gsgs
Registered User
> February 14, 2022, 12:28 PM
>> but how likely is it that one of the rare ancient viruses acquires
>> mutations and becomes dominant rather than one of the widespread
>> alrady more transmissable viruses ?
> I do not know as we do not have data to go on but I would guess it
> is low probability which is why I suspect a different mechanism
> for Omicron.
yes, that's what I wanted to indicate. It's something special, unusual.
Which includes mice or other animals or prolonged evolution in
immunodeficient people.
> There are a number of possible reasons/confounding factors.
> As you know exactly where you add a new sequence into a phylogenetic
> tree is dependent on the algorithm used and becomes increasingly dodgy
> with large jumps in the sequence so the current rooting may just
> be the best fit to the previously sequenced samples and not the
> actual ancestry.
well, typically every single mutation-marker has an origin and then
replicates. And these can be traced. It's less reliable in spike
> This pandemic has occurred at a time where the technology has
> advanced to a point that we can sequence and observe change
> in a way we could not before so we have never been able to
> observe evolution in real time like this previously.
I would not formulate it this way. It's been gratly enhanced,
i.e. with cog_UK, but we did observe genetic evolution before,
> In addition medical technology has allowed unprecedented numbers
> of immunocompromised individuals to live amongst us who would not
> have survived had they caught HIV or needed a transplant in 1918.
> The enormous number of viral replications occurring when you have
> daily new cases measured in millions makes the mutation permutations
> staggering. This also makes me wonder about molecular clock
> calculations which are showing very high rates for SARS-CoV-2
> but how much of this is due to the exceptionally high propagation
> rate in the middle of a pandemic wave rather than an intrinsic
> property of an endemic virus?
it's pretty stable at 2 mutations per month, if we ignore these rare jumps
I see no big difference between outbreaks in small and lasge communities
>> Re. The BA1/2 difference
> I suspect one source but two introductions.
I wanted to examine the origin of BA.2, checking RKI,cog-UK,
genbank ... but gave up. Too many sequences, too big files, not aligned,
and the important sequences from Africa are only at _nonpublic_ GISAID.
Shall others do it and write papers (in some months ...)
>> Re. The political problem.
> I think the answer is probably in education of the public.
> The data is clear enough but we are not acting on it.
> Is this due to people not being able to understand relative risk
> calculations?
> In terms of US deaths
> Pearl Harbour 2k,
> WW2 418k,
> 9/11 3k,
> 1918 flu 675k,
> COVID 918k and counting.
I first noticed birdflu in 2004? when our newspaper reported on
a terroristic train attack in Spain with 200 deaths all over the first page
and then a tiny article on page 2 about 200M possible deaths from birdflu
So I searched the web, emails with Fedson, Fluwiki, Flutrackers etc.
And I first became political after the WMD-lying campaign in 2002/3
However, when comparing these numbers we should also consider the age.
Old people dying is better than young people dying.
With a special calculation for children, infants when we consider their
high mortality in still intact societies in past centuries.
> It is fairly apparent where the danger lies but this is not reflected
> in the preparedness investment.
we need numbers and probability estimates to make reasonable decisions.
Maybe China does this.
The general public does not understand this and these people indirectly
determine the politics in a democracy through their votes, protests.
Talking about risks and spending money on preparation is not popular.
> I would recommend this Mayo clinic video which concisely lays out
> the US data.
> Year Three of COVID-19: Harsh Truths, Realities, and Glimmers of Hope
> https://www.youtube.com/watch?v=32IAD5NyqWg
> I think he is wrong in his comment about the flu vaccine H1N1
> component and disagree with part of his take on routes to
> endemicity but otherwise I agree - some of his conclusions
> will not go down well with the anti-mandaters.
I don't like long videos/audios. Can't be searched,quoted,discussed
hard to understand for non-English.
------------------------------------------
i don't do google,youtube - long list of terms and privacy
------------------------------------------
here a new paper about BA.2 : (--> worse than BA.1)
https://www.biorxiv.org/content/10.1101/2022.02.14.480335v1
>> but how likely is it that one of the rare ancient viruses acquires
>> mutations and becomes dominant rather than one of the widespread
>> alrady more transmissable viruses ?
> I do not know as we do not have data to go on but I would guess it
> is low probability which is why I suspect a different mechanism
> for Omicron.
yes, that's what I wanted to indicate. It's something special, unusual.
Which includes mice or other animals or prolonged evolution in
immunodeficient people.
> There are a number of possible reasons/confounding factors.
> As you know exactly where you add a new sequence into a phylogenetic
> tree is dependent on the algorithm used and becomes increasingly dodgy
> with large jumps in the sequence so the current rooting may just
> be the best fit to the previously sequenced samples and not the
> actual ancestry.
well, typically every single mutation-marker has an origin and then
replicates. And these can be traced. It's less reliable in spike
> This pandemic has occurred at a time where the technology has
> advanced to a point that we can sequence and observe change
> in a way we could not before so we have never been able to
> observe evolution in real time like this previously.
I would not formulate it this way. It's been gratly enhanced,
i.e. with cog_UK, but we did observe genetic evolution before,
> In addition medical technology has allowed unprecedented numbers
> of immunocompromised individuals to live amongst us who would not
> have survived had they caught HIV or needed a transplant in 1918.
> The enormous number of viral replications occurring when you have
> daily new cases measured in millions makes the mutation permutations
> staggering. This also makes me wonder about molecular clock
> calculations which are showing very high rates for SARS-CoV-2
> but how much of this is due to the exceptionally high propagation
> rate in the middle of a pandemic wave rather than an intrinsic
> property of an endemic virus?
it's pretty stable at 2 mutations per month, if we ignore these rare jumps
I see no big difference between outbreaks in small and lasge communities
>> Re. The BA1/2 difference
> I suspect one source but two introductions.
I wanted to examine the origin of BA.2, checking RKI,cog-UK,
genbank ... but gave up. Too many sequences, too big files, not aligned,
and the important sequences from Africa are only at _nonpublic_ GISAID.
Shall others do it and write papers (in some months ...)
>> Re. The political problem.
> I think the answer is probably in education of the public.
> The data is clear enough but we are not acting on it.
> Is this due to people not being able to understand relative risk
> calculations?
> In terms of US deaths
> Pearl Harbour 2k,
> WW2 418k,
> 9/11 3k,
> 1918 flu 675k,
> COVID 918k and counting.
I first noticed birdflu in 2004? when our newspaper reported on
a terroristic train attack in Spain with 200 deaths all over the first page
and then a tiny article on page 2 about 200M possible deaths from birdflu
So I searched the web, emails with Fedson, Fluwiki, Flutrackers etc.
And I first became political after the WMD-lying campaign in 2002/3
However, when comparing these numbers we should also consider the age.
Old people dying is better than young people dying.
With a special calculation for children, infants when we consider their
high mortality in still intact societies in past centuries.
> It is fairly apparent where the danger lies but this is not reflected
> in the preparedness investment.
we need numbers and probability estimates to make reasonable decisions.
Maybe China does this.
The general public does not understand this and these people indirectly
determine the politics in a democracy through their votes, protests.
Talking about risks and spending money on preparation is not popular.
> I would recommend this Mayo clinic video which concisely lays out
> the US data.
> Year Three of COVID-19: Harsh Truths, Realities, and Glimmers of Hope
> https://www.youtube.com/watch?v=32IAD5NyqWg
> I think he is wrong in his comment about the flu vaccine H1N1
> component and disagree with part of his take on routes to
> endemicity but otherwise I agree - some of his conclusions
> will not go down well with the anti-mandaters.
I don't like long videos/audios. Can't be searched,quoted,discussed
hard to understand for non-English.
------------------------------------------
i don't do google,youtube - long list of terms and privacy
------------------------------------------
here a new paper about BA.2 : (--> worse than BA.1)
https://www.biorxiv.org/content/10.1101/2022.02.14.480335v1
