Don't Blame Birds for 1918 Flu

[gsgs]

Re: Don't Blame Birds for 1918 Flu

the parents are decades younger than the child ?
just name one segment and polymorphism

 

[HenryN]

Re: Don't Blame Birds for 1918 Flu

the parents are decades younger than the child ?
just name one segment and polymorphism

A little over 1 decade. They represent the non-pandemic strains and have 90% of the 1918 polymorphisms (in 1917 they probably had close to 100%). The relationship is the same for all 8 gene segments.

 

[gsgs]

Re: Don't Blame Birds for 1918 Flu

OK, so I assume you don't want me to verify it.

 

[HenryN]

Re: Don't Blame Birds for 1918 Flu

OK, so I assume you don't want me to verify it.

You have the info required for verification. It will be up at Nature Precedings soon.

 

[super_flu]

Re: Don't Blame Birds for 1918 Flu

silly IMO to use phylo-trees to detect recombination.
Write a program and let the computer do it.

There are phylogenetic methods to detect recombination. But again, this has to do with major topology changes - as pointed out by pjie2. I'm sure some new methods are being developed. Again methods to detect recombination that work within a phylogenetic framework are more powerful than those that do not. But no method can detect single nucleotide polymorphisms.

 

[super_flu]

Re: Don't Blame Birds for 1918 Flu

From new PNAS paper:



Can we interpret this to disagree with ?experts? advice that those of us born before 1957 have some protection against the novel H1N1, because of our exposure to the earlier H1N1?

-------------------------

Regarding the ?BEAST? - can this system be aimed ?forward? to look at the current pandemic & derive some information that would assist in reducing severe illness and death? (e.g., some data regarding choice of an appropriate anti-viral therapy)

If they had strategic samples could the system perform a ?forward-analysis??

.

I don't think you can make that interpretation from what they said. The fact that older people were exposed to a virus that more closely resembles the current virus should not be affect by the argument that seasonal and pandemic influenza co-circulated.

As for predictive analysis, there are a number of simulation studies that try to model evolutionary behavior of many different aspects of pandemic viruses. Certainly the information from a BEAST analysis could inform a model so that it's more realistic.

 

[super_flu]

Re: Don't Blame Birds for 1918 Flu

You have the info required for verification. It will be up at Nature Precedings soon.

Since it's a comment directly on the PNAS paper why don't you send it to PNAS or to NATURE so it can be peer reviewed. In fact it's a good time to publish as a flu scientist since there is lots of interest. It'll probably be sent for peer review.

 

[gsgs]

Re: Don't Blame Birds for 1918 Flu

I do claim, that SNP-recombination can be detected statistically,
if they are frequent
---------------------
why not upload (partial) papers to a webpage or post it here,
so it can be discussed and improved
---------------------------
we need more and better summaries of papers
---------------------------
see my updated post#61 above with the picture

 

[gsgs]

Re: Don't Blame Birds for 1918 Flu

just an idea to be discussed - don't put too much into it yet :

the reason for the 1918 pandemic was maybe a mixing of segments
from Eurasian and American avian-flus.

Just as the reason for the 2009 pandemic was a mixture of Eurasian
and American swine-flus

this created enough diversity and changes so the virus could jump to mammals.

And as in 2009 it was a rare strain, rare reassortment that changed species.
Maybe it was related to the extinction of passenger pigeons which
changed bird-ecology in North America and thus also avian flu.

http://www.setbb.com/fluwiki2/viewtopic.php?t=424&mforum=fluwiki2


best possible ancestor for BM18 is A/turkey/Ontario/6118/1968(H8N4)
with 102,085,080,430,126,347,052,035 promille difference to BM18,
HA,NP,NA were acquired from elsewhere, or 6118-ancestors reassorted since 1918.

 

[HenryN]

Re: Don't Blame Birds for 1918 Flu

Since it's a comment directly on the PNAS paper why don't you send it to PNAS or to NATURE so it can be peer reviewed. In fact it's a good time to publish as a flu scientist since there is lots of interest. It'll probably be sent for peer review.

I agree that now is the time to send these out for peer review. Nature Precedings allows for rapid publication and the data can be referenced. Since most of the data that has been made public is at Nature Precedings, it is a lot easier to put the data into a proper framework by citing the related data. I have had requests from peer reviewed Journals for the swine data (but the data is fairly old now, so it also requires some work to make it current -which includes data showing that the swine pandemic was predicted in 2007 by acquistions in seasonal flu).

http://precedings.nature.com/documents/385/version/1

 

[HenryN]

Re: Don't Blame Birds for 1918 Flu

just an idea to be discussed - don't put too much into it yet :

the reason for the 1918 pandemic was maybe a mixing of segments
from Eurasian and American avian-flus.

Just as the reason for the 2009 pandemic was a mixture of Eurasian
and American swine-flus

this created enough diversity and changes so the virus could jump to mammals.

And as in 2009 it was a rare strain, rare reassortment that changed species.
Maybe it was related to the extinction of passenger pigeons which
changed bird-ecology in North America and thus also avian flu.

http://www.setbb.com/fluwiki2/viewtopic.php?t=424&mforum=fluwiki2


best possible ancestor for BM18 is A/turkey/Ontario/6118/1968(H8N4)
with 102,085,080,430,126,347,052,035 promille difference to BM18,
HA,NP,NA were acquired from elsewhere, or 6118-ancestors reassorted since 1918.

There is ZERO evidence for an avian precursor just prior to 1918. The sequence of 1917 avian has been published and it is avian and quite distinct from 1918, swine H1N1 or human H1N1, which of course are all mammalian. The 2005 Nature paper describe 10 key changes (including E627K) and ALL 10 were mammalian and found not only in 1918, but seasonal H1N1 and swine H1N1.
The relationship between ALL 8 gene segments of 1918 and mammalian and swine H1N1 can be EASILY seen through phylogenetic analysis.
1918 is a recombinant between MAMMALIAN flu (H1N1) genomes.

 

[pjie2]

Re: Don't Blame Birds for 1918 Flu

There is ZERO evidence for an avian precursor just prior to 1918. The sequence of 1917 avian has been published and it is avian and quite distinct from 1918, swine H1N1 or human H1N1, which of course are all mammalian.

I have no opinion on the mammalian/bird origin of the 1918 pandemic, but I don't see how you can rule it out from a (single?) 1917 bird sequence. Birds have lots of strains of flu! Unless you have lots of sequences from 1917, sufficient to give a good picture of all the different circulating avian strains, I don't see how you can rule out an avian origin.

I mean, if a human gets H5N1 in 2009, you can't point to an H7N9 sequence from 2008 and say "this is quite distinct from 2008, therefore H5N1 must be mammalian". The logic is just flat out wrong.

 

[gsgs]

Re: Don't Blame Birds for 1918 Flu

1918 is clearly avian by AT-score

also similar to 7 bird sequences e.g. Turkey/6118

 

[HenryN]

Re: Don't Blame Birds for 1918 Flu

1918 is clearly avian by AT-score

also similar to 7 bird sequences e.g. Turkey/6118

Please. The phylogenetic analysis is VERY clear.
1918 is OBVIOUSLY mammalian.

 

[HenryN]

Re: Don't Blame Birds for 1918 Flu

1918 is clearly avian by AT-score

also similar to 7 bird sequences e.g. Turkey/6118

Here is a phylogenetic tree with the 1917 avian sequence. Pandemic 1918 isolates are between human H1N1 and swine H1N1 and are mammalian.

The mammalian sequences are EASILY distinguished from avian, including 1917 avian.

http://jvi.asm.org/cgi/content-nw/full/76/15/7860/F1

 

[HenryN]

Re: Don't Blame Birds for 1918 Flu

Here is a phylogenetic tree with the 1917 avian sequence. Pandemic 1918 isolates are between human H1N1 and swine H1N1 and are mammalian.

The mammalian sequences are EASILY distinguished from avian, including 1917 avian.

http://jvi.asm.org/cgi/content-nw/full/76/15/7860/F1

It is worth noting that on this tree, as well as trees involving longer sequences, show WSN/33 as the closest human H1N1 sequences, and swine/Iowa/15/1930 as the closest swine H1N1 sequence ( a similar tree is in the January 2005 issue of Scientific American on the "Mystery of 1918" as noted in this 2004 commentary

http://www.recombinomics.com/News/12140401/WSN33_1918_pandemic.html

 

[HenryN]

Re: Don't Blame Birds for 1918 Flu

I have no opinion on the mammalian/bird origin of the 1918 pandemic, but I don't see how you can rule it out from a (single?) 1917 bird sequence. Birds have lots of strains of flu! Unless you have lots of sequences from 1917, sufficient to give a good picture of all the different circulating avian strains, I don't see how you can rule out an avian origin.

I mean, if a human gets H5N1 in 2009, you can't point to an H7N9 sequence from 2008 and say "this is quite distinct from 2008, therefore H5N1 must be mammalian". The logic is just flat out wrong.

The data are VERY clear. This is not your area of expertise, which is VERY obvious.
Here is DATA, which is QUITE unambigous (which uses H1N1 sequences)

http://jvi.asm.org/cgi/content-nw/full/76/15/7860/F1

H7N9 and H5N1 have NOTHING to do with H1N1 sequences, or each other. As indicate in their names, they are COMPLETELY different serotypes. ALL eight genes of 1918 are mammalian H1N1 genes.

 

[gsgs]

Re: Don't Blame Birds for 1918 Flu

Here is a phylogenetic tree with the 1917 avian sequence. Pandemic 1918 isolates are between human H1N1 and swine H1N1 and are mammalian.

The mammalian sequences are EASILY distinguished from avian, including 1917 avian.

http://jvi.asm.org/cgi/content-nw/full/76/15/7860/F1

ahh, only HA. Look at PB1 and you see the 7 bird sequences.
Look at PA and there are more.

Of course, SW30 and WS33 are closer, but they are later.
They clearly almost descend from BM18 , common ancestor
~1916,~1913 (if not 1918) see previous posts.
You can watch how the AT-score increases over time,
see the Rabadan papers

 

[pjie2]

Re: Don't Blame Birds for 1918 Flu

I knew I shouldn't have mentioned H7N9. I was only using it to illustrate the flaw in the logic.

From that tree we see that yes, there was an avian H1N? strain circulating in goose in 1917 whose H sequence is more similar to current avian H1N1 than to 1918 pandemic H1N1. We can therefore rule out the 1917 goose sequence as the ancestor of the H segment of the 1918 pandemic virus. I still don't see how you can conclusively rule out avian ancestry without a much more comprehensive survey of 1917 bird sequences. There may have been more than one H1N? bird flu in circulation in 1917. You're extrapolating a single 1917 sequence to claim that no 1917 bird flu could be the ancestor of the 1918 pandemic.

I'm not of course claiming avian ancestry for it - as I said I'm agnostic on the issue. I just don't think the data are conclusive.

 

[gsgs]

Re: Don't Blame Birds for 1918 Flu

the sequences before 1918 were almost withdrawn, Taubenberger
said it was probably contamination