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J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

Giuseppe

Giuseppe

Emeritus
J Clin Microbiol. 2009 Mar 4. [Epub ahead of print]

Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

Tamura D, Mitamura K, Yamazaki M, Fujino M, Nirasawa M, Kimura K, Kiso M, Shimizu H, Kawakami C, Hiroi S, Takahashi K, Hatta M, Minagawa H, Kimura Y, Kaneda S, Sugita S, Horimoto T, Sugaya N, Kawaoka Y. - Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; Department of Pediatrics, Eijyu General Hospital, Tokyo, Japan; Department of Pediatrics, Zama Children's Clinic, Kanagawa, Japan; Department of Pediatrics, Saiseikai Central Hospital, Tokyo, Japan; Department of Pediatrics, Isehara Kyodo Hospital, Kanagawa, Japan; Kawasaki City Institute of Public Health, Kanagawa, Japan; Yokohama City Institute of Public Health, Kanagawa, Japan; Osaka Prefectural Institute of Public Health, Osaka, Japan; Aichi Prefectural Institute of Public Health, Aichi, Japan; Tottori Prefectural Institute of Public Health and Environmental Science, Tottori, Japan; Equine Research Institute, Japan Racing Association, Tochigi, Japan; Department of Pediatrics, Keiyu Hospital, Kanagawa, Japan; Interenational Research Center for Infectious Disease, Institute of Medical Science, University of Tokyo, Tokyo, Japan; Department of Pathobiological Science, School of Veterinary Medicine, University of Wisconsin- Madison, Wisconsin, USA.

Surveillance studies of influenza viruses circulating in Europe and other countries in 2007-2008 have revealed rates of resistance to oseltamivir of up to 67% among H1N1 viruses.
Here, we examined 202 clinical samples obtained from patients infected with H1N1 virus in Japan in 2007-2008 for oseltamivir resistance and found that three were oseltamivir-resistant (1.5%).
The IC50 values, as measured by a sialidase inhibition assay of these drug-resistant viruses, were >100-fold higher than those of the non-resistant viruses (a median of 12.6 nmol/L).
The His274Tyr (N2 numbering) mutation of the neuraminidase protein, which is known to confer oseltamivir resistance, was detected in these three isolates.
A phylogenetic analysis showed that one virus belonged to a lineage that is composed of drug-resistant viruses isolated in Europe and North America and that the other two viruses independently emerged in Japan.
Continued surveillance studies are necessary to observe whether these viruses will persist.

PMID: 19261802 [PubMed - as supplied by publisher]

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GISAID Discussion

GISAID Discussion

> A phylogenetic analysis showed that one virus belonged
> to a lineage that is composed of drug-resistant viruses
> isolated in Europe

it would be interesting to know the exact timing and mutations
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

gsgs said:
> A phylogenetic analysis showed that one virus belonged
> to a lineage that is composed of drug-resistant viruses
> isolated in Europe

it would be interesting to know the exact timing and mutations
Click to expand...
This is public information. Japan has published multiple phylogenetic trees with sequences that greatly expand the three sequences in this paper. As indicated in this small subset, there were multiple introductions. Moreover, Japan has published multiple phylogenetic trees of samples from THIS season, and have deposited something like 100 sequences from THIS season at GISAID (in addition to public sequences at Genbank).
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

so, when was that one virus isolated which is similar to the European ones ?

who says they have deposited 100 sequences at GISAID?



this season is not critical. We want to know, where/when H275Y emerged first in 2007
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

gsgs said:
so, when was that one virus isolated which is similar to the European ones ?

who says they have deposited 100 sequences at GISAID?



this season is not critical. We want to know, where/when H275Y emerged first in 2007
Click to expand...
There was a series (labeled "northern EU") that were in phylogenetic trees published some time ago (late spring?) as well as more recently (late fall).

The sequences at GISAID can be seen by anyone registered.
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

when you register at GISAID, you are no longer allowed to talk
about these things at FT, right ?
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

gsgs said:
when you register at GISAID, you are no longer allowed to talk
about these things at FT, right ?
Click to expand...
Most of the sequences in the isolates in the phylogenetic trees that you ignore (showing MULTIPLE independent introductions) are at GISAID, as well as many other H1N1 sequences, including MANY from Japan.
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

gsgs said:
when you register at GISAID, you are no longer allowed to talk
about these things at FT, right ?
Click to expand...

These things can be talked about at FT.
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

Florida1 said:
These things can be talked about at FT.
Click to expand...
I believe, GSGS is referring to restrictions by GISAID. The sequences are "public", but only to those who resister, which places limitations on the dissemination of the information to non-members.

However, as is seen in public phylogenetic tress, the sequences are displayed in a way that gives out general information (the name of the sequences as well as their relationships with other sequences), but doesn't release the actual sequence.

Similarly, Indonesia said that human H5N1 sequences would be deposited at GISAID, and such sequences are available to members. Similarly, these sequences were on the recent WHO phylogenetic tree of vaccine targets, so relationships to public sequences are also public.

Thus, much of the information is in the public domain, and of course anything in the public domain can me discussed by anyone, without restrictions.

Therefore, I find it somewhat annoying when the public data is ignored to try to make a point that has no scientific basis, as well as try to create an illusion that the public data is "secret" and controlled by mysterious forces with evil intent, which appears to come up again and again from the same poster (here and throughout the internet) on a VERY regular basis.

For this thread, the public data (and discussion) has demonstrated time and again that H274Y has been independently introduced multiple times, yet he wants to find the origin, based on a collections dates in a VERY limited database (most of which he ignores).
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

when it is at GISAID, it is not really "public".

We had a discussion.

about their terms and conditions (which I decided _not_ to sign)

they intervened and required any quotes from their terms and
conditions to be deleted !


are you the same niman who loudly required in 2006 that data should be published
from the password protected WHO-databases and uploaded to genbank ?


-----edit-------
same question to http://www.offlu.net/ , BTW. Capua apparantly won't reply to emails.
 
Last edited by a moderator:
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

gsgs said:
when it is at GISAID, it is not really "public".

We had a discussion.

about their terms and conditions (which I decided _not_ to sign)

they intervened and required any quotes from their terms and
conditions to be deleted !


are you the same niman who loudly required in 2006 that data should be published
from the password protected WHO-databases and uploaded to genbank ?


-----edit-------
same question to OFFLU.com , BTW. Capua apparantly won't reply to emails.
Click to expand...
As noted, GISAID sequences are quite public (and include sequences from Capua). GISAID is VERY distinct from the password protected WHO database, which REMAINS quite PRIVATE.
 
Last edited by a moderator:
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

gsgs said:
may GISAID-sequences be posted to FT or uploaded to genbank or made public ?
I haven't seen any yet.


http://platform.gisaid.org/dante-cm...AAAJIDLNLAGPMCM&window=&aid=1131&node_id=3520

> You will not copy, reverse engineer, disseminate or disclose any part of the Database Platform.
Click to expand...
As noted, GISAID sequences are quite public and support the information at additional public sites, including Genbank and multiple phylogenetic trees released by agencies in the US, England, Japan, and Italy showing how H1N1 sequences with H274Y related to other public sequences.

The data show that H274Y was initially introduced onto multiple clade 2C backgrounds in China in 2006, followed by multiple clade 1 backgrounds in the US and England in 2006/2007, followed by multiple clade 2B backgrounds worldwide in the 2007/2008, and fixing on a clade 2B background that began to emerge in 2007 in the US and Europe.

The earliest collection date for clade 2B public sequences with H274Y was in isolates in Hawaii in Oct, 2007.
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

niman said:
As noted, GISAID sequences are quite public and support the information at additional public sites, including Genbank and multiple phylogenetic trees released by agencies in the US, England, Japan, and Italy showing how H1N1 sequences with H274Y related to other public sequences.

The data show that H274Y was initially introduced onto multiple clade 2C backgrounds in China in 2006, followed by multiple clade 1 backgrounds in the US and England in 2006/2007, followed by multiple clade 2B backgrounds worldwide in the 2007/2008, and fixing on a clade 2B background that began to emerge in 2007 in the US and Europe.

The earliest collection date for clade 2B public sequences with H274Y was in isolates in Hawaii in Oct, 2007.
Click to expand...
Actually, the earliest US isolate was in Hawaii. An isolate from Australia, was also collected in Oct, 2007 but a couple weeks prior to the Hawaii isolates. These clade 2B isolates were independent of each other, as well as the sub-clade that led to world-wide fixing of H274Y.
In 2007, H274Y in Japan was VERY rare.
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

the Hawaii-isolates (nor does A/Yokohama/91/2007/11/14)
don't quite qualify as ancestors of Norway/European
resistant viruses in 2007/8, they have some markers which were
not seen in Europe.

Earliest for me is
A/Sydney/142/2007/11/02

then
A/Paris/341/2007/11/12

it would be interesting to see, if possible ancestors appeared earlier in Asia
or Oceania
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

gsgs said:
the Hawaii-isolates (nor does A/Yokohama/91/2007/11/14)
don't quite qualify as ancestors of Norway/European
resistant viruses in 2007/8, they have some markers which were
not seen in Europe.

Earliest for me is
A/Sydney/142/2007/11/02

then
A/Paris/341/2007/11/12

it would be interesting to see, if possible ancestors appeared earlier in Asia
or Oceania
Click to expand...
Right, They were INDEPENDENT introductions, as was the sequence in Australia.

That is the POINT. There were MULTIPLE INDEPENDENT introductions.
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

they were single events, didn't spread.
The vast majority in Europe 2007/8 was one specific strain
whose origin should be tracked (and should have been in 2007,
early 2008 already !)

Sydney/142 looks very European/2007-8 like
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

gsgs said:
they were single events, didn't spread.
The vast majority in Europe 2007/8 was one specific strain
whose origin should be tracked (and should have been in 2007,
early 2008 already !)

Sydney/142 looks very European/2007-8 like
Click to expand...
The strain that spread was tracked almost a year ago. It included multiple isolates in the US and Europe collected in 2007. Like the earlier isoaltes which you ignore, it was found in patients not taking Tamiflu and the resistance was limited to H274Y in H1N1. These isolates were presented in phylogentic trees which you also ignore, as well as multiple recombinomics comentaries, which you also ignore.

All of the above were deatiled here which includes isolates from THIS season)

http://precedings.nature.com/documents/2832/version/1
 
Re: J Clin Microbiol. Oseltamivir-Resistant Influenza A Viruses Circulating in Japan.

gsgs said:
they were single events, didn't spread.
The vast majority in Europe 2007/8 was one specific strain
whose origin should be tracked (and should have been in 2007,
early 2008 already !)

Sydney/142 looks very European/2007-8 like
Click to expand...
WRONG. Several of the independent introductions spread, but not as commonly or widely as the strain that eventually dominated (but spread did jump continents and included North America and Europe).

Limited spread is also demonstrated here

http://precedings.nature.com/documents/2832/version/1
 
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