makes this newsworthy. As far as we know. Except that it was apparently his team that posted the new samples.

 

[DrGriz]

If his statement was about the new samples altogether, then I'm afraid that's plainly wrong (as I will show below), and not a very promising sign for the potentially upcoming article of Gao. However it is not obvious from the literal quote what exactly he was referring to in that sentence.



The samples that were posted recently have animal DNA/RNA in the same single sample that is virus-positive. That's the news, as examined by an international team of researchers. There is nothing else that makes this worth talking about, that's the whole point, so better be clear about it. The samples that were posted previously didn't have that. In chinese pre-prints those were more associated with having been in the vicinity of human DNA (see below).



This is about February 2022, in Science, referring to Gao's team:
"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."

That's a completely different message isn't it? And with completely different conclusions by Gao's team.

For reference, this is a link to the pre-print of their article: Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market



However the news isn't about what George Gao has said. On the contrary. That is context for the story, the background on which this happened and continues. The Science article however is lot about that context, which is why I posted it. I was using the words "regarding the whole situation".

George Gao himself indeed hasn't said anything so far that makes this newsworthy. As far as we know. Except that it was apparently his team that posted the new samples.

I do hear what you are saying.

The presentations from China CDC and invited international researchers indicated that there were newly available data from the Huanan Seafood Wholesale Market. This included metagenomic data of environmental samples from various stalls and wastewater collection sites collected as early as January 2020. Analyses of these data suggest that apart from SARS-CoV-2 sequences, some samples also contained human DNA, as well as mitochondrial DNA of several animal species, including some that are known to be susceptible to SARS-CoV-2.

Before, we had Human and Covid genetic material together, but no combination of Covid with susceptible animals. Now we have both.

Probably, because SAGO carefully concludes

The findings suggest that animals were present at the market...

(my emphasis)

If this is evidence, why did they say it only "suggests" the animals were present? Why is that not conclusive? And:

However, the presence of high levels of raccoon dog mitochondrial DNA in the metagenomics data from environmental samples identified in the new analysis, suggest that raccoon dog and other animals may have been present before the market was cleaned as part of the public health intervention.

(again, my emphasis)

Why only "suggest" and "may?" And why only mDNA and not regular old DNA like we had with humans?
Why not say "shows" instead?

SAGO is being cautious about this new data, and so am I.

 

[Norbert]

Before, we had Human and Covid genetic material together, but no combination of Covid with susceptible animals. Now we have both.

I'd guess if this market is the place where animals infected humans, then it is not surprising to find both.

Why only "suggest" and "may?" And why only mDNA and not regular old DNA like we had with humans?
Why not say "shows" instead?

SAGO is being cautious about this new data, and so am I.

I don't know what those uncertainties might be, and how large they are. I guess the situation is still very new for everyone and that the report will give more information about any remaining uncertainties when it is peer-reviewed and/or published.

Being cautious is generally a good idea about all the origin theories. However that doesn't mean this isn't significant.

 

[DrGriz]

I'd guess if this market is the place where animals infected humans, then it is not surprising to find both.



I don't know what those uncertainties might be, and how large they are. I guess the situation is still very new for everyone and that the report will give more information about any remaining uncertainties when it is peer-reviewed and/or published.

Being cautious is generally a good idea about all the origin theories. However that doesn't mean this isn't significant.

Chicken or egg?

It might be significant. It might not. I would wait until the rest of the information is in before doing a victory dance. Not that you are. It's just that I have learned to be skeptical.

Why was there nuclear human DNA found mixed with covid, but only mitochondrial DNA from susceptible animal species? What caused that difference? Is it relevant and how?

 

[shinytop]

It does not really matter where the bug came from. What matters is that we learn from it how to be ready for the next one. Will Big Pharm have a play book that may work faster on getting vaccines? Will the vulnerable be identified so they can be better protected? Will WHO develop means and methods for operation of labs that have viral material? These are the issues that need working on so that next we get a new deadly virus we can react faster and smarter. Oh, and get rid of the anti science politicos. They will kill us all just to win an election.

 

[Norbert]

Maybe to be fair to China, we shouldn't dismiss the theory that it originated somewhere else, either, and consider the possibility that the outbreak in Wuhan was just where COVID-19 was first recognized as such.

 

[AlanSubie4Life]

For that you would need some evidence of a (very) close ancestor somewhere else, which does not exist. So basically impossible with existing evidence.

Viruses get sequenced a lot.

 

[Norbert]

For that you would need some evidence of a (very) close ancestor somewhere else, which does not exist. So basically impossible with existing evidence.

Viruses get sequenced a lot.

How about things like this? Unexpected detection of SARS-CoV-2 antibodies in the prepandemic period in Italy - PubMed

 

[bkp_duke]

How about things like this? Unexpected detection of SARS-CoV-2 antibodies in the prepandemic period in Italy - PubMed

That's an antibody binding study. I would be very cautious drawing conclusions from that. Antibody cross-reactivity is notorious.


I.e. these people could have antibodies to an S-protein from one of the 6 other Coronaviruses, and there is enough cross-reactivity to flag as positive in the sample. If these were genetic tests proving actual SARS-CoV-2 virus, that would be a smoking gun, but anti-body cross-reactivity is notorious. Every paper I ever published with antibody results had to have secondary tests for confirmation.

 

[AlanSubie4Life]

How about things like this? Unexpected detection of SARS-CoV-2 antibodies in the prepandemic period in Italy - PubMed

That’s all fine and good but in the end you need sequenced virus. And as has been noted this is pretty unreliable.

Sequenced virus showing there was an immediate ancestor elsewhere is what is needed. And if such evidence existed you can be sure it would be trumpeted far and wide!

There are likely many swab samples in various places frozen in Italy (and elsewhere!), and they have been looked at extensively. Nothing.

There are many virologists/physicians who routinely freeze samples from patients with unknown illnesses (very common), so that they can maybe figure out later what it was. So there are samples everywhere ripe for sequencing.

 

[Norbert]

That's an antibody binding study. I would be very cautious drawing conclusions from that. Antibody cross-reactivity is notorious.


I.e. these people could have antibodies to an S-protein from one of the 6 other Coronaviruses, and there is enough cross-reactivity to flag as positive in the sample. If these were genetic tests proving actual SARS-CoV-2 virus, that would be a smoking gun, but anti-body cross-reactivity is notorious. Every paper I ever published with antibody results had to have secondary tests for confirmation.

It would be a sign that *some* Coronavirus was going around in September 2019? Why doesn't the abtract say that?

It claims the antibodies are "SARS-CoV-2 RBD-specific". That sounds seriously misleading to the non-expert if what you are saying is true.

 

[Norbert]

That’s all fine and good but in the end you need sequenced virus. And as has been noted this is pretty unreliable.

Sequenced virus showing there was an immediate ancestor elsewhere is what is needed. And if such evidence existed you can be sure it would be trumpeted far and wide!

There are likely many swab samples in various places frozen in Italy, and they have been looked at extensively. Nothing.

Well to me it would seem to mean that publication should not have survived peer-review.

 

[AlanSubie4Life]

Well to me it would seem to mean that publication should not have survived peer-review.

I think it is fine. They don’t claim to have found that the SARS2 virus was circulating early. Just that it was possible. Which it is! There is just no direct evidence of it!