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PostPosted: Thu Feb 03, 2011 7:11 am 
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The first 2011 H5N1 sequence, A/whooper swan/Hokkaido/4/2011, has been released by Hokkaido University at Genbank. The sequence is clade 2.3.2, as expected (Fujian strain circulating in wild birds), but it has RBD change S227R. The acquisition of S227N led to the first reported human infection by the Qinghai strain (clade 2.2) in Turkey in 2006. In addition, the recent clade 2.3.2 sequences have the additional RBD chnages V223I and M230I, which were present in the Gharbya cluster in Egypt in late 2006.

The acquistion of S227R raises concerns of human transmission.

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PostPosted: Thu Feb 03, 2011 7:18 am 
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LOCUS AB610972 1743 bp cRNA linear VRL 03-FEB-2011
DEFINITION Influenza A virus (A/whooper swan/Hokkaido/4/2011(H5N1)) viral
cRNA, segment 4, complete sequence.
ACCESSION AB610972
VERSION AB610972.1 GI:321267415
KEYWORDS .
SOURCE Influenza A virus (A/whooper swan/Hokkaido/4/2011(H5N1))
ORGANISM Influenza A virus (A/whooper swan/Hokkaido/4/2011(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1
AUTHORS Kida,H., Sakoda,Y. and Okamatsu,M.
TITLE Characterization of H5N1 influenza viruses isolated from waterbirds
in Japan in 2010-2011
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1743)
AUTHORS Makiko,J., Kida,H., Sakoda,Y. and Okamatsu,M.
TITLE Direct Submission
JOURNAL Submitted (31-JAN-2011) Contact:Jizou Makiko Hokkaido University,
Graduate School of Veterinary Medicine; kita-ku, kita18 nishi9,
Sapporo, Hokkaido 060-0818, Japan
FEATURES Location/Qualifiers
source 1..1743
/organism="Influenza A virus (A/whooper
swan/Hokkaido/4/2011(H5N1))"
/mol_type="viral cRNA"
/strain="A/whooper swan/Hokkaido/4/2011"
/serotype="H5N1"
/db_xref="taxon:980042"
/segment="4"
/country="Japan:Hokkaido"
/collection_date="2011"
gene 16..1719
/gene="HA"
CDS 16..1719
/gene="HA"
/codon_start=1
/product="haemagglutinin"
/protein_id="BAJ72684.1"
/db_xref="GI:321267416"
/translation="MEKIVLLFTTISLVKSDHICIGYHANNSTEQVDTIMEKNVTVTH
AQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPLCDEFINVPEWSYIVEKANPA
NDLCYPGNFNDYEELKHLLSRINHFEKIQIIPKDSWSDHEASLGVSAACSYQGNSSFF
RNVVWLIKKDNAYPTIKKGYNNTNQEDLLVLWGIHHPNDEAEQTRLYQNPTTYISIGT
STLNQRLVPKIATRSKINGQRGRIDFFWTILKPNDAIHFESNGNFIAPEYAYKIVKKG
DSTIMKSEVEYGNCNTRCQTPIGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLR
NSPQRERRRKRGLFGAIAGFIEGGWQGMIDGWYGYHHSNEQGSGYAADKESTQKAIDG
VTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENE
RTLDFHDSNVKNLYDKVRLQLKDNAKELGNGCFEFYHKCNNECMESVRNGTYDYPQYS
EEAKLKREEISGVKLESIGIYQILSIYSTVASSLVLAIMMAGLSLWMCSNGSLQCRIC
I"
ORIGIN
1 gttcactctg tcaaaatgga gaaaatagtg cttctcttta caacaatcag ccttgttaaa
61 agcgatcata tttgcattgg ttatcatgca aataactcga cagagcaggt tgacacaata
121 atggaaaaga acgttactgt tacacatgcc caagacatac tggaaaagac acacaacggg
181 aagctctgcg atctaaatgg agtgaagcct ctgattttaa aagattgtag tgtagcggga
241 tggctcctcg gaaacccatt gtgtgacgaa ttcatcaatg tgccagaatg gtcttacata
301 gtagagaagg ccaatccagc caatgacctc tgttacccag ggaatttcaa cgattatgaa
361 gaattgaaac acctattgag caggataaac cattttgaga aaatacagat catccccaaa
421 gactcttggt cagatcatga agcctcattg ggggtgagcg cagcatgttc ataccaggga
481 aattcctcct tcttcagaaa tgtggtatgg cttatcaaaa aggacaatgc atacccaaca
541 ataaagaaag gctacaataa taccaaccaa gaagatctct tggtactgtg ggggattcac
601 caccctaatg atgaggcaga gcagacaagg ctctatcaaa acccaaccac ctatatttcc
661 attgggacat caacactaaa ccagagattg gtaccaaaaa tagccactag atccaaaata
721 aacgggcaaa ggggcaggat agatttcttc tggacaattt taaagccgaa tgatgcaatc
781 cacttcgaga gtaatggaaa tttcattgct ccagaatatg catacaaaat tgtcaagaaa
841 ggagactcca caattatgaa aagtgaagtg gaatatggta actgcaacac caggtgtcag
901 actccgatag gggcgataaa ctctagtatg ccattccaca acatacaccc tctcaccatc
961 ggagaatgtc ccaaatatgt gaaatcaaac aaattagtcc ttgcgactgg gctcagaaat
1021 agtcctcaaa gagagagaag aagaaaaaga ggactgtttg gagctatagc aggttttata
1081 gagggaggat ggcagggaat gatagatggt tggtatgggt accaccacag caatgagcag
1141 gggagtgggt acgctgcaga caaagaatct actcaaaagg caatagacgg agtcaccaat
1201 aaggtcaact cgatcattga caaaatgaac actcagtttg aggccgtagg aagggaattt
1261 aacaacttag agaggagaat agagaattta aacaagaaga tggaagacgg attcctagat
1321 gtttggactt ataatgctga acttctggtt ctcatggaaa atgagagaac tctagatttc
1381 catgactcaa atgtcaagaa cctttacgat aaggtcagac tacagcttaa ggataatgca
1441 aaagagttgg gtaacggttg tttcgagttc tatcacaaat gtaataatga atgtatggaa
1501 agtgtaagaa acggaacgta tgactacccg cagtattcag aagaagcaaa actaaaaaga
1561 gaggaaataa gtggagtaaa attggaatca ataggaatct accaaatact gtcaatttat
1621 tcaacagtgg cgagttccct agtgctggca atcatgatgg ctggtctgtc tttatggatg
1681 tgttccaacg gatcgttaca gtgcagaatt tgcatttaag tctgtgagtt caaattgtgg
1741 tta

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PostPosted: Thu Feb 03, 2011 8:39 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 28247
Location: Pittsburgh, PA USA
AVIAN INFLUENZA (11): JAPAN (KAGOSHIMA, AICHI, MIYAZAKI), POULTRY AND
WILD BIRDS
***********************************************
A ProMED-mail post
<http://www.promedmail.org>
ProMED-mail is a program of the
International Society for Infectious Diseases
<http://www.isid.org>

Date: Wed 2 Feb 2011
Source: The Japan Times [edited]
<http://search.japantimes.co.jp/cgi-bin/nn20110202a3.html>


The Miyazaki Prefectural Government said Tuesday [1 Feb 2011] that
191 chickens died at a poultry farm in the city of Miyazaki and that
6 of the 7 dead birds tested positive for avian influenza in a
preliminary exam.

Officials decided to launch more detailed examinations on the 6 dead
birds to confirm whether they were infected with bird flu. It would
be the prefecture's 7th outbreak.

In Tottori Prefecture, meanwhile, officials said the highly virulent
strain of the H5N1 virus was detected in 2 wild birds that tested
positive for avian flu in earlier tests.

The infection, involving a tufted duck and hooded gull found in a
weakened state in Yonago last month [January 2011], marks the 2nd
outbreak of a highly virulent strain of bird flu in Tottori this
winter.

No signs of infection have been confirmed so far among the 924 000
chickens at 18 poultry farms within 10 km of where the 2 wild birds
were found, the prefectural government said.

The Hokkaido government said detailed tests on a dead whooper swan
recovered in the town of Hamanaka in mid-January 2011 were positive
for the H5N1 virus, the 6th case of a wild bird infected with bird
flu in Hokkaido.

In Aichi Prefecture, 2 quail farms in Toyohashi resumed shipping
quail eggs for the 1st time in 6 days after a ban was put in place on
transporting birds and eggs following the outbreak of highly
pathogenic avian influenza at a chicken farm there.

The prefecture authorized quail farms within a 10-km radius of where
the bird flu had broken out to restart egg shipments after confirming
the farms had taken measures to prevent infection.

--
Communicated by:
ProMED-mail <promed@promedmail.org>

[Japan submitted to the OIE its 6th follow-up report on HPAI H5N1 in
poultry on 2 Feb 2011 (today), notifying 5 new outbreaks (one each in
Kagoshima and Aichi; 3 in Miyazaki), their epidemiological diagnosis,
and comments.

The following epidemiological comments are derived from the said
follow-up report:

"1. Izumi city, Kagoshima:
On 25 Jan 2011, poultry were tested positive for influenza A with
rapid test at a farm in Izumi city in Kagoshima prefecture. Virus was
identified as H5 with RT-PCR on 26 Jan 2011 and as H5N1 on 29 Jan
2011. Mandatory movement restriction has been enforced within 10 km
around the affected farm since 25 Jan 2011. All of the poultry at the
farm was destroyed by 26 Jan 2011.

2. Toyohashi city, Aichi:
On 26 Jan 2011, poultry were tested positive for influenza A with
rapid test at a farm in Toyohashi city in Aichi prefecture. Virus was
identified as H5 with RT-PCR on 27 Jan 2011 and as H5N1 on 30 Jan
2011. Mandatory movement restriction has been enforced within 10 km
around the affected farm since 26 Jan 2011. All of the poultry at the
farm was destroyed by 31 Jan 2011.

3. Tsuno-cho Koyu-gun, Miyazaki:
On 27 Jan 2011, poultry from a farm in Tsuno-cho Koyu-gun were tested
positive for influenza A with rapid test at a poultry abattoir in
Kawaminami-cho. Virus was identified as H5 with RT-PCR on 28 Jan 2011
and as H5N1 on 31 Jan 2011. Mandatory movement restriction has been
enforced within 10 km around the affected farm and within 5 km around
the poultry abattoir since 27 Jan 2011. All of the poultry at the
farm was destroyed by 28 Jan 2011.

4. Kawaminami-cho Koyu-gun, Miyazaki:
On 28 Jan 2011, poultry were tested positive for influenza A with
rapid test at a farm in Kawaminami-cho Koyu-gun in Miyazaki
prefecture. Virus was identified as H5 with RT-PCR on 29 Jan 2011.
Mandatory movement restriction has been enforced within 10 km around
the affected farm since 28 Jan 2011. All of the poultry at the farm
was destroyed by 29 Jan 2011.

5. Kitakawa-cho Nobeoka city, Miyazaki:
On 28 Jan 2011, poultry were tested positive for influenza A with
rapid test at a farm in Kitakawa-cho Nobeoka city in Miyazaki
prefecture. Virus was identified as H5 with RT-PCR on 29 Jan 2011.
Mandatory movement restriction has been enforced within 10 km around
the affected farm since 28 Jan 2011. All of the poultry at the farm
was destroyed by 29 Jan 2011."

A summary of the event since its start on 27 Nov 2010, including a
map with the accumulated (9) outbreaks, is available at
<http://web.oie.int/wahis/public.php?page=event_summary&reportid=9999>.
- Mod.AS]

[see also:
Avian influenza (10): Japan (AI), poultry 20110129.0349
Avian influenza (08): Japan (MZ), H5N1, poultry, wild birds 20110125.0303
Avian influenza (06): Japan (FS), H5N1, wild birds 20110121.0245
2010
----
Avian influenza, poultry vs migratory birds (07): Japan 20101227.4562
Avian influenza (64): Japan (TY) HPAI H5, OIE 20101221.4492
Avian influenza (58): Japan (SM) HPAI H5N1 20101206.4366
Avian influenza (56): Japan (SM) HPAI H5, OIE 20101202.4330
Avian influenza (55): Japan (SM) susp, RFI 20101130.4303]
......................................................arn/msp/lm

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PostPosted: Thu Feb 03, 2011 8:43 am 
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http://web.oie.int/wahis/public.php?pag ... rtid=10205

Information received on 02/02/2011 from Dr Toshiro Kawashima, CVO, Animal Health Division, Ministry of Agriculture, Forestry and Fisheries, Tokyo , Japan

Summary

Report type Follow-up report No. 6
Start date 27/11/2010
Date of first confirmation of the event 29/11/2010
Report date 02/02/2011
Date submitted to OIE 02/02/2011
Reason for notification Reoccurrence of a listed disease
Date of previous occurrence 01/04/2009
Manifestation of disease Clinical disease
Causal agent Highly pathogenic avian influenza virus
Serotype H5N1
Nature of diagnosis Clinical, Laboratory (basic), Laboratory (advanced), Necropsy
This event pertains to the whole country
Related reports Immediate notification (02/12/2010)
Follow-up report No. 1 (09/12/2010)
Follow-up report No. 2 (16/12/2010)
Follow-up report No. 3 (21/12/2010)
Follow-up report No. 4 (27/12/2010)
Follow-up report No. 5 (23/01/2011)
Follow-up report No. 6 (02/02/2011)


New outbreaksOutbreak 1 Nobeoka city, MIYAZAKI
Date of start of the outbreak 28/01/2011
Outbreak status Resolved (30/01/2011)
Epidemiological unit Farm
Affected animals Species Susceptible Cases Deaths Destroyed Slaughtered
Birds 6600 67 67 6533 0

Outbreak 2 Tsuno-cho Koyu-gun, MIYAZAKI
Date of start of the outbreak 27/01/2011
Outbreak status Resolved (29/01/2011)
Epidemiological unit Farm
Affected animals Species Susceptible Cases Deaths Destroyed Slaughtered
Birds 10401 300 300 10101 0

Outbreak 3 Izumi city, KAGOSHIMA
Date of start of the outbreak 25/01/2011
Outbreak status Resolved (26/01/2011)
Epidemiological unit Farm
Affected animals Species Susceptible Cases Deaths Destroyed Slaughtered
Birds 8600 84 84 8516 0

Outbreak 4 Toyohashi city, AICHI
Date of start of the outbreak 26/01/2011
Outbreak status Continuing (or date resolved not provided)
Epidemiological unit Farm
Affected animals Species Susceptible Cases Deaths Destroyed Slaughtered
Birds 150000 120 120 149880 0

Outbreak 5 Kawaminami-cho Koyu-gun, MIYAZAKI
Date of start of the outbreak 28/01/2011
Outbreak status Resolved (31/01/2011)
Epidemiological unit Farm
Affected animals Species Susceptible Cases Deaths Destroyed Slaughtered
Birds 92000 428 428 91572 0

Summary of outbreaks Total outbreaks: 5
Total animals affected Species Susceptible Cases Deaths Destroyed Slaughtered
Birds 267601 999 999 266602 0

Outbreak statistics Species Apparent morbidity rate Apparent mortality rate Apparent case fatality rate Proportion susceptible animals lost*
Birds 0.37% 0.37% 100.00% 100.00%

* Removed from the susceptible population through death, destruction and/or slaughter


EpidemiologySource of the outbreak(s) or origin of infection Unknown or inconclusive

Epidemiological comments Izumi city, Kagoshima:
On 25 January 2011, poultry were tested positive for influenza A with rapid test at a farm in Izumi city in Kagoshima prefecture. Virus was identified as H5 with RT-PCR on 26 January and as H5N1 on 29 January. Mandatory movement restriction has been enforced within 10 km around the affected farm since 25 January 2011. All of the poultry at the farm was destroyed by 26 January.
Toyohashi city, Aichi:
On 26 January 2011, poultry were tested positive for influenza A with rapid test at a farm in Toyohashi city in Aichi prefecture. Virus was identified as H5 with RT-PCR on 27 January and as H5N1 on 30 January. Mandatory movement restriction has been enforced within 10 km around the affected farm since 26 January 2011. All of the poultry at the farm was destroyed by 31 January.
Tsuno-cho Koyu-gun, Miyazaki:
On 27 January 2011, poultry from a farm in Tsuno-cho Koyu-gun were tested positive for influenza A with rapid test at a poultry abattoir in Kawaminami-cho. Virus was identified as H5 with RT-PCR on 28 January and as H5N1 on 31 January. Mandatory movement restriction has been enforced within 10 km around the affected farm and within 5 km around the poultry abattoir since 27 January 2011. All of the poultry at the farm was destroyed by 28 January.
Kawaminami-cho Koyu-gun, Miyazaki:
On 28 January 2011, poultry were tested positive for influenza A with rapid test at a farm in Kawaminami-cho Koyu-gun in Miyazaki prefecture. Virus was identified as H5 with RT-PCR on 29 January. Mandatory movement restriction has been enforced within 10 km around the affected farm since 28 January 2011. All of the poultry at the farm was destroyed by 29 January.
Kitakawa-cho Nobeoka city, Miyazaki:
On 28 January 2011, poultry were tested positive for influenza A with rapid test at a farm in Kitakawa-cho Nobeoka city in Miyazaki prefecture. Virus was identified as H5 with RT-PCR on 29 January. Mandatory movement restriction has been enforced within 10 km around the affected farm since 28 January 2011. All of the poultry at the farm was destroyed by 29 January.


Control measuresMeasures applied Stamping out
Movement control inside the country
Screening
Disinfection of infected premises/establishment(s)
No vaccination
No treatment of affected animals

Measures to be applied No other measures



Diagnostic test resultsLaboratory name and type Aichi Livestock Hygiene Centre (Local laboratory)
Tests and results Species Test Test date Result
Birds reverse transcription - polymerase chain reaction (RT-PCR) 27/01/2011 Positive

Laboratory name and type Kagoshima Livestock Hygiene Centre (Local laboratory)
Tests and results Species Test Test date Result
Birds reverse transcription - polymerase chain reaction (RT-PCR) 26/01/2011 Positive

Laboratory name and type Miyazaki Livestock Hygiene Centre (Local laboratory)
Tests and results Species Test Test date Result
Birds reverse transcription - polymerase chain reaction (RT-PCR) 28/01/2011 Positive
Birds reverse transcription - polymerase chain reaction (RT-PCR) 29/01/2011 Positive

Laboratory name and type National Institute of Animal Health (National laboratory)
Tests and results Species Test Test date Result
Birds gene sequencing 26/01/2011 Positive
Birds gene sequencing 28/01/2011 Positive
Birds gene sequencing 29/01/2011 Positive
Birds gene sequencing 31/01/2011 Positive
Birds haemagglutination inhibition test (HIT) 28/01/2011 Positive
Birds haemagglutination inhibition test (HIT) 29/01/2011 Positive
Birds haemagglutination inhibition test (HIT) 30/01/2011 Positive
Birds haemagglutination inhibition test (HIT) 31/01/2011 Positive
Birds neuraminidase inhibition assay 27/01/2011 Positive
Birds neuraminidase inhibition assay 29/01/2011 Positive
Birds neuraminidase inhibition assay 30/01/2011 Positive
Birds neuraminidase inhibition assay 31/01/2011 Positive



Future ReportingThe event is continuing. Weekly follow-up reports will be submitted.

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PostPosted: Thu Feb 03, 2011 9:17 am 
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Commentary

http://www.recombinomics.com/News/02031 ... Japan.html

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PostPosted: Thu Feb 03, 2011 11:23 am 
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Joined: Thu Dec 10, 2009 1:14 pm
Posts: 548
Ye, this change is of real concern and it's also significant the evolution towards a more able H5 to begin transmitting human to human. This hightlights the importance of timely release of sequences.

I strongly suspect that in the coming months we will see large clusters of bird flu in human population and possibly the next pandemic unfolding.

Thank you for sharing it with the scientific community.

Thank you for your good work, Henry.


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