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niman
PostPosted: Sat Feb 11, 2012 5:00 am 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27558
Location: Pittsburgh, PA USA
niman wrote:
niman wrote:
niman wrote:
AVIAN INFLUENZA (14): H5N1, WHO MEETING ANNOUNCEMENT
****************************************************

[The WHO is concerned that the Pandemic Influenza Preparedness (PIP) Framework, a multi-country agreement ratified last spring 2011, has not been damaged by this research work. That apart, perhaps the most interesting information in this announcement are the facts that the avian A/(H5N1) influenza virus used by the Dutch group of Ron Fouchier at the Erasmus Medical Center in Rotterdam, the Netherlands was an isolate obtained from Indonesia, whereas the virus used by Yoshihiro Kawaoka at the University of Wisconsin-Madison had been isolated in Viet Nam. The outcome of this meeting may shed light on the similarity of these 2 isolates and the extent to which this may have determined the outcome of the projects. - Mod.CP]


Rather bizarre comment at ProMED. Although the two groups independently acheived efficient transmission, the approaches were VERY different. Fouchier used an isolate from Indonesia, which would be clade 2.1 which has never been isolated outside of Indonesia. Kawaoka has published papers on reassortants between an H5N1 isolate from Hanoi, A/Vietnam/HN31604/2009, which is clade 2.3.4.2 and H1N1pdm09 (A/California/04/2009) and the censored paper in Nature descibes transmission that does not kill ferrets, in contrast to Fouchier, who creates and evolved H5N1 which transmits and kills.

Thus, it is unlikely that the two distinct approaches produce the same set of receptor binding domain changes.

Sequences from the initial clade 2.1 cases in Indonesia have been known for years. The sequence from first case (38M), A/Indonesia/5/05, has been at Genbank since 2007, and anyone with an internet connection can get the HA sequence
http://www.ncbi.nlm.nih.gov/nuccore/EF541394.1
LOCUS EF541394 1729 bp cRNA linear VRL 01-MAY-2008
DEFINITION Influenza A virus (A/Indonesia/5/05(H5N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION EF541394
VERSION EF541394.1 GI:145284449
KEYWORDS .
SOURCE Influenza A virus (A/Indonesia/5/2005(H5N1))
ORGANISM Influenza A virus (A/Indonesia/5/2005(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1729)
AUTHORS Smith,C.
TITLE Direct Submission
JOURNAL Submitted (19-MAR-2007) Centers for Disease Control and Prevention,
1600 Clifton Road, Mailstop G-16, Atlanta, GA 30329, USA
COMMENT Sequence entered by GenBank staff on behalf of submitter.
FEATURES Location/Qualifiers
source 1..1729
/organism="Influenza A virus (A/Indonesia/5/2005(H5N1))"
/mol_type="viral cRNA"
/strain="A/Indonesia/5/05"
/serotype="H5N1"
/isolation_source="38 year-old male"
/host="Homo sapiens"
/db_xref="taxon:400788"
/segment="4"
/country="Indonesia"
/collection_date="2005"
/note="passage level E"
misc_feature 1..1729
/db_xref="IRD:EF541394"
gene 9..1715
/gene="HA"
CDS 9..1715
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ABP51969.1"
/db_xref="GI:145284450"
or any of the 8 gene segments
http://www.ncbi.nlm.nih.gov/nuccore/?term=txid400788

Initial cluster included 3 fatal cases, which were initially denied and not all three familiy members have been offially classified as confirmed cases, although the cluster clearly involved human to human tranmission and the sequence from the index case was used as a pandemic vaccine target.

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niman
PostPosted: Sat Feb 11, 2012 5:07 am 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27558
Location: Pittsburgh, PA USA
niman wrote:
niman wrote:
niman wrote:
AVIAN INFLUENZA (14): H5N1, WHO MEETING ANNOUNCEMENT
****************************************************

[The WHO is concerned that the Pandemic Influenza Preparedness (PIP) Framework, a multi-country agreement ratified last spring 2011, has not been damaged by this research work. That apart, perhaps the most interesting information in this announcement are the facts that the avian A/(H5N1) influenza virus used by the Dutch group of Ron Fouchier at the Erasmus Medical Center in Rotterdam, the Netherlands was an isolate obtained from Indonesia, whereas the virus used by Yoshihiro Kawaoka at the University of Wisconsin-Madison had been isolated in Viet Nam. The outcome of this meeting may shed light on the similarity of these 2 isolates and the extent to which this may have determined the outcome of the projects. - Mod.CP]


Rather bizarre comment at ProMED. Although the two groups independently acheived efficient transmission, the approaches were VERY different. Fouchier used an isolate from Indonesia, which would be clade 2.1 which has never been isolated outside of Indonesia. Kawaoka has published papers on reassortants between an H5N1 isolate from Hanoi, A/Vietnam/HN31604/2009, which is clade 2.3.4.2 and H1N1pdm09 (A/California/04/2009) and the censored paper in Nature descibes transmission that does not kill ferrets, in contrast to Fouchier, who creates and evolved H5N1 which transmits and kills.

Thus, it is unlikely that the two distinct approaches produce the same set of receptor binding domain changes.

Sequences from the initial clade 2.1 cases in Indonesia have been known for years. The sequence from first case (38M), A/Indonesia/5/05, has been at Genbank since 2007, and anyone with an internet connection can get the HA sequence
http://www.ncbi.nlm.nih.gov/nuccore/EF541394.1
LOCUS EF541394 1729 bp cRNA linear VRL 01-MAY-2008
DEFINITION Influenza A virus (A/Indonesia/5/05(H5N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION EF541394
VERSION EF541394.1 GI:145284449
KEYWORDS .
SOURCE Influenza A virus (A/Indonesia/5/2005(H5N1))
ORGANISM Influenza A virus (A/Indonesia/5/2005(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1729)
AUTHORS Smith,C.
TITLE Direct Submission
JOURNAL Submitted (19-MAR-2007) Centers for Disease Control and Prevention,
1600 Clifton Road, Mailstop G-16, Atlanta, GA 30329, USA
COMMENT Sequence entered by GenBank staff on behalf of submitter.
FEATURES Location/Qualifiers
source 1..1729
/organism="Influenza A virus (A/Indonesia/5/2005(H5N1))"
/mol_type="viral cRNA"
/strain="A/Indonesia/5/05"
/serotype="H5N1"
/isolation_source="38 year-old male"
/host="Homo sapiens"
/db_xref="taxon:400788"
/segment="4"
/country="Indonesia"
/collection_date="2005"
/note="passage level E"
misc_feature 1..1729
/db_xref="IRD:EF541394"
gene 9..1715
/gene="HA"
CDS 9..1715
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ABP51969.1"
/db_xref="GI:145284450"
or any of the 8 gene segments
http://www.ncbi.nlm.nih.gov/nuccore/?term=txid400788

H5N1Bird Flu Exported to Indonesia from Hong Kong or India?
Recombinomics Commentary
July 13, 2005

A father and his little daughter have died at a hospital in the western Java town of Tangerang from suspected avian influenza, local media reports said Wednesday.

Iwan Siswara Rafei, a staff with the Supreme Audit Body (BPK), died at the Siloam Gleneagles Hospital Tuesday afternoon after showing bird flu symptoms, reported the Detikcom online news service.

His daughter Thalita Nurul Azizah died earlier Saturday with similar symptoms, it said. Another daughter Sabrina Nurul Aisyah, who was first detected with the symptoms, is still under intensive treatment at the same hospital, around 20 km south of Jakarta.

She suffers high fever and respiratory problems.

The reports were first released by Metro TV, which reported that the family suffered the disease after their trip to Hong Kong and India.
The above familial cluster of bird flu is of concern for many reasons. Since a family of three has symptoms, human-to-human transmission is a major consideration.........
http://www.recombinomics.com/News/07130 ... nesia.html

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niman
PostPosted: Sat Feb 11, 2012 5:11 am 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27558
Location: Pittsburgh, PA USA
niman wrote:
niman wrote:
niman wrote:
AVIAN INFLUENZA (14): H5N1, WHO MEETING ANNOUNCEMENT
****************************************************

[The WHO is concerned that the Pandemic Influenza Preparedness (PIP) Framework, a multi-country agreement ratified last spring 2011, has not been damaged by this research work. That apart, perhaps the most interesting information in this announcement are the facts that the avian A/(H5N1) influenza virus used by the Dutch group of Ron Fouchier at the Erasmus Medical Center in Rotterdam, the Netherlands was an isolate obtained from Indonesia, whereas the virus used by Yoshihiro Kawaoka at the University of Wisconsin-Madison had been isolated in Viet Nam. The outcome of this meeting may shed light on the similarity of these 2 isolates and the extent to which this may have determined the outcome of the projects. - Mod.CP]


Rather bizarre comment at ProMED. Although the two groups independently acheived efficient transmission, the approaches were VERY different. Fouchier used an isolate from Indonesia, which would be clade 2.1 which has never been isolated outside of Indonesia. Kawaoka has published papers on reassortants between an H5N1 isolate from Hanoi, A/Vietnam/HN31604/2009, which is clade 2.3.4.2 and H1N1pdm09 (A/California/04/2009) and the censored paper in Nature descibes transmission that does not kill ferrets, in contrast to Fouchier, who creates and evolved H5N1 which transmits and kills.

Thus, it is unlikely that the two distinct approaches produce the same set of receptor binding domain changes.

Sequences from the initial clade 2.1 cases in Indonesia have been known for years. The sequence from first case (38M), A/Indonesia/5/05, has been at Genbank since 2007, and anyone with an internet connection can get the HA sequence
http://www.ncbi.nlm.nih.gov/nuccore/EF541394.1
LOCUS EF541394 1729 bp cRNA linear VRL 01-MAY-2008
DEFINITION Influenza A virus (A/Indonesia/5/05(H5N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION EF541394
VERSION EF541394.1 GI:145284449
KEYWORDS .
SOURCE Influenza A virus (A/Indonesia/5/2005(H5N1))
ORGANISM Influenza A virus (A/Indonesia/5/2005(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1729)
AUTHORS Smith,C.
TITLE Direct Submission
JOURNAL Submitted (19-MAR-2007) Centers for Disease Control and Prevention,
1600 Clifton Road, Mailstop G-16, Atlanta, GA 30329, USA
COMMENT Sequence entered by GenBank staff on behalf of submitter.
FEATURES Location/Qualifiers
source 1..1729
/organism="Influenza A virus (A/Indonesia/5/2005(H5N1))"
/mol_type="viral cRNA"
/strain="A/Indonesia/5/05"
/serotype="H5N1"
/isolation_source="38 year-old male"
/host="Homo sapiens"
/db_xref="taxon:400788"
/segment="4"
/country="Indonesia"
/collection_date="2005"
/note="passage level E"
misc_feature 1..1729
/db_xref="IRD:EF541394"
gene 9..1715
/gene="HA"
CDS 9..1715
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ABP51969.1"
/db_xref="GI:145284450"
or any of the 8 gene segments
http://www.ncbi.nlm.nih.gov/nuccore/?term=txid400788

Fatal H5N1 Bird Flu in Suburban Jakarta Family Confirmed
Recombinomics Commentary
July 20, 2005

Health Minister Siti Fadilah Supari told reporters lab tests from Hong Kong showed the 38-year-old man and his two children, 9 and 1, had the deadly H5N1 strain of bird flu.

She said the tests done in Hong Kong were based on specimens from the father and one of the daughters, but it could be concluded that all three had died of the deadly H5N1 strain of bird flu.

"We don't distinguish between the three," she said.
The above comments confirm initial reports of fatal H5N1 in a three member family cluster. The disease onset dates were bimodal, strongly suggesting human-to-human transmission within the family. This distribution is found in virtually every familial cluster in Vietnam, Thailand, and Cambodia, further confirming widespread human-to-human transmission of fatal bird flu.........
http://www.recombinomics.com/News/07200 ... irmed.html

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 Profile  
 
niman
PostPosted: Sat Feb 11, 2012 5:17 am 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27558
Location: Pittsburgh, PA USA
niman wrote:
niman wrote:
niman wrote:
AVIAN INFLUENZA (14): H5N1, WHO MEETING ANNOUNCEMENT
****************************************************

[The WHO is concerned that the Pandemic Influenza Preparedness (PIP) Framework, a multi-country agreement ratified last spring 2011, has not been damaged by this research work. That apart, perhaps the most interesting information in this announcement are the facts that the avian A/(H5N1) influenza virus used by the Dutch group of Ron Fouchier at the Erasmus Medical Center in Rotterdam, the Netherlands was an isolate obtained from Indonesia, whereas the virus used by Yoshihiro Kawaoka at the University of Wisconsin-Madison had been isolated in Viet Nam. The outcome of this meeting may shed light on the similarity of these 2 isolates and the extent to which this may have determined the outcome of the projects. - Mod.CP]


Rather bizarre comment at ProMED. Although the two groups independently acheived efficient transmission, the approaches were VERY different. Fouchier used an isolate from Indonesia, which would be clade 2.1 which has never been isolated outside of Indonesia. Kawaoka has published papers on reassortants between an H5N1 isolate from Hanoi, A/Vietnam/HN31604/2009, which is clade 2.3.4.2 and H1N1pdm09 (A/California/04/2009) and the censored paper in Nature descibes transmission that does not kill ferrets, in contrast to Fouchier, who creates and evolved H5N1 which transmits and kills.

Thus, it is unlikely that the two distinct approaches produce the same set of receptor binding domain changes.

Sequences from the initial clade 2.1 cases in Indonesia have been known for years. The sequence from first case (38M), A/Indonesia/5/05, has been at Genbank since 2007, and anyone with an internet connection can get the HA sequence
http://www.ncbi.nlm.nih.gov/nuccore/EF541394.1
LOCUS EF541394 1729 bp cRNA linear VRL 01-MAY-2008
DEFINITION Influenza A virus (A/Indonesia/5/05(H5N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION EF541394
VERSION EF541394.1 GI:145284449
KEYWORDS .
SOURCE Influenza A virus (A/Indonesia/5/2005(H5N1))
ORGANISM Influenza A virus (A/Indonesia/5/2005(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1729)
AUTHORS Smith,C.
TITLE Direct Submission
JOURNAL Submitted (19-MAR-2007) Centers for Disease Control and Prevention,
1600 Clifton Road, Mailstop G-16, Atlanta, GA 30329, USA
COMMENT Sequence entered by GenBank staff on behalf of submitter.
FEATURES Location/Qualifiers
source 1..1729
/organism="Influenza A virus (A/Indonesia/5/2005(H5N1))"
/mol_type="viral cRNA"
/strain="A/Indonesia/5/05"
/serotype="H5N1"
/isolation_source="38 year-old male"
/host="Homo sapiens"
/db_xref="taxon:400788"
/segment="4"
/country="Indonesia"
/collection_date="2005"
/note="passage level E"
misc_feature 1..1729
/db_xref="IRD:EF541394"
gene 9..1715
/gene="HA"
CDS 9..1715
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ABP51969.1"
/db_xref="GI:145284450"
or any of the 8 gene segments
http://www.ncbi.nlm.nih.gov/nuccore/?term=txid400788

United States Selects Indonesian H5N1 for Pandemic Vaccine

Recombinomics Commentary
March 11, 2006

The selection of a new pandemic vaccine candidate by the United States is not a surprise. When initial results of the first candidate vaccine was announced, it was clear that H5N1 was evolving away from that target, which was a 2004 isolate from Vietnam. The Qinghai version of H5N1 was spreading rapidly in Russia, Kazakhstan, and Mongolia, and further spread was anticipated.

However, an Indonesian strain has been selected as the next target. It is unlikely that a vaccine against an Indonesian isolate would offer significant protection for the Qinghai H5N1 strain of bird flu........
http://www.recombinomics.com/News/03110 ... nesia.html

_________________
www.twitter.com/hniman
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 Profile  
 
niman
PostPosted: Sat Feb 11, 2012 5:21 am 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27558
Location: Pittsburgh, PA USA
niman wrote:
niman wrote:
niman wrote:
AVIAN INFLUENZA (14): H5N1, WHO MEETING ANNOUNCEMENT
****************************************************

[The WHO is concerned that the Pandemic Influenza Preparedness (PIP) Framework, a multi-country agreement ratified last spring 2011, has not been damaged by this research work. That apart, perhaps the most interesting information in this announcement are the facts that the avian A/(H5N1) influenza virus used by the Dutch group of Ron Fouchier at the Erasmus Medical Center in Rotterdam, the Netherlands was an isolate obtained from Indonesia, whereas the virus used by Yoshihiro Kawaoka at the University of Wisconsin-Madison had been isolated in Viet Nam. The outcome of this meeting may shed light on the similarity of these 2 isolates and the extent to which this may have determined the outcome of the projects. - Mod.CP]


Rather bizarre comment at ProMED. Although the two groups independently acheived efficient transmission, the approaches were VERY different. Fouchier used an isolate from Indonesia, which would be clade 2.1 which has never been isolated outside of Indonesia. Kawaoka has published papers on reassortants between an H5N1 isolate from Hanoi, A/Vietnam/HN31604/2009, which is clade 2.3.4.2 and H1N1pdm09 (A/California/04/2009) and the censored paper in Nature descibes transmission that does not kill ferrets, in contrast to Fouchier, who creates and evolved H5N1 which transmits and kills.

Thus, it is unlikely that the two distinct approaches produce the same set of receptor binding domain changes.

Sequences from the initial clade 2.1 cases in Indonesia have been known for years. The sequence from first case (38M), A/Indonesia/5/05, has been at Genbank since 2007, and anyone with an internet connection can get the HA sequence
http://www.ncbi.nlm.nih.gov/nuccore/EF541394.1
LOCUS EF541394 1729 bp cRNA linear VRL 01-MAY-2008
DEFINITION Influenza A virus (A/Indonesia/5/05(H5N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION EF541394
VERSION EF541394.1 GI:145284449
KEYWORDS .
SOURCE Influenza A virus (A/Indonesia/5/2005(H5N1))
ORGANISM Influenza A virus (A/Indonesia/5/2005(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1729)
AUTHORS Smith,C.
TITLE Direct Submission
JOURNAL Submitted (19-MAR-2007) Centers for Disease Control and Prevention,
1600 Clifton Road, Mailstop G-16, Atlanta, GA 30329, USA
COMMENT Sequence entered by GenBank staff on behalf of submitter.
FEATURES Location/Qualifiers
source 1..1729
/organism="Influenza A virus (A/Indonesia/5/2005(H5N1))"
/mol_type="viral cRNA"
/strain="A/Indonesia/5/05"
/serotype="H5N1"
/isolation_source="38 year-old male"
/host="Homo sapiens"
/db_xref="taxon:400788"
/segment="4"
/country="Indonesia"
/collection_date="2005"
/note="passage level E"
misc_feature 1..1729
/db_xref="IRD:EF541394"
gene 9..1715
/gene="HA"
CDS 9..1715
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ABP51969.1"
/db_xref="GI:145284450"
or any of the 8 gene segments
http://www.ncbi.nlm.nih.gov/nuccore/?term=txid400788

H5N1 Indonesian Pandemic Vaccine Sequence Released

Recombinomics Commentary
March 26, 2006

The human H5N1 sequence selected for the next US pandemic vaccine target was just released at Los Alamos (A/Indonesia/5/2005). It is from the father of the index case in Indonesia. Samples from the index case and her sister were not collected, but H5N1 was isolated from her father. Media reports of the familial cluster were in mid-July, and the sequences of the HA and NA were deposited at Los Alamos by the CDC on August 1. 2005 at 9:29 GMT. The sequence was just updated and released to the public, although the other 6 gene segments are still locked up in the password protected side of the database, along with dozens of other H5N1 sequences from around the world.............
http://www.recombinomics.com/News/03260 ... uence.html

_________________
www.twitter.com/hniman
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 Profile  
 
niman
PostPosted: Sat Feb 11, 2012 5:25 am 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27558
Location: Pittsburgh, PA USA
niman wrote:
niman wrote:
niman wrote:
AVIAN INFLUENZA (14): H5N1, WHO MEETING ANNOUNCEMENT
****************************************************

[The WHO is concerned that the Pandemic Influenza Preparedness (PIP) Framework, a multi-country agreement ratified last spring 2011, has not been damaged by this research work. That apart, perhaps the most interesting information in this announcement are the facts that the avian A/(H5N1) influenza virus used by the Dutch group of Ron Fouchier at the Erasmus Medical Center in Rotterdam, the Netherlands was an isolate obtained from Indonesia, whereas the virus used by Yoshihiro Kawaoka at the University of Wisconsin-Madison had been isolated in Viet Nam. The outcome of this meeting may shed light on the similarity of these 2 isolates and the extent to which this may have determined the outcome of the projects. - Mod.CP]


Rather bizarre comment at ProMED. Although the two groups independently acheived efficient transmission, the approaches were VERY different. Fouchier used an isolate from Indonesia, which would be clade 2.1 which has never been isolated outside of Indonesia. Kawaoka has published papers on reassortants between an H5N1 isolate from Hanoi, A/Vietnam/HN31604/2009, which is clade 2.3.4.2 and H1N1pdm09 (A/California/04/2009) and the censored paper in Nature descibes transmission that does not kill ferrets, in contrast to Fouchier, who creates and evolved H5N1 which transmits and kills.

Thus, it is unlikely that the two distinct approaches produce the same set of receptor binding domain changes.

Sequences from the initial clade 2.1 cases in Indonesia have been known for years. The sequence from first case (38M), A/Indonesia/5/05, has been at Genbank since 2007, and anyone with an internet connection can get the HA sequence
http://www.ncbi.nlm.nih.gov/nuccore/EF541394.1
LOCUS EF541394 1729 bp cRNA linear VRL 01-MAY-2008
DEFINITION Influenza A virus (A/Indonesia/5/05(H5N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION EF541394
VERSION EF541394.1 GI:145284449
KEYWORDS .
SOURCE Influenza A virus (A/Indonesia/5/2005(H5N1))
ORGANISM Influenza A virus (A/Indonesia/5/2005(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1729)
AUTHORS Smith,C.
TITLE Direct Submission
JOURNAL Submitted (19-MAR-2007) Centers for Disease Control and Prevention,
1600 Clifton Road, Mailstop G-16, Atlanta, GA 30329, USA
COMMENT Sequence entered by GenBank staff on behalf of submitter.
FEATURES Location/Qualifiers
source 1..1729
/organism="Influenza A virus (A/Indonesia/5/2005(H5N1))"
/mol_type="viral cRNA"
/strain="A/Indonesia/5/05"
/serotype="H5N1"
/isolation_source="38 year-old male"
/host="Homo sapiens"
/db_xref="taxon:400788"
/segment="4"
/country="Indonesia"
/collection_date="2005"
/note="passage level E"
misc_feature 1..1729
/db_xref="IRD:EF541394"
gene 9..1715
/gene="HA"
CDS 9..1715
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ABP51969.1"
/db_xref="GI:145284450"
or any of the 8 gene segments
http://www.ncbi.nlm.nih.gov/nuccore/?term=txid400788

Indonesia Pledges to Release H5N1 Bird Flu Sequences
Recombinomics Commentary
August 3, 2006

Indonesia's health minister, Siti Fadilah Supari, said the country will deposit avian flu virus data in GenBank, a public database of genetic sequences, according to today's Bloomberg report. She said data from the recent family case cluster in Sumatra involving person-to-person transmission would be included.

The journal Nature reported Jul 28 that until very recently, Indonesia had shared few, if any, H5N1 virus samples from birds over the past year.

The above comments indicate Indonesia has pledge to release the H5N1 sequences in the private WHO database at Los Alamos. These sequences can be released by simply removing the password protection. This was recently done for the human H5N1 sequences from Turkey, which were sumitted by the WHO H5 group and have the characteristic ISDN numbers assigned at Los Alamos.. Earlier, this was also done for H5N1 from the first human case in Indonesia. Although that sequence was deposited in the WHO data base on August 1, 2005, it was not released until March 25, 2006..........
http://www.recombinomics.com/News/08030 ... ledge.html

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niman
PostPosted: Sat Feb 11, 2012 5:30 am 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27558
Location: Pittsburgh, PA USA
niman wrote:
niman wrote:
niman wrote:
AVIAN INFLUENZA (14): H5N1, WHO MEETING ANNOUNCEMENT
****************************************************

[The WHO is concerned that the Pandemic Influenza Preparedness (PIP) Framework, a multi-country agreement ratified last spring 2011, has not been damaged by this research work. That apart, perhaps the most interesting information in this announcement are the facts that the avian A/(H5N1) influenza virus used by the Dutch group of Ron Fouchier at the Erasmus Medical Center in Rotterdam, the Netherlands was an isolate obtained from Indonesia, whereas the virus used by Yoshihiro Kawaoka at the University of Wisconsin-Madison had been isolated in Viet Nam. The outcome of this meeting may shed light on the similarity of these 2 isolates and the extent to which this may have determined the outcome of the projects. - Mod.CP]


Rather bizarre comment at ProMED. Although the two groups independently acheived efficient transmission, the approaches were VERY different. Fouchier used an isolate from Indonesia, which would be clade 2.1 which has never been isolated outside of Indonesia. Kawaoka has published papers on reassortants between an H5N1 isolate from Hanoi, A/Vietnam/HN31604/2009, which is clade 2.3.4.2 and H1N1pdm09 (A/California/04/2009) and the censored paper in Nature descibes transmission that does not kill ferrets, in contrast to Fouchier, who creates and evolved H5N1 which transmits and kills.

Thus, it is unlikely that the two distinct approaches produce the same set of receptor binding domain changes.

Sequences from the initial clade 2.1 cases in Indonesia have been known for years. The sequence from first case (38M), A/Indonesia/5/05, has been at Genbank since 2007, and anyone with an internet connection can get the HA sequence
http://www.ncbi.nlm.nih.gov/nuccore/EF541394.1
LOCUS EF541394 1729 bp cRNA linear VRL 01-MAY-2008
DEFINITION Influenza A virus (A/Indonesia/5/05(H5N1)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION EF541394
VERSION EF541394.1 GI:145284449
KEYWORDS .
SOURCE Influenza A virus (A/Indonesia/5/2005(H5N1))
ORGANISM Influenza A virus (A/Indonesia/5/2005(H5N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1729)
AUTHORS Smith,C.
TITLE Direct Submission
JOURNAL Submitted (19-MAR-2007) Centers for Disease Control and Prevention,
1600 Clifton Road, Mailstop G-16, Atlanta, GA 30329, USA
COMMENT Sequence entered by GenBank staff on behalf of submitter.
FEATURES Location/Qualifiers
source 1..1729
/organism="Influenza A virus (A/Indonesia/5/2005(H5N1))"
/mol_type="viral cRNA"
/strain="A/Indonesia/5/05"
/serotype="H5N1"
/isolation_source="38 year-old male"
/host="Homo sapiens"
/db_xref="taxon:400788"
/segment="4"
/country="Indonesia"
/collection_date="2005"
/note="passage level E"
misc_feature 1..1729
/db_xref="IRD:EF541394"
gene 9..1715
/gene="HA"
CDS 9..1715
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ABP51969.1"
/db_xref="GI:145284450"
or any of the 8 gene segments
http://www.ncbi.nlm.nih.gov/nuccore/?term=txid400788


Human H5N1 Indonesian Sequences Available at Los Alamos

Recombinomics Commentary
August 4, 2006

Yesterday Indonesia pledged to release the H5N1 human sequence sequestered in the WHO private database. Today the password protection on the sequences was removed and the sequences became publicly available. Analysis of the sequences can help determine origins and predict targets for vaccines. Orgins can be traced by monitoring informative polymorphisms.

Below is one such series, showing the similarity between the various human isolates and relationship to other H5N1 bird flu sequences at Genbank or Los Alamos.


ISDN136817 A/Feline/Indonesia/CDC1/2006 2006 H5N1
ISDN136812 A/Indonesia/CDC326/2006 2006 H5N1
ISDN136810 A/Indonesia/CDC326N/2006 2006 H5N1
ISDN136811 A/Indonesia/CDC326N2/2006 2006 H5N1
ISDN136813 A/Indonesia/CDC326T/2006 2006 H5N1
ISDN136814 A/Indonesia/CDC326T/2006 2006 H5N1
ISDN136815 A/Indonesia/CDC329/2006 2006 H5N1
ISDN136816 A/Indonesia/CDC357/2006 2006 H5N1
ISDN136908 A/Indonesia/CDC370/2006 2006 H5N1
ISDN136909 A/Indonesia/CDC370E/2006 2006 H5N1
ISDN137412 A/Indonesia/CDC370P/2006 2006 H5N1
ISDN137413 A/Indonesia/CDC370T/2006 2006 H5N1
ISDN181365 A/Indonesia/CDC523/2006 2006 H5N1
ISDN183297 A/Indonesia/CDC523E/2006 2006 H5N1
ISDN183305 A/Indonesia/CDC523T/2006 2006 H5N1
ISDN183313 A/Indonesia/CDC582/2006 2006 H5N1
ISDN140835 A/Indonesia/CDC594/06 2006 H5N1
ISDN140843 A/Indonesia/CDC595/06 2006 H5N1
ISDN140851 A/Indonesia/CDC596/06 2006 H5N1
ISDN140859 A/Indonesia/CDC597/06 2006 H5N1
ISDN140866 A/Indonesia/CDC599/06 2006 H5N1
ISDN183782 A/Indonesia/CDC599N/2006 2006 H5N1
ISDN183698 A/Indonesia/CDC610/2006 2006 H5N1
ISDN183706 A/Indonesia/CDC623/2006 2006 H5N1
ISDN183714 A/Indonesia/CDC623E/2006 2006 H5N1
ISDN183722 A/Indonesia/CDC624/2006 2006 H5N1
ISDN183730 A/Indonesia/CDC624E/2006 2006 H5N1
ISDN183738 A/Indonesia/CDC625/2006 2006 H5N1
ISDN183770 A/Indonesia/CDC625L/2006 2006 H5N1
ISDN183746 A/Indonesia/CDC634/2006 2006 H5N1
ISDN183754 A/Indonesia/CDC634P/2006 2006 H5N1
ISDN183762 A/Indonesia/CDC634T/2006 2006 H5N1
DQ497667 A/chicken/Dairi/BPPVI/2005 2005 H5N1
DQ497668 A/chicken/Deli Serdang/BPPVI/2005 2005 H5N1
DQ497651 A/chicken/Gunung Kidal/BBVW/2005 2005 H5N1
DQ497652 A/chicken/Kulon Progo/BBVW/2005 2005 H5N1
DQ497643 A/chicken/Magetan/BBVW/2005 2005 H5N1
DQ497648 A/chicken/Purworejo/BBVW/2005 2005 H5N1
DQ320928 A/chicken/Salatiga/BBVet-I/2005 2005 H5N1
DQ497665 A/chicken/Simalanggang/BPPVI/2005 2005 H5N1
DQ497669 A/chicken/Tarutung/BPPVI/2005 2005 H5N1
DQ497666 A/chicken/Tebing Tinggi/BPPVI/2005 2005 H5N1
DQ320933 A/chicken/Wajo/BBVM/2005 2005 H5N1
DQ497659 A/duck/Parepare/BBVM/2005 2005 H5N1
ISDN125873 A/Indonesia/5/05 2005 H5N1
ISDN136806 A/Indonesia/CDC287E/2005 2005 H5N1
ISDN136807 A/Indonesia/CDC287T/2005 2005 H5N1
ISDN136808 A/Indonesia/CDC292N/2005 2005 H5N1
ISDN136809 A/Indonesia/CDC292T/2005 2005 H5N1
DQ497662 A/chicken/Kupang-1-NTT/BPPV6/2004 2004 H5N1
DQ497663 A/chicken/Pangkalpinang/BPPV3/2004 2004 H5N1
DQ320930 A/chicken/Yogjakarta/BBVet-IX/2004 2004 H5N1................
http://www.recombinomics.com/News/08040 ... lease.html

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niman
PostPosted: Sat Feb 11, 2012 5:41 am 
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Top 100 HA matches
EPI124067 A/Indonesia/5/2005 (A/H5N1) segment 4 (HA) 3151.5 0.000000e+00 1706/1706 (100%)
EPI116487 A/Indonesia/5/2005 (A/H5N1) segment 4 (HA) 3147.8 0.000000e+00 1704/1704 (100%)
EPI181390 A/Indonesia/5/2005 (A/H5N1) segment 4 (HA) 3142.3 0.000000e+00 1703/1704 (99%)
EPI226651 A/Chicken/Murao Jambi/BBPV-II/2005 (A/H5N1) segment 4 (HA) 3125.7 0.000000e+00 1700/1704 (99%)
EPI119998 A/Indonesia/TLL007/2006 (A/H5N1) segment 4 (HA) 3125.7 0.000000e+00 1700/1704 (99%)
EPI226652 A/Chicken/Pakun Baru/BPPV-II/2005 (A/H5N1) segment 4 (HA) 3123.8 0.000000e+00 1701/1706 (99%)
EPI123831 A/Chicken/Indonesia/Rejang Lebong1631-22/2006 (A/H5N1) segment 4 (HA) 3123.8 0.000000e+00 1701/1706 (99%)
EPI225050 A/chicken/West Java/TASIKSOB/2006 (A/H5N1) segment 4 (HA) 3114.6 0.000000e+00 1698/1704 (99%)
EPI224608 A/Chicken/West Java/TASIKSOL/2006 (A/H5N1) segment 4 (HA) 3114.6 0.000000e+00 1698/1704 (99%)
EPI124201 A/Indonesia/283H/2006 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1697/1704 (99%)
EPI120006 A/Indonesia/TLL011/2006 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1697/1704 (99%)
EPI120004 A/Indonesia/TLL010/2006 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1697/1704 (99%)
EPI119996 A/Indonesia/TLL006/2006 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1697/1704 (99%)
EPI119994 A/Indonesia/TLL005/2006 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1697/1704 (99%)
EPI123832 A/Chicken/Indonesia/Lampung1631-23/2006 (A/H5N1) segment 4 (HA) 3107.2 0.000000e+00 1698/1706 (99%)
EPI124253 A/Indonesia/304H/2006 (A/H5N1) segment 4 (HA) 3105.3 0.000000e+00 1698/1706 (99%)
EPI41399 A/Indonesia/CDC523/2006 (A/H5N1) segment 4 (HA) 3105.3 0.000000e+00 1696/1704 (99%)
EPI124217 A/Indonesia/286H/2006 (A/H5N1) segment 4 (HA) 3103.5 0.000000e+00 1696/1704 (99%)
EPI120000 A/Indonesia/TLL008/2006 (A/H5N1) segment 4 (HA) 3103.5 0.000000e+00 1696/1704 (99%)
EPI124143 A/Indonesia/195H/2005 (A/H5N1) segment 4 (HA) 3101.6 0.000000e+00 1689/1694 (99%)
EPI123828 A/Chicken/Indonesia/Belitung Timor1631-18/2006 (A/H5N1) segment 4 (HA) 3101.6 0.000000e+00 1697/1706 (99%)
EPI120002 A/Indonesia/TLL009/2006 (A/H5N1) segment 4 (HA) 3101.6 0.000000e+00 1695/1704 (99%)
EPI224706 A/Muscovy Duck/Jakarta/HABWIN/2006 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1695/1704 (99%)
EPI124475 A/Indonesia/567H/2006 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1689/1695 (99%)
EPI124421 A/Indonesia/542H/2006 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1695/1704 (99%)
EPI119990 A/Indonesia/TLL003/2006 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1695/1704 (99%)
EPI41820 A/Indonesia/CDC669P/2006 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1695/1704 (99%)
EPI234502 A/Swan/Indonesia/Malang1631-61/2007 (A/H5N1) segment 4 (HA) 3096.1 0.000000e+00 1696/1706 (99%)
EPI123833 A/Muscovy Duck/Indonesia/Kedri1631-24/2006 (A/H5N1) segment 4 (HA) 3096.1 0.000000e+00 1696/1706 (99%)
EPI41801 A/Indonesia/CDC669/2006 (A/H5N1) segment 4 (HA) 3094.3 0.000000e+00 1694/1704 (99%)
EPI321366 A/chicken/Magelang/BBVW-662-764/2007 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1694/1704 (99%)
EPI321321 A/chicken/Flores Timur/BBVD-256/2007 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1694/1704 (99%)
EPI321280 A/chicken/Badung/BBVD-175/2007 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1694/1704 (99%)
EPI123734 A/Chicken/West Java/TASIK1/2006 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1694/1704 (99%)
EPI123732 A/Chicken/West Java/TASIK2/2006 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1694/1704 (99%)
EPI49202 A/Indonesia/CDC835/2006 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1694/1704 (99%)
EPI123825 A/Chicken/Indonesia/Agam1631-3/2006 (A/H5N1) segment 4 (HA) 3090.6 0.000000e+00 1695/1706 (99%)
EPI124271 A/Indonesia/292H/2006 (A/H5N1) segment 4 (HA) 3088.7 0.000000e+00 1688/1696 (99%)
EPI119992 A/Indonesia/TLL004/2006 (A/H5N1) segment 4 (HA) 3088.7 0.000000e+00 1693/1704 (99%)
EPI321749 A/peaceful dove/Badung/BBVD-493/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321408 A/chicken/Tabanan/BBVD-339/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321339 A/chicken/Klungkung/BBVD-417/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321335 A/chicken/Jembrana/BBVD-298b/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321334 A/chicken/Jembrana/BBVD-298/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321333 A/chicken/Jembrana/BBVD-273/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321293 A/chicken/Bangli/BBVD-387ab/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321292 A/chicken/Bangli/BBVD-343/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321287 A/chicken/Badung/BBVD-319ac/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321283 A/chicken/Badung/BBVD-219/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321282 A/chicken/Badung/BBVD-216/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI321281 A/chicken/Badung/BBVD-205/2007 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI49240 A/Indonesia/CDC836T/2006 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI49221 A/Indonesia/CDC836/2006 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI41839 A/Indonesia/CDC699/2006 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI234497 A/Pigeon/Indonesia/Rokhit1631-6/2006 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1694/1706 (99%)
EPI123842 A/Chicken/Indonesia/Semerang1631-62/2007 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1694/1706 (99%)
EPI123836 A/Chicken/Indonesia/Gunung Kidul1631-33/2006 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1694/1706 (99%)
EPI123822 A/Chicken/Indonesia/Padang1631-1/2006 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1694/1706 (99%)
EPI123728 A/Quail/Jakarta/JU1/2006 (A/H5N1) segment 4 (HA) 3083.2 0.000000e+00 1687/1696 (99%)
EPI41948 A/Indonesia/CDC759/2006 (A/H5N1) segment 4 (HA) 3083.2 0.000000e+00 1692/1704 (99%)
EPI321750 A/peaceful dove/Denpasar/BBVD-480/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321583 A/duck/Sleman/BBVW-599-33290/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321581 A/duck/Sleman/BBVW-599-33288/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321579 A/duck/Sleman/BBVW-598-32237/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321543 A/duck/Magelang/BBVW-604-44402/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321541 A/duck/Magelang/BBVW-604-44401/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321520 A/duck/Bantul/BBVW-358-24381/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321399 A/chicken/Sleman/BBVW-626-234/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321397 A/chicken/Sleman/BBVW-626-233/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321351 A/chicken/Kulon Progo/BBVW-610-11020/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321341 A/chicken/Klungkung/BBVD-484/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321337 A/chicken/Klungkung/BBVD-225/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321318 A/chicken/Denpasar/BBVD-494/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321313 A/chicken/Denpasar/BBVD-291/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI321311 A/chicken/Denpasar/BBVD-145/2007 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI124234 A/Indonesia/298H/2006 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1686/1695 (99%)
EPI41915 A/Indonesia/CDC739/2006 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1693/1705 (99%)
EPI123827 A/Chicken/Indonesia/Pekenbaru1631-11/2006 (A/H5N1) segment 4 (HA) 3079.5 0.000000e+00 1693/1706 (99%)
EPI321577 A/duck/Sleman/BBVW-598-32226/2007 (A/H5N1) segment 4 (HA) 3077.6 0.000000e+00 1691/1704 (99%)
EPI321582 A/duck/Sleman/BBVW-599-33289/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI321576 A/duck/Sleman/BBVW-379-34423/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI321409 A/chicken/Tabanan/BBVD-461/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI321350 A/chicken/Kulon Progo/BBVW-610-11019/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI321322 A/chicken/Gianyar/BBVD-429/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI321306 A/chicken/Bantul/BBVW-482-22235/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI321304 A/chicken/Bantul/BBVW-482-22233/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI321300 A/chicken/Bantul/BBVW-446-24454/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI321299 A/chicken/Bantul/BBVW-446-24453/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI321298 A/chicken/Bantul/BBVW-446-24452/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI321294 A/chicken/Bangli/BBVD-555ab/2007 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI49183 A/Indonesia/CDC940/2006 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI123839 A/Chicken/Indonesia/Garut1631-51/2006 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1692/1706 (99%)
EPI123838 A/Chicken/Indonesia/Bandung1631-49/2006 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1692/1706 (99%)
EPI124309 A/Indonesia/341H/2006 (A/H5N1) segment 4 (HA) 3072.1 0.000000e+00 1685/1696 (99%)
EPI321364 A/chicken/Magelang/BBVW-662-762A/2007 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1690/1704 (99%)
EPI321348 A/chicken/Kulon Progo/BBVW-537-11099/2007 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1690/1704 (99%)
EPI321347 A/chicken/Kulon Progo/BBVW-453-11055/2007 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1690/1704 (99%)
EPI321346 A/chicken/Kulon Progo/BBVW-453-11054/2007 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1690/1704 (99%)
EPI321345 A/chicken/Kulon Progo/BBVW-453-11053/2007 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1690/1704 (99%)
EPI321344 A/chicken/Kulon Progo/BBVW-453-11052/2007 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1690/1704 (99%)

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niman
PostPosted: Sat Feb 11, 2012 5:49 am 
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Although Indonesia stopped releasing human sequences in early 2007, sequences from the recent bali cluster were rapidly released (prior to WHO confirmation). These sequences had a number of receptor binding domain changes, as well as clear evidence of recombination between family members.

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niman
PostPosted: Sat Feb 11, 2012 5:55 am 
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niman wrote:
Although Indonesia stopped releasing human sequences in early 2007, sequences from the recent bali cluster were rapidly released (prior to WHO confirmation). These sequences had a number of receptor binding domain changes, as well as clear evidence of recombination between family members.

RBD Changes In 2011 H5N1 Fatal Cluster In Bali Indonesia
Recombinomics Commentary 14:30
November 7, 2011


The Indonesian Ministry of Health, (NIHRD-MOH) has released HA sequences (A/Indonesia/NIHRD11766/2011, A/Indonesia/NIHRD11771/2011, A/Indonesia/NIHRD11815/2011) at GISAID from the H5N1 cluster (5F, 10M, 25F) in Bali (collected on October 7 and 16). The Indonesian MoH is commended for the rapid release of these important sequences.

The sequences had a series of receptor binding domain changes flanking position 190 (D187N, A188G, R193M).......
http://www.recombinomics.com/News/11071 ... _Bali.html

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