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HUNT FOR DUCK?S FECES - Collection of avian flu virus

HUNT FOR DUCK?S FECES
Source: http://www.asahi.com/jinmyakuki/TKY200903050203.html

Dr. Hiroshi Kida, 65, professor of the graduate school of veterinary, Hokkaido
University, has completed his collection of all subtypes of the avian influenza
A virus, which he had been collecting for 30 years.

In 1978, Kida discovered the avian influenza A virus lurks in the duck?s
intestine. Without falling sick, ducks migrate north and south scattering virus-
containing feces everywhere.

Kida thought if he collected many subtypes of flu virus before an outbreak of
pandemic flu, it might be helpful in making vaccine quickly. By collecting
feces, he can collect viruses.

Kida accompanied hunting groups to duck hunting, only he hunted for duck?s
feces instead. Some subtypes were easily found, some were very scarce. He
collected feces like a child scooping up junk foods to collect freebies.

In 1997, the avian flu H5N1 killed six people in Hong Kong. WHO suspected an
outbreak of pandemic flu and called Kida to request for the H5N1 virus.
However, Kida didn?t have the virus in his collection at that time.

He thought an incomplete collection had little use and extended areas for
collecting as far as to Alaska and Siberia where ducks spend summers. If he
cannot possibly find a subtype, he generated it by himself by mixing subtypes
already in his collection.

Kida posted on his laboratory wall a chart of 144 boxes, 16 boxes horizontally
and 9 boxes vertically. Each time he found a new subtype, he drew a circle in
the chart.

Last November, he succeeded in incubating H16N1, the last remaining
subtype of his collection. It was then the world?s first and only collection of
all subtypes of the avian influenza A virus was completed.

Dr. Yoshihiro Sakoda, associate professor, Kida?s right hand man, created a
virus database and released it on the internet so that researchers around the
world could use it at once.

Dr. Kouichi Yamanishi, 67, is a researcher who was anxiously awaiting the
completion of Kida?s collection. As president of the National Institute of
Biomedical Innovation, he is responsible for the development of a pandemic
flu vaccine. ?We can go to any direction using this collection.?

Japanese government currently produces a vaccine for H5N1. But there is no
assurance that H5N1 will mutate into pandemic flu. Just last week in Aichi,
quails were found infected with H7N6. Yamanishi considers it dangerous to
pick a single subtype as candidate for a pandemic and only prepare for it.

This year, Yamanishi starts the development of a nasal-spray (inactivated)
vaccine. The vaccine will be very easy to use and effective. Using Kida?s
collection, we can prepare for a pandemic no matter what subtype will trigger
it.
(END OF ARTICLE)


NOTE: As far as I understand, a pandemic flu vaccine will be developed from
virus samples of the actual patient and not from virus samples of Kida?s
collection. Kida?s collection will be useful for the veterinarian and virological
research but not for the pandemic flu vaccine. I wrote to the newspaper for
a confirmation but no response.
Dr. Kida, as chairman of the poultry disease subcommittee of the Ministry of
Agriculture, Forestry and Fisheries, is working on the bird flu outbreaks in
Aichi.

____________________
SN1987A
 
Re: HUNT FOR DUCK?S FECES - Collection of avian flu virus

a pandemic flu vaccine will likely resemble to some of Kida's
HAs, but hard to predict which.
By studying the database we can find hints, how the virus spreads,
reassorts and what the most likely candidates for a pandemic are.

However, by keeping his samples secret and not uploading to genbank
the development, spread and advance of this knowledge is restricted
to Kida's own lab, which represents only a small fraction of the
world's research capabilities.
Other labs may have their own databases and so each is required to
hunt all the ducks - instead of just exchanging their data.

However, there is hope that sequencing becomes much cheaper in the
near future and multi-viruses maybe are isolated from sediments
or feces-mixes and thus databases larger than Kida's may become
available to everyone.

When a pandemic happens earlier, then Kida will have to reply to
speculations how many deaths the delay in research due to his secrecy
had caused...
 
Re: HUNT FOR DUCK?S FECES - Collection of avian flu virus

Thank you gsgs for clarification.

Actually, Kida's database is reportedly for everyone's use.

Dr. Yoshihiro Sakoda, associate professor, Kida?s right hand man, created a
virus database and released it on the internet so that researchers around the
world could use it at once.

Considering rapid and frequent changes in flu virus, I assume Kida's database has to be updated and bolstered all the time.

____________________
SN1987A
 
Re: HUNT FOR DUCK?S FECES - Collection of avian flu virus

hmm, seaching...

it could be this:
http://www.ddbj.nig.ac.jp/ddbjingtop-e.html

?!


...
downloading
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/fasta
ddbjvrl1

100MB, takes 20min
...


wondering whether they have sequences which are not at genbank...



> Last November, he succeeded in incubating H16N1, the last remaining
> subtype of his collection.


> DDBJ is the sole DNA data bank in Japan, which is officially certified to collect DNA sequences
> from researchers and to issue the internationally recognized accession number to data submitters.
> We collect data mainly from Japanese researchers, but of course accept data and issue the
> accession number to researchers in any other countries. Since we exchange the collected data
> with EMBL/EBI and GenBank/NCBI on a daily basis, the three data banks share virtually the
> same data at any given time.


doesn't look as if they had extra sequences, not available at genbank

but no H16N1 at genbank


76256 flu-sequences there, looks like a copy of genbank

sent email to Kida

----edit-------------
hey, I got reply from Sakoda !
The webpage is available Monday, here is a google cache:
(hard to load for me)

http://209.85.129.132/search?q=cach...sdb.czc.hokudai.ac.jp/&hl=en&ie=UTF-8&strip=1


-------------------------------------------
About this Database
Influenza Virus Database System presents data of influenza viruses isolated from birds and mammals including humans, established in 2006 by the Laboratory of Microbiology, Graduate School of Veterinary Medicine and the Research Center for Zoonosis Control at Hokkaido University. The aim of the database is to share the data and biological materials for research and development of vaccines and diagnostic use for the control of animal and human influenza.

The database consists of five parts, (1) virus stock information, (2) sequence data of the virus, (3) primer information for gene cloning, (4) plasmid clones containing viral genomes, and (5) reference in the scientific publications.
The data will be updated when the viruses are isolated in the course of surveillance and outbreaks.
Go to page top
Copyright(c) Graduate School of Vaterinary Medicine and Research Center for Zoonosis Control, Hokkaido University. All rights reserved.
 
Re: HUNT FOR DUCK?S FECES - Collection of avian flu virus

GOOD FOR YOU!!

Actually, I was to call Hokkaido University Monday morning.
You saved me a long distance call. Thanks.

Hope you will find the H16N1 sequence.

Do you know why you couldn't find their data at genbank?


________________
SN1987A
 
Re: HUNT FOR DUCK?S FECES - Collection of avian flu virus

368 avian flu sequences from Hokkaido at genbank from 33 serotypes:

H1N1 ,15
H2N2 ,10
H2N3 ,24
H2N5 ,2
H3N2 ,4
H3N6 ,3
H3N8 ,25
H4N2 ,2
H4N5 ,8
H4N6 ,1
H4N6 ,16
H4N9 ,1
H5N1 ,24
H5N3 ,88
H6N1 ,18
H6N2 ,17
H6N5 ,2
H6N8 ,6
H7N1 ,3
H7N7 ,6
H8N4 ,9
H9N2 ,38
H9N4 ,2
H10N2 ,4
H10N4 ,8
H10N5 ,4
H10N6 ,2
H10N7 ,2
H10N8 ,8
H11N6 ,1
H11N9 ,7
H12N5 ,7
H13N6 ,1

all flu sequences at genbank:

Code:
        N1    N2    N3    N4    N5    N6    N7    N8    N9
----------------------------------------------------------
H01: 11185, 1048,   31,-----,   14,   24,    4,    1,   25
H02:   111,  872,  286,    8,   74,    1,   36,   26,  145
H03:   142,24420,   77,   14,   63,  515,   24, 1617,   14
H04:    33,  126,   40,   26,   24,  967,   10,  278,   35
H05: 12638, 1304,  383,    5,   11,   12,   58,   30,   56
H06:  1309,  884,   44,   44,  137,   77,    3,  336,   22
H07:   565, 2371,  822,   31,    9,    2,  390,   25,   22
H08: -----,    3,    1,  126,-----,-----,    2,-----,-----
H09:    75, 5826,    8,    6,   32,   25,    4,    6,    7
H10:    15,    9,   44,   26,   30,   20,  406,   39,   20
H11:    50,   69,   50,   11,-----,   37,-----,   26,  326
H12:     9,    5,    1,   14,  167,-----,-----,    1,   17
H13: -----,   39,   10,-----,-----,   98,-----,    9,   19
H14: -----,-----,    1,-----,   12,    4,-----,-----,-----
H15: -----,    3,-----,-----,-----,    1,-----,    8,   25
H16: -----,-----,   52,-----,-----,-----,-----,-----,-----
 
Re: HUNT FOR DUCK?S FECES - Collection of avian flu virus

From the database web page....

(Quote)
Influenza viruses of 61 combinations of HA and NA subtypes have been isolated from fecal samples of waterfowl in surveillance studies. So far, 83 other combinations have been generated by the genetic reassortment procedure in chicken embryonated eggs. Thus, non-pathogenic avian influenza viruses of all 144 combinations of HA and NA subtypes have been stocked in our library. The library will be updated when novel viruses are isolated in future global surveillance studies.
(Unquote)

photo_usefulness03.jpg


_______________
SN1987A
 
Re: HUNT FOR DUCK?S FECES - Collection of avian flu virus

yes, they created them in the laboratory, with reassortment as I assume.
So, this gives no new sequences - just new combinations of exosting
sequeences.

I assume all their (non-lab) sequences are at genbank.
I checked for the 14 Hokkaido H5, the H16


it makes sense to distinguish 2 different NS also, so that gives another table of 144...
 
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