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**HenryN** · July 11, 2008, 08:13 PM

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

Originally posted by gsgs View Post

Y removed. That was my first idea to mark H274Y, but indentation
seems better. It shows how resistant and non-resistant isolates alternate.

In my mutation tables this would look like vertically sprenkled
dots or multiple short lines or dots in the same column,
which is rare

Recent H5N1 would look the same for G743A

**gsgs** · July 11, 2008, 08:50 PM

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

not quite. 4 distant spots not this sprenkling (English?). -edit--(scattered)

my current theory is, that it's due to drug use.
Not (necessarily) in the sampled patients but
earlier, undetected.
The prevalent strain this year may have some other mutations
not seen before which counterbalances the earlier found
worse spreading of strains with H274Y.
I hope this will be determined.

But the reason for the establishing of Amantadine-resistance
some years ago was never found, AFAIK.

**gsgs** · July 11, 2008, 08:56 PM

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

I don't really know, how these phylo-trees are generated.
The rules, the source-code.
Maybe we could generate the sequences from the tree,
modulo the exact positions of the mutations, which is not
so important.

The most natural ordering of sequences would be to
always add as next one the closest sequence to the last selected one
out of the remaining ones.

**HenryN** · July 11, 2008, 09:06 PM

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

Originally posted by gsgs View Post

not quite. 4 distant spots not this sprenkling (English?).

my current theory is, that it's due to drug use.
Not (necessarily) in the sampled patients but
earlier, undetected.
The prevalent strain this year may have some other mutations
not seen before which counterbalances the earlier found
worse spreading of strains with H274Y.
I hope this will be determined.

But the reason for the establishing of Amantadine-resistance
some years ago was never found, AFAIK.

The problem is that you don't know how to generate or read the trees, which clearly show the H274Y was acquired AFTER the branches were formed.
Same story for G743A.
The data and sequences are CLEAR.
Case is closed.

**gsgs** · July 11, 2008, 09:20 PM

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

cause I consider the trees less informative and inferior to
computer-available direct data.
Presumably that's why they give trees in non-computer-readable .pdf
but withhold sequences

**HenryN** · July 11, 2008, 09:44 PM

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

Originally posted by gsgs View Post

cause I consider the trees less informative and inferior to
computer-available direct data.
Presumably that's why they give trees in non-computer-readable .pdf
but withhold sequences

The trees can be generated with free public software, as long as you have the sequences.
The tree from Japan, as well as the others I linked had public sequences, so it was easy to map the public and non-public sequences and see the H274Y was appended onto MULTIPLE branches AFTER the branches were formed.
The data have been made public and are easily interpreted.

**Oracle** · July 11, 2008, 10:06 PM

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

"cause I consider the trees less informative and inferior to
computer-available direct data.
Presumably that's why they give trees in non-computer-readable .pdf
but withhold sequences"

Wrong. Phylogenetic relationships have been mapped as 'trees' for decades by Systematics and Cladistics Biologists. The input data can be physical (morphological or anatomical features), biochemical (enzyme assay, protein structure), or genetic, or a combination thereof (treated as 'layers' within a cladistics analysis model). The goal is to map the characteristics of individuals to the best fit evolutionary relationships when comparing members of a group.

As Niman *patiently* points out, the software is within the public domain, as are websites that explain their use. The sequence data is also published within the public domain - as you well know.

The output file forms vary according to use. Pdf format has nothing to do with tree making.

**HenryN** · July 11, 2008, 10:30 PM

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

Originally posted by Oracle View Post

"cause I consider the trees less informative and inferior to
computer-available direct data.
Presumably that's why they give trees in non-computer-readable .pdf
but withhold sequences"

Wrong. Phylogenetic relationships have been mapped as 'trees' for decades by Systematics and Cladistics Biologists. The input data can be physical (morphological or anatomical features), biochemical (enzyme assay, protein structure), or genetic, or a combination thereof (treated as 'layers' within a cladistics analysis model). The goal is to map the characteristics of individuals to the best fit evolutionary relationships when comparing members of a group.

As Niman *patiently* points out, the software is within the public domain, as are websites that explain their use. The sequence data is also published within the public domain - as you well know.

The output file forms vary according to use. Pdf format has nothing to do with tree making.

Yes, the phylogenetic trees are the "industry standard" and although they have shortcomings (they can't handle recombination very well), they do provide a basis for analysis.

The trees from Japan included several public sequences (from the US), so it was fairly easy to take a tree of the public data, see where the public sequences on the Japan tree mapped, and figure out where the unpublished sequences would map. The same is true for the other trees that I linked.

As a result, I listed the isolates that would be on the branch labled "Northern EU-like"

404

http://www.who.int/csr/disease/influenza/japan_2008_06_25.pdf

Error 404

on the tree from Japan.

Influenza Virus A/h1n1 Resistant To Oseltamivir: W.h.o. Preliminary Summary - FluTrackers News and Information

http://www.flutrackers.com/forum/showpost.php?p=168413&postcount=29

Since all isolates on this branch have H274Y, they all could have originated from a single sequence with H274Y. As can be seen by the length of the list and the locations, this is the major version of Bisbane/59 with H274Y.

However, it is the isolates with H274Y that are NOT on this branch that represent independent acquistion of H274Y and these other isolates are on branches that have isolates with and without the change. Since some of the branch members do NOT have H274Y, those branches were formed BEFORE H274Y was acquired (because if H274Y came first, all branch members would have H274 - except for rare revertants).

As was described in earlier commentaries, in the US there are two such branches. One has isolates from Hawaii and California, but only two of the Hawaii isolates have the change (one of the Hawaii isolates with the chnage is listed on the tree from Japan, as well as the other trees I linked).

Another branch is formed by isoates from Florida. Two of the Florida isolates are from 2007 and they don't have the change, while the isolate from 2008 does, indicating the 2008 acquistion was in Florida (or on a Florida-like sequence).

The tree from Japan has several additional branches which have some isolates from Japan without the change, and others from Japan with the change, indicating these were also acquisitions AFTER these other branches were formed, and were independent of the acquisitions on the other branches.

Most of the isolates in Japan were from patients who either definitely did not have Tamiflu prior to collection, or probably did not have Tamiflu prior to collection. Only 2 of 22 isolates definitely had Tamiflu prior to collection and one of the two is in group 2A, which isn't included in the above analysis.

The story is in the sequence, and the sequence is an EASY read.

**Oracle** · July 11, 2008, 10:59 PM

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

Phylogenetic relationships are on the edge of applicability for microbial (bacterial, viral, plasmid) isolate comparisons because of that issue of host-environment interaction causing active 'editing' of genes, even within just a few generations.

Which brings us to an interesting conundrum when comparing a small number of outbreak samples and making assumptions on their geographic representativeness, given the exceptional plasticity of these viruses in susceptible hosts (human, mammal, avian).

Also of comparing sequences for all three pandemics of the last century, given that paucity of samples for all three (6, 3, and I believe 3-4 for the last one, 1968). Furthermore, the last two pandemics have isolates have been 'passed' repeatedly while maintained in culture. Taubenberger mentions this in a 2003 paper analyzing the two 1918 variants.

It's not surprising, for instance, to read that the Marburg virus isolate from the Dutch patient (deceased) is 'different' than the type isolate from the outbreak in Uganda in 2007. Despite being from very nearly the same locale.

They are different for a reason other temporal, locale or arising from different patients groups.

**gsgs** · July 12, 2008, 02:10 AM

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

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.

**gsgs** · July 12, 2008, 04:02 AM

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

google has it in html:

http://209.85.135.104/search?q=cache:KV_7H-FKgwEJ:www.fda.gov/ohrms/dockets/AC/08/slides/2008-4348S2-3.pdf+%22A/Denmark/4/2008%22&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 &#226;—„ Oct
A/Guam/6495/2007 &#226;—„ Oct LR
A/Oregon/07/2007 Dec LR
A/Oregon/06/2007 &#226;—„ Dec
A/Lyon/1388/2007 &#226;—„ Dec LR
A/Hong Kong/4703/2007 &#226;—„ Sep LR
A/Cambodia/0371/2007 &#226;—„ Aug #
niid A/Hiroshima/93/2007 Oct LR #
A/Korea/6612/2007 &#226;—„ Oct
aus A/Philippines/3150/2007 &#226;—„ Sep
A/Hong Kong/2652/2006 &#226;—„ Jul LR #
A/Ulaanbaatar/116/2007 &#226;—„ Jan #
niid A/Yokohama/75/2007 Oct LR
niid A/Hiroshima/109/2007 Dec #
A/Minnesota/25/2007 &#226;—„ Oct
A/Hawaii/19/2007 &#226;—„ 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 &#226;—„ Oct
A/Oregon/07/2007 &#226;—„ Dec
A/Oregon/06/2007 &#226;—„ Dec
A/Guam/6495/2007 &#226;—„ Oct LR
A/Cambodia/0371/2007 &#226;—„ Aug #
A/Lyon/1388/2007 &#226;—„ Dec
A/Hong Kong/4703/2007 &#226;—„ Sep
A/Ulaanbaatar/116/07 &#226;—„ Jan #
A/Hong Kong/2652/2006 &#226;—„ Jul #
A/Liaoning/Huanggu1183/2007 Oct #
niid A/Yokohama/75/2007 Oct LR
niid A/Hiroshima/109/2007 Dec #
A/Minnesota/25/2007 &#226;—„ Oct
A/Hawaii/19/2007 &#226;—„ 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

**gsgs** · July 12, 2008, 04:59 AM

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

I just found this:

[Page Not Found]

https://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 #

**HenryN** · July 12, 2008, 05:48 AM

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

Originally posted by gsgs View Post

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 #

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.

**HenryN** · July 12, 2008, 05:54 AM

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

Originally posted by gsgs View Post

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.

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.

**gsgs** · July 12, 2008, 05:58 AM

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

Announcement

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

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