Published Date: 2006-03-19 23:50:00
Subject: PRO/AH> Avian influenza virus: sequence database (02)
Archive Number: 20060319.0855

AVIAN INFLUENZA VIRUS: SEQUENCE DATABASE (02)
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A ProMED-mail post
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Date: Sat 18 Mar 2006
From: Poul Jorgensen <phj@dfvf.dkand> & Anders Fomsgaard <AFO@ssi.dk>
Source: The Danish Institute for Food and Veterinary Research (DFVF)
& Statens Seruminstitut (SSI) [edited]

[Sequencing information is not normally carried by ProMED-mail, but
the following communication is posted, as it demonstrates a link
between high pathogenic avian influenza viruses isolated in Astrakhan
and Denmark which would not otherwise be immediately apparent.
Furthermore, it demonstrates the value of depositing sequence
information in an open access database, as proposed recently in
ProMED-mail and elsewhere by Ilaria Capua. It also illustrates the
ever increasing technical advances in speed and accuracy of whole
genome sequencing. - Mod.CP]

Full genomic sequencing of HP H5N1 Avian Influenza virus isolated
from a buzzard in Denmark
-------------------------
On Tue 14 Mar 2006, an H5 avian influenza virus was detected in
respiratory tissues from a dead buzzard (_Buteo buteo_) found in the
southern part of the island of Zealand (Sjaelland) in Denmark. The
identification of the virus is A/Buzzard/Denmark/6370/06 (H5N1).
Sequencing of the cleavage site of the HA gene revealed that the
virus is highly pathogenic for fowl.
On Wed 15 Mar 2006, a virus isolate was obtained from SPF [specific
pathogen free] chicken embryos. The entire viral genome has been
sequenced now in a collaborative work between the Danish Institute
for Food and Veterinary Research (DFVF) and Statens Seruminstitut
(SSI).
The sequence has been made accessible at the home page of the
Danish Influenza Research Network, formed by DFVF and SSI:
<http://home.no.net/difn>.
Preliminary analysis of the sequences indicates that the HA gene has
high homology with A/Cygnus olor/Astrakhan/Ast05-2-4/2005 (H5N1) and
the NA gene with A/Cygnus olor/Astrakhan/Ast05-2-7/2005 (H5N1). There
are no neuraminidase substitutions in the NA gene. [_Cygnus olor_ is the
common mute swan. - Mod.JW]
[Russia's authorities reported the mortality of 558 swans (out of a
population estimated to be 15 000) in the hunting refuge
"Astradelta," in the Volga delta area, Astrakhan, in November 2005.
The data, presented in a table, were included in Russia's official
follow-up report No. 5 to the OIE for 2005; see
<http://www.oie.int/eng/info/hebdo/aIS_38.htm#Sec4>.
The report included also phylogenetic trees constructed from
fragments of the HA gene (nucleotides 801-1113) and NA gene
(nucleotides 605-937) showing that "Russian isolates of the year 2005
exhibited greatest sequence similarity with the A/Qinghai/05 H5N1
group of isolates." The HA gene homology was shown, among others, in
the isolate A/swan/Astrakhan/04/05. For further details, see posting
20060120.0191. - Mod.AS]
Further analysis of the genome will be performed. This is the 1st
time highly pathogenic avian influenza has been detected in Denmark.
The virus isolate was submitted to the EU reference laboratory in the
UK on Thu 16 Mar 2006 for confirmation.
--
Poul H. Jorgensen (DFVF)
<phj@dfvf.dk>
Anders Fomsgaard
<AFO@ssi.dk>
[An initial media report on the discovery of H5 in an (unspecified)
wild fowl in Denmark was included in post 20060315.0803. It appears
now that the affected bird was a buzzard. So far, no information on
this case is available on the OIE website. - Mod.AS]
[Buzzard (_Buteo buteo_)
<http://www.waarneming.nl/fotonew/2/1532.jpg>
Denmark locator map:
<http://www.mapsofworld.com/denmark/maps/denmark.jpg>
Detailed map -- see island on right of map:
<http://www.alltraveldenmark.com/images/destin_map.gif>

See Also

Avian influenza - worldwide (53): Europe 20060315.0803
Avian influenza virus: sequence database proposal 20060309.0750
2005
----
Avian influenza - Eurasia (94): Ukraine, Russia 20051207.3529
Avian influenza - Eurasia (108): FAO, update 20051223.3674
Avian influenza - Eurasia (27): Russia, wild birds 20060120.0191
..............................cp/arn/msp/jw
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