Re: Don't Blame Birds for 1918 Flu

[gsgs]

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does someone understand table 1 ?
what's "nodes"
do they claim all human H1N1 descended directly from BM18
in 2,3,5,6 but from human flu in the other segments with
reassortments in ~1910,1913,1911,1915 (expectation value) ?
the years in brackets give their 95% confidence interval ? ---edit: yes, 95%,
they call it Bayesian credible interval(BCI)----------

do they claim classical swine (e.g. SW/31) descendd directly
from BM18 in 1,7,8 but from another virus(es) in 2,3,4,5,6
with reassortment between 1918 and 1931 ?

what's TMRCA of one virus (BM18), node 2
what's swine/human in node 1, they didn't mix after 1918, did they

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OK, the nodes must be the numbers in the phylo-charts
of figure 1, each segment has its own chart and the numbers are included

http://www.pnas.org/content/early/2009/07/10/0904991106.full.pdf

node 1 = common ancestor of early classical swine(1931) and early human H1N1 (1935)
node 2 = common ancestor of classical swine and BM/1918
node 3 = common ancestor of early human and BM/1918

(?)

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keywords:


Zitation
Discussion
Dating the emergence of pandemic influenza viruses.
Smith GJ, Bahl J, Vijaykrishna D, Zhang J, Poon LL, Chen H, Webster RG, Peiris JS, and Guan Y

Our results indicate that genetic components of the 1918 H1N1 pandemic virus circulated in mammalian hosts


1918

A/Brevig Mission/1/1918(H1N1)

origin

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Smith et al get for the TMRCA

sw-hu:1881,1906,1904,1885,1884,1907,1884,1899
BM-hu:1903,1914,1914,1916,1909,1913,1896,1908
BM-sw:1910,bm18,bm18,1913,bm18,bm18,1911,1915

I get:
sw-hu : 1908,1908,1908,----,1908
BM-hu : 1912,1918,1914,1916,1916,1916,1916,1917
BM-sw : 1911,1913,1910,1914,1915,1916,1912,1911

[gsgs]

Re: Don't Blame Birds for 1918 Flu

amino-differences from the bird-index:

BM:08,07,10,--,09,--,07,05
hu:13,08,16,--,17,--,09,12
sw:18,13,16,--,07,--,08,19

suggesting that a new NP (and M?) jumped from wild birds to swine
~1930.

an NP similar to the one from 1918 but close relatives
are not found in available bird sequences

[gsgs]

Re: Don't Blame Birds for 1918 Flu

http://www.ncbi.nlm.nih.gov/pubmed/20723216

It was found that the 1918 pandemic H1N1 virus contained genes with mammalian-like
viral codon usage patterns, indicating that the introduction of this virus to humans was
not through in toto transfer of an avian influenza virus
...
reduced the overall GC content and the usage of G at the third codon position

[gsgs]

Re: Don't Blame Birds for 1918 Flu

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2772961/?tool=pubmed

Our model suggests that the eight RNA segments which eventually became the 1918 viral genome were introduced into a mammalian host around 1882–1913. The viruses later diverged into the classical swine and human H1N1 influenza lineages around 1913–1915. The last common ancestor of human strains dates from February 1917 to April 1918. Because pigs are more readily infected with avian influenza viruses than humans, it would seem that they were the original recipient of the virus. This would suggest that the virus was introduced into humans sometime between 1913 and 1918.

with four of the segments (PA, HA, NP, NA) supporting this topology. The segments encoding the PB2 and PB1 proteins place the 1918 sequence at the bottom of the swine virus lineage
the only possibility is that there were two different strains circulating in 1918 that reassorted to form the 1918 pandemic virus
This reassortant would have been replaced later by a non-reassortant some time before the earliest post-1918 human isolates of the 1930s. While this is an intriguing possibility, in the absence of more convincing statistical support we agree with Worobey’s (2008) view that the 1918 sequence is much more reasonably placed on the human lineage
the HA and NP segments seem to have been introduced earlier (pre-1890) than the polymerase genes (post-1900).
We intentionally avoid given specific ages to the individual segments, as the branches projecting from the host shift node are highly correlated (Fig. 7), making the estimation of the individual host transfer dates highly uncertain
(ahh, why then write a paper about it ?)

[gsgs]

Re: Don't Blame Birds for 1918 Flu

http://rnajournal.cshlp.org/content/17/1/64.full.pdf

http://rnajournal.cshlp.org/content/17/1/64.full

swine H1N1 virus had crossed the species barrier from pigs to humans
shortly before the pandemic of 1918.
The highly pathogenic swine virus that was detected in the pig population
after the human pandemic outbreaks had started (Koen 1919; Chun 1919)
is most likely not the precursor of the H1N1 classical swine virus lineage,
1918 virus is rather of swine virus origin
RSCU (relative synonymous codon usage )
signature of the PB1 gene of the 1918 virus is identical to that of the
classical swine and human H1N1 viruses


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I don't understand. I thought that i.e. in PB1 the situation were clear
and an avian PB1 entered into BM18 shortly before.
We have 7 birds from the 60s-80s with similar PB1.
That strain is now extinct.

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ahhhhh - I haven't read the whole paper, and I haven't checked the
sequences, but it seems that they misinterpreted these "clade 1" viruses as avian.
But they are swine viruses : a turkey farm close to a swine farm
and they got an H1N1 outbreak in turkeys. But those viruses never
did spread nor were they introduced by wild birds.

> What we can say for sure is that the 1918 H1N1 virus
> is not related to one of the known avian influenza viruses,
> except the clade 1 viruses.

clade 1 is swine, in PB1 BM1918 is quite similar to their
7 clade-2 viruses. So similar, that there is not much room
for mammalean adaptation - the most recent common
ancestor should be ~1910 or later.
We saw earlier that BM1918 was probably a multi-
reassortant virus with the segments crossing from birds to
swine or humans~3-30 years before, depending on the segment.