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Influenza Virus A/h1n1 Resistant To Oseltamivir: W.h.o. Preliminary Summary

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

google has it in html:
http://209.85.135.104/search?q=cach...A/Denmark/4/2008"&hl=en&ct=clnk&cd=2&ie=UTF-8
from 21.Febr.2008
not much sprinkling of the indentations at that time.
Full genomes are better to determine the distances, we got many full genomes of
H1N1 from USA season 2006/7 in Oct.2007 , so maybe we'll get them in 3 months for 2007/8
http://www.setbb.com/fluwiki2/viewtopic.php?t=196&mforum=fluwiki2

the German report also has phylo-trees, last year the deadline was 15.July,
http://influenza.rki.de/agi/GetBericht?id=180 (page 36)
so this year's report may appear soon


with months ,
â—„ :Amantadine resistant
@ : Oseltamivir resistant
#: egg isolate

phylo-sorted (algorithm unclear to me)

Code: 
HA
------
niid A/Toyama/108/2007 Oct LR
aus A/Guam/1/2007 â—„ Oct
A/Guam/6495/2007 â—„ Oct LR
A/Oregon/07/2007 Dec LR
A/Oregon/06/2007 â—„ Dec
A/Lyon/1388/2007 â—„ Dec LR
A/Hong Kong/4703/2007 â—„ Sep LR
A/Cambodia/0371/2007 â—„ Aug #
niid A/Hiroshima/93/2007 Oct LR #
A/Korea/6612/2007 â—„ Oct
aus A/Philippines/3150/2007 â—„ Sep
A/Hong Kong/2652/2006 â—„ Jul LR #
A/Ulaanbaatar/116/2007 â—„ Jan #
niid A/Yokohama/75/2007 Oct LR
niid A/Hiroshima/109/2007 Dec #
A/Minnesota/25/2007 â—„ Oct
A/Hawaii/19/2007 â—„ Oct #
A/Liaoning/Huanggu1183/2007 Oct #
A/Lyon/1350/2007 Dec LR
  nimr A/Norway/1630/2007 @
  A/Illinois/10/2007 Dec @
  A/Lyon/1337/2007 Dec LR @
A/South Dakota/06/2007 Jul #
  A/New Jersey/16/2007 Dec LR @
A/Florida/10/2007 Dec #
A/Toulouse/1401/2007 Nov
A/Texas/70/2007 Dec #
A/Texas/74/2007 Nov
A/Illinois/11/2007 Dec LR
A/Arizona/07/2007 Dec LR
A/Nepal/4606/2007 Jul LR
A/Alaska/13/2007 Dec LR
A/Texas/78/2007 Dec
A/Massachusetts/14/2007 Dec
A/New York/16/2007 Dec LR
A/Washington/34/2007 Dec
niid A/Hiroshima/99/2007 Nov #
A/Pennsylvania/01/2008 Jan LR
A/Qatar/1124/2007 Nov LR
A/Hawaii/31/2007 Oct #
  A/Hawaii/21/2007 Oct @
A/Iowa/04/2007 Nov
A/Florida/15/2007 Dec
aus A/Brisbane/59/2007 IVR148 #
aus A/Brisbane/59/2007 Jul #
A/Illinois/13/2007 Dec
A/Colorado/21/2007 Nov #
A/California/40/2007 Dec LR
A/Fukushima/141/2006 #
A/Solomon Islands/03/2006 #
A/Solomon Islands/03/2006 IVR145 #
A/Florida/3/2006 #
A/El Salvador/582/2007 Sep LR
A/Honduras/643/2007 Oct LR
A/New Caledonia/20/1999

Code: 
NA
---
niid A/Toyama/108/2007 Oct LR
niid A/Hiroshima/93/2007 Oct LR #
A/Korea/6612/2007 â—„ Oct
A/Oregon/07/2007 â—„ Dec
A/Oregon/06/2007 â—„ Dec
A/Guam/6495/2007 â—„ Oct LR
A/Cambodia/0371/2007 â—„ Aug #
A/Lyon/1388/2007 â—„ Dec
A/Hong Kong/4703/2007 â—„ Sep
A/Ulaanbaatar/116/07 â—„ Jan #
A/Hong Kong/2652/2006 â—„ Jul #
A/Liaoning/Huanggu1183/2007 Oct #
niid A/Yokohama/75/2007 Oct LR
niid A/Hiroshima/109/2007 Dec #
A/Minnesota/25/2007 â—„ Oct
A/Hawaii/19/2007 â—„ Oct #
A/Texas/70/2007 Dec #
A/Texas/74/2007 Nov
A/Arizona/07/2007 Dec LR
A/Illinois/11/2007 Dec LR
A/Toulouse/1401/2007 Nov
A/Nepal/4606/2007 Jul LR
A/Washington/34/2007 Dec
A/Florida/10/2007 Dec #
A/Lyon/1350/2007 Dec
A/South Dakota/06/2007 Jul #
  nimr A/Norway/1630/2007 @
  A/Lyon/1337/2007 Dec @
  A/Illinois/10/2007 Dec @
  A/New Jersey/16/2007 Dec @
A/Pennsylvania/01/2008 Jan
A/Qatar/1124/2007 Nov LRniid 
A/Hiroshima/99/2007 Nov #
A/Colorado/21/2007 Nov #
  A/Hawaii/21/2007 Oct @
A/Hawaii/31/2007 Oct #
A/Brisbane/59/2007 Jul #
A/California/40/2007 Dec
A/Illinois/13/2007 Dec
A/Iowa/04/2007 Nov
A/Massachusetts/14/2007 Dec
A/Fukushima/141/2006 #
A/Solomon Islands/03/2006 #
A/Solomon Islands/3/06 IVR-145 #
A/Florida/3/2006 #
A/El Salvador/582/2007 Sep
A/Honduras/643/2007 Oct
A/New Caledonia/20/1999
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

I just found this:

www.idsociety.org/WorkArea/downloadasset.aspx?id=11382

Gubareva,CDC about Amantadine and Oseltamivir resistance, May,19,2008


H1N1-NA phylo tree on page 24
(protected .pdf , needs handwork :-( )
I assume that all these sequences are available in some non-public database
to subscribed members and they may publish phylo-trees from it but not the sequences
themselves.

Code: 
A/Hong Kong/36/2008 < Jan LR
A/Japan/763/2008 < Jan
  niid A/Yokohama/91/2007 @
A/Hawaii/05/2008 < Jan
A/Liaoning/Huanggu1183/2007 < Oct LR
A/Hong Kong/2652/2006 < Jul #
  A/Gansu/Chengguan1129/2007 < @ Jan
A/Cambodia/0371/2007 < Aug #
A/Hawaii/38/2007 < Nov #
A/Ulaanbatar/0607/2008 < Jan
A/Massachusetts/01/2008 < Jan
  A/Arizona/15/2007 @ Dec
  A/Norway/1747/07 @ Dec
  A/Indiana/01/2008 @ Jan
  A/British Columbia/RV1585/07 @ Dec
  niid A/Yokohama/78/2008 @
  A/StPetersburg/16/2008 @ Feb #
  nimr A/Lisbon/3/2008 @
  aus A/Sydney/142/2007 @
  A/Trinidad/1448/2008 @ Feb
  A/New Jersey/06/2008 @ Feb
  nimr A/England/557/2007 @
nimr A/Berlin/1/08
A/Hong Kong/179/2008 Feb LR
A/South Dakota06/2007 Jul #
A/Bucuresti/136/2008 Jan #
swe A/Stockholm/5/08
A/Kuwait/1070/2008 Jan
A/Oklahoma/03/2008 Feb
  niid A/Yamagata/68/2008 @
  niid A/Tottori/29/2008 @
  niid A/Yokohama/30/2008 @
  A/Thailand/1577/2007 @ Nov
A/louisiana/03/2008 Jan #
A/Brisbane/59/2007 Jul #
  niid A/Aichi/76/2008 @
  A/Hawaii/28/2007 @ Oct
  niid A/Gifu-C/38/2008 @
  niid A/Tottori/23/2008 @
A/Kaliningrad/07/2008 Feb
A/New Jersey/08/2008 Jan
A/Pennsylvania/01/2008 Jan
aus A/Thailand/39/2008 ZR
A/Alaska/02/2008 Jan
A/Moscow/04/2008 Feb
A/Fukushima/141/2006 #
A/Solomon Islands/03/2006 Aug #
A/Solomon Islands/3/06 IVR-145 #
A/Florida/3/2006 Oct#
A/New Caledonia/20/1999 #
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

gsgs said:
I just found this:

www.idsociety.org/WorkArea/downloadasset.aspx?id=11382

Gubareva,CDC about Amantadine and Oseltamivir resistance, May,19,2008


H1N1-NA phylo tree on page 24
(protected .pdf , needs handwork :-( )
I assume that all these sequences are available in some non-public database
to subscribed members and they may publish phylo-trees from it but not the sequences
themselves.

Code: 
A/Hong Kong/36/2008 < Jan LR
A/Japan/763/2008 < Jan
  niid A/Yokohama/91/2007 @
A/Hawaii/05/2008 < Jan
A/Liaoning/Huanggu1183/2007 < Oct LR
A/Hong Kong/2652/2006 < Jul #
  A/Gansu/Chengguan1129/2007 < @ Jan
A/Cambodia/0371/2007 < Aug #
A/Hawaii/38/2007 < Nov #
A/Ulaanbatar/0607/2008 < Jan
A/Massachusetts/01/2008 < Jan
  A/Arizona/15/2007 @ Dec
  A/Norway/1747/07 @ Dec
  A/Indiana/01/2008 @ Jan
  A/British Columbia/RV1585/07 @ Dec
  niid A/Yokohama/78/2008 @
  A/StPetersburg/16/2008 @ Feb #
  nimr A/Lisbon/3/2008 @
  aus A/Sydney/142/2007 @
  A/Trinidad/1448/2008 @ Feb
  A/New Jersey/06/2008 @ Feb
  nimr A/England/557/2007 @
nimr A/Berlin/1/08
A/Hong Kong/179/2008 Feb LR
A/South Dakota06/2007 Jul #
A/Bucuresti/136/2008 Jan #
swe A/Stockholm/5/08
A/Kuwait/1070/2008 Jan
A/Oklahoma/03/2008 Feb
  niid A/Yamagata/68/2008 @
  niid A/Tottori/29/2008 @
  niid A/Yokohama/30/2008 @
  A/Thailand/1577/2007 @ Nov
A/louisiana/03/2008 Jan #
A/Brisbane/59/2007 Jul #
  niid A/Aichi/76/2008 @
  A/Hawaii/28/2007 @ Oct
  niid A/Gifu-C/38/2008 @
  niid A/Tottori/23/2008 @
A/Kaliningrad/07/2008 Feb
A/New Jersey/08/2008 Jan
A/Pennsylvania/01/2008 Jan
aus A/Thailand/39/2008 ZR
A/Alaska/02/2008 Jan
A/Moscow/04/2008 Feb
A/Fukushima/141/2006 #
A/Solomon Islands/03/2006 Aug #
A/Solomon Islands/3/06 IVR-145 #
A/Florida/3/2006 Oct#
A/New Caledonia/20/1999 #
Click to expand...
Slide 17 also has additional isolates with H274Y, which are not on the earlier list of isolates labeled Northern EU-like, and of course there aree many public sequences from the US with H274Y.
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

gsgs said:
so, why do they give trees but withhold sequences ?

is there software to construct the sequences from the trees, modulo locations ?

is there OCR software to read trees into the computer ?



Obviously the trees are less informative than my mutation tables wrt.
some (most) aspects. Are such tables and pictures used elsewhere ?
You can't track single polymorphisms with the trees.
Click to expand...
These latest trees have changes at the protein level, so you could create the protein sequence from the trees. However, only the number of nucleotide changes can be obtained from the trees without the actual sequences.

The sequences are withheld for publication, which is not a new story.

The recent Science paper on seasonal H3 emerging from Asia had sequences that had been held for five years, and the sequences were primarily from WHO consultants, as well as Klaus Stohr who used to run the WHO influenza program (and even then only partials of H3 were released).

The blaming of the resident country is just hocus pocus for media writers and the general public, espcially for seasonal flu.
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

> The sequences are withheld for publication

so there must be someone who pays for this exclusive publishing.
Do the journals pay for this and thus indirectly reward
withholding ?

however, sequencing is becoming cheap and more people can easily
do it, so this might change soon
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

gsgs said:
> The sequences are withheld for publication

so there must be someone who pays for this exclusive publishing.
Do the journals pay for this and thus indirectly reward
withholding ?

however, sequencing is becoming cheap and more people can easily
do it, so this might change soon
Click to expand...
You really don't understand who does the sequencing and why. Almost all of the sequencing is done with GOVERNMENT funds and for infleunza, most is done by public health agencies.
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

and they reward withholding for some reason which is withheld


someone with access please just create the whole N1-phylo-tree for 2007/8
and post the digital resistence pattern for the generated ordering.

That won't reveal too much secret material
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

gsgs said:
and they reward withholding for some reason which is withheld


someone with access please just create the whole N1-phylo-tree for 2007/8
and post the digital resistence pattern for the generated ordering.

That won't reveal too much secret material
Click to expand...
They are looking for publication in peer reviewed journals, not internet message boards.
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

The additional isolates on the various phylogenetic trees have expanded the number of "Northern EU-like" isolates to other countries, including Canada, Russia, Trinidad. However, these trees also expanded the number of countries with isolates that form additional branches, including Spain, Thailand, Greece.

Here is the expanded "Northern EU-like" list

Arizona/3/07
Arizona/13/07
Arizona/14/07
Arizona/15/07
British Columbia/RV1585/07
England/557/07
Illinois/10/07
Maryland/04/07
New Jersey/15/07
New Jersey/16/07
New Jersey/20/07
Norway/1630/07
Norway/1651/07
Norway/1684/07
Norway/1687/07
Norway/1701/07
Norway/1731/07
Norway/1736/07
Norway/1743/07
Norway/1745/07
Norway/1747/07
Ontario/RV0131/2007
Paris/0577/07
Paris/0644/07

Hawaii/1/08
Hawaii/2/08
Indiana/1/08
Memphis/3/08
Minnesota/1/08
New Jersey/05/08
New Jersey/06/08
New Jersey/10/08
North Carolina/2/08
Pennsylvania/2/08
St Petersburg/16/2008
Trinadad/14/2008
Washington/1/08
Wisconsin/01/08
Yokohama/77/08
Yokohama/78/08
Yokohama/79/08
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

can we make a maximal 2008 phylo-sorted list
(all sources, joined segments, estimated orderings)
with indented resistant viruses ?

> They are looking for publication in peer reviewed journals,
> not internet message boards.

they could easily have both. The internet boards are gratis
and increase their popularity. You see this in other
science, but the only online virologist I'm aware of is you
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

gsgs said:
can we make a maximal 2008 phylo-sorted list
(all sources, joined segments, estimated orderings)
with indented resistant viruses ?

> They are looking for publication in peer reviewed journals,
> not internet message boards.

they could easily have both. The internet boards are gratis
and increase their popularity. You see this in other
science, but the only online virologist I'm aware of is you
Click to expand...
The trees are generated through the actual sequences. There is free public software that will generate a tree, but the actual sequences are required. The software first aligns the sequences with a program like clustal w and then genrates a tree based on which sequences are most closely related to each other, and the x axis shows how many differences there are from branch to branch. The only real trick is to trim the sequences so all have the same start and stop point.

Since everyone uses similar software, it is pretty easy to compare one tree with another and see which sequences fall on which branches (although of course such analysis is most accurate if a tree is generated with all of the raw sequence data).

However, as noted, most of teh sequences from isolates outside of teh US have not been released. Most of the US sequences have been released by the CDC (primarily HA and NA). There are partials from Turkey and a full sequence from England, but all others are only available via the trees in the variosu PDF files used in power point presentations.

The tree from Japan has the largest number of sequences that are not in the "northern EU category" and that tree pretty much answers teh question about independent introductions (almost all of the branches have isolates with and without H274Y, indicating they are all independent introductions, and the associated text indicates the patients were not known to be taking Tamiflu - most are definitely not, while a few do not yet have data).

I will be doing a commentary with the updated info from the other trees, which pretty much explains how and why H274Y is going global. It will have links to existing trees, but the only tree I can generate is one using public sequences, which are virtually all from the US and have three distinct branches (Northern EU-like, Hawaii, and Florida). The only branch that isn't in the public trees is one from Florida, which is a branch with three Florida isolates. The two from 2007 do not have H274Y, while the one from 2008 does.

http://www.recombinomics.com/News/05210804/H274Y_Florida.html

Free software to generate phylogenetic trees can be downloaded here

http://www.clcbio.com/index.php?id=28
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

there should be some software to merge several trees with some commons.
But the problem is to make the trees computer-readable,
when they are posted as .pdf files
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

gsgs said:
there should be some software to merge several trees with some commons.
But the problem is to make the trees computer-readable,
when they are posted as .pdf files
Click to expand...
I doubt it. Most software requires the raw sequence data.
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Tree-building software has output that is 'computer readable', but that output isn't used in formal journal publications, it's presented as a graphic representation within submitted papers. The pdf format is widely used by publishers for electronic document construction to ensure uniform document access. Pdf file format readers are incorporated into internet browsers to ensure compatibility for access to the finished on-line and to streamline processing of print journal versions. The pdf builder/output software accepts tables, text and graphic file inputs that are incorporated into the document as universally readable document output.

You want to read up on PHYLIP and Newick file formats for phylogenetic analysis software input/output.

evolution.genetics.washington.edu/phylip/general.html
evolution.genetics.washington.edu/phylip/newicktree.html

This is an example of software that utilizes these tree-builder file output formats for tree-comparison.

http://bioinformatics.oxfordjournals.org/cgi/content/full/23/12/1556
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

doesn't look good for Tamiflu and N1.

Compare here with Amantadine resistance in H3N2:
o:resistant (S31N)


1.) phylogenically sorted
Code: 
............................................................
............................................o...............
............................................................
....................o..............................o........
............................................................
.......................................................o....
............................................................
......................o......................oo.............
............................................................
.....o......................................................
..................................o..............o..........
............................................................
............................................................
............................................................
..........................................................oo
............................................................
............................................................
............................................o..ooooo........
............................................................
............................................................
..............o..................o.........................o
oooooooooooooooooooooooooooooooooo.ooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooo...
............................................................
...................o........................................
......................................o..o..................
..


2.) sorted by time

Code: 
..................................
.......................................................o....
....o.......................................................
............................................................
.....................................o......................
................o......................o....................
...............o............................................
............................................................
............................................................
............................................................
............................................................
............................................................
.....o......................o...............................
............................................................
..................o.........o....................o..........
............................................................
o...........................................................
............................................................
............................................................
.........................o..................................
......o.ooooo......o.o.o.oo.o...o.o.o...oooo...o...oooooo..o
......o....o....o..o.....oo......ooooooooooooooooooooooooooo
oooooooooooooooooooooooooo..oooooooooooooooo.ooo.ooooooo.ooo
oooooo.oo


and now H275Y (H274Y in N2-numbering) in phylogenetically sorted full NA of
human H1N1 since 1977 (only NA, not full genomes)

Code: 
............................................................
............................................................
............................................................
............................................................
............................................................
............................................................
............................................................
............................................................
............................................................
....o.................................o.........oo..........
..............................................ooo...........
............................................................
......ooo..............................ooooooooooooooooooooo
............................................................
........oo..................................................
............................................................
............................................................
...............................


and while I'm at it, here is G743A (G723A in coding region of N1) in H5N1,
phylo-sorted in NA

Code: 
.......................oo...................................
ooo.....oo..................................................
........................................o...................
........................ooooooooooooo...............ooo.....
..........ooooooooooooooooooooooooooooo.................oo..
.....o......ooooo............oo......o...o..............oo..
...........................................................o
............................................................
.......................oo...................................
.......oooooooooooooooooooooooooooooooooooooooooooo.........
...........ooo...oo....................ooo......oooooooooo..
.o.....................ooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
.o.......o..................o............................o..
.o.....................o.......................o.ooooooooooo
o...........................................................
.............o........oo................................o.oo
.......o....................................................
........................o...................................
........................oo....ooo.............oooo.

pretty much scattered, not only in Qinghai-background
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

earlier H274Y was reported in A/Texas/36/1991 and A/Mississippi/3/2001.
Most seasons were H3N2 dominated, so there was not so much H1N1.
And samples in 2006/7 greatly increased. I'm not sure yet, whether we can
say that H274Y first emerged in 2006/7.
I don't see a connection with H5N1
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

gsgs said:
doesn't look good for Tamiflu and N1.

Compare here with Amantadine resistance in H3N2:
o:resistant (S31N)


1.) phylogenically sorted
Code: 
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............................................o...............
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....................o..............................o........
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.......................................................o....
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......................o......................oo.............
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.....o......................................................
..................................o..............o..........
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............................................................
..........................................................oo
............................................................
............................................................
............................................o..ooooo........
............................................................
............................................................
..............o..................o.........................o
oooooooooooooooooooooooooooooooooo.ooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooo...
............................................................
...................o........................................
......................................o..o..................
..


2.) sorted by time

Code: 
..................................
.......................................................o....
....o.......................................................
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.....................................o......................
................o......................o....................
...............o............................................
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.....o......................o...............................
............................................................
..................o.........o....................o..........
............................................................
o...........................................................
............................................................
............................................................
.........................o..................................
......o.ooooo......o.o.o.oo.o...o.o.o...oooo...o...oooooo..o
......o....o....o..o.....oo......ooooooooooooooooooooooooooo
oooooooooooooooooooooooooo..oooooooooooooooo.ooo.ooooooo.ooo
oooooo.oo


and now H275Y (H274Y in N2-numbering) in phylogenetically sorted full NA of
human H1N1 since 1977 (only NA, not full genomes)

Code: 
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....o.................................o.........oo..........
..............................................ooo...........
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......ooo..............................ooooooooooooooooooooo
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........oo..................................................
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and while I'm at it, here is G743A (G723A in coding region of N1) in H5N1,
phylo-sorted in NA

Code: 
.......................oo...................................
ooo.....oo..................................................
........................................o...................
........................ooooooooooooo...............ooo.....
..........ooooooooooooooooooooooooooooo.................oo..
.....o......ooooo............oo......o...o..............oo..
...........................................................o
............................................................
.......................oo...................................
.......oooooooooooooooooooooooooooooooooooooooooooo.........
...........ooo...oo....................ooo......oooooooooo..
.o.....................ooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
.o.......o..................o............................o..
.o.....................o.......................o.ooooooooooo
o...........................................................
.............o........oo................................o.oo
.......o....................................................
........................o...................................
........................oo....ooo.............oooo.

pretty much scattered, not only in Qinghai-background
Click to expand...
G743A has been around for awhile and is now on multiple backgrounds. The jumps can be easily seen with phylogenetic trees.
H5N1 knows what it is doing and its evolution is NOT random.
 
Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

Re: _|INFLUENZAVIRUS A/H1N1 RESISTANT TO OSELTAMIVIR: W.H.O. PRELIMINARY SUMMARY|_

gsgs said:
you keep saying this, yet noone seems to agree.
And noone including you could so far predict flu-evolution.

You can't distinguish the mutations with phylo-trees, only their counts.
Click to expand...
The phylo trees provide a background for annotation. Of course they don't handle recombination well because the recombination creates discordance.
The startled and baffled experts may have some problems understand the data, but the story is pretty straight forward.
The trees are like using wall maps to show that the earth is round (which also applies to the representations you post).
 
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