Rhiza Labs FluTracker Forum

R193M and RBD Changes In H5N1 Fatal Bali Indonesia Cluster
Recombinomics Commentary 16:45
November 7, 2011


189, which corresponds to antigenic site B of H3N2, may represent an immunodominant epitope,

The above comments, regarding the receptor binding domain change R193M (H3 numbering), found in an escape mutant from A/Indonesia/05/2005, from the second confirmed H5N1 case (37F, fatal) in Indonesia, are from a paper entitled “Broad Cross-Protection against H5N1 Avian Influenza Virus Infection by Means of Monoclonal Antibodies that Map to Conserved Viral Epitopes”. A position 193 change (S193F) was associated with the fixing of adamantine resistance (S31N in M2) in seasonal H3N2, as well as the fixing of oseltamivir resistance (H274Y in NA) in seasonal H1N1, as detailed in “Emergence and Fixing of Antiviral Resistance in Influenza A Via Recombination and Hitchhiking”. Thus, the finding of R193M in all of the 2008 and 2011 human H5N1 sequences from Indonesia (see list here) signals the importance of position 193 in seasonal H3N2, seasonal H1N1, and pandemic H5N1..............
http://www.recombinomics.com/News/11071 ... _Bali.html

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viewtopic.php?f=5&t=7693

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Health experts, scientists to discuss bird flu studies
by Staff Writers
Geneva (AFP) Feb 10, 2012

The World Health Organization said Friday it will meet next week to determine whether scientists can publish research on a bird flu virus that may be easily passed among humans.

The two-day discussion will relate to research on a mutation of the H5N1 virus that international scientists halted on January 20 citing fears of the devastation it could wreak were it to escape the laboratory.

According to WHO, avian influenza H5N1 is primarily transmitted between birds, and very rarely to humans.

Two separate teams of researchers, one in the Netherlands and the other in the United States, found ways late last year to engineer the H5N1 virus so that it is transmitted among mammals, something that has been rare.

The breakthrough raised alarm that the method could fall into the wrong hands and unleash a massive flu pandemic that could cost millions of lives.

A US advisory panel in December urged that key details remain unpublished.

WHO said it will hold a technical meeting on Wednesday and Thursday on the specific circumstances and results of the two studies.

"There will be 22 participants: two teams of researchers, representatives of the influenza laboratory network and representatives of the scientific newspapers Science and Nature" said WHO spokeswoman Fadela Chaib.

They will try to reach a consensus about practical actions to resolve the most urgent issues, particularly those related to access to and dissemination of the results of this research, WHO said.

http://www.terradaily.com/reports/Healt ... s_999.html

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No way of stopping leak of deadly new flu, says terror chief
US biosecurity board expert warns against details of H5N1 bird flu getting into wrong hands


The bioterrorism expert responsible for censoring scientific research which could lead to the creation of a devastating pandemic has admitted the information "is going to get out" eventually.

Professor Paul Keim, chairman of the US National Science Advisory Board for Biosecurity, controversially recommended that researchers be stopped from publishing the precise mutations needed to transform the H5N1 strain of birdflu virus into a human-transmissible version.

In an exclusive interview with The Independent, he argued it had been necessary to limit the release of the scientific details because of fears that terrorists may use the information to create their own H5N1 virus that could be spread easily between people.

Professor Keim said that it was necessary to slow down the release of scientific information because it was clear that the world is not yet prepared for a strain of highly lethal H5N1 influenza that can be transmitted by coughs and sneezes.

“We recognised that, in the long term certainly, the information is going to get out, and maybe even in the mid term. But if we can restrict it in the short term and motivate governments to start getting busy in terms of building up the flu-defence infrastructure, then we’ve succeeded at a certain level,” he said.

“If we can slow down the release of the specific information that would enable somebody to reconstruct this virus and do something nefarious, even for a while, then that was a good thing.”

By withholding key details of the mutations needed to make an airborne strain of H5N1, this would give time for governments to prepare for and prevent a possible pandemic, he added.

“The infrastructure to stop a pandemic in this area is not there. We just don’t have the capabilities. The very first time we knew that the swine flu virus [coming out of Mexico] was there, it was already in 18 countries. I’m not confident at all that we have the surveillance capability to spot an emerging virus in time to stop it,” he said.

“And even if we did spot it early on, I don’t think we have sufficient vaccines. The vaccines aren’t good enough, and the drugs are not good enough to stop this emerging and being a pandemic.”

Although H5N1 spreads rapidly between birds, it has so far affected only about 600 people worldwide who have had direct contact with infected poultry. However, two teams of researchers have shown independently that it only requires five mutations for H5N1 to become an airborne pathogen for laboratory ferrets, the standard animal model for human influenza.

Professor Keim said that the biosecurity board was asked by the US Government to review the two independent studies because they had already been submitted to the journals Science and Nature. The board had to make a recommendation on whether any or all of the information should be published.

Scientists involved in showing how the H5N1 birdflu virus can be transmitted in the air between ferrets have criticised the biosecurity board’s decision to part-censor their research on the grounds that it would hinder the development of new vaccines and drugs.

However, Professor Keim dismissed the criticism as disingenuous. “The argument that we need this information to make better vaccines and better drugs does not ring true,” he said. “There are lots of ways to make drugs against this virus. The very drugs they were using against this virus were the very same ones used against other flu viruses. The drug-invention problem has nothing to do with having this virus to hand,” he added.

Professor Keim revealed that although he is personally in favour of the research that led to the creation of airborne strains of H5N1, some other members of the board were not convinced. “I’m personally in favour of this research but that opinion is not universal on the board. Some people on the board wanted to stop this research and destroy the virus,” he said.

“I don’t think we need this virus to prove that Tamiflu works against it. And we know that the H5 antigen is not a great antigen for vaccines, we don’t need the virus to tell us that. But there are some experiments that can only be done with the live virus and I’m in favour of keeping the virus for those type of experiments.”

http://www.independent.co.uk/news/scien ... 60997.html

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J Gen Virol. 2010 October; 91(Pt 10): 2485–2490.
doi: 10.1099/vir.0.021659-0
PMCID: PMC3052597
Pathogenicity of highly pathogenic avian H5N1 influenza A viruses isolated from humans between 2003 and 2008 in northern Vietnam

Quynh Mai Le,1 Mutsumi Ito,2 Yukiko Muramoto,2,3 Phuong Vu Mai Hoang,1 Cuong Duc Vuong,1 Yuko Sakai-Tagawa,2 Maki Kiso,2 Makoto Ozawa,4,5 Ryo Takano,2,3 and Yoshihiro Kawaoka2,3,4,5,6

1National Institute of Hygiene and Epidemiology (NIHE), Hanoi, Vietnam

2Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

3ERATO Infection-Induced Host Responses Project, Japan Science and Technology Agency, Saitama 332-0012, Japan

4International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

5Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA

6Division of Zoonosis, Department of Microbiology and Infectious Diseases, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan

Correspondence: Yoshihiro Kawaoka: Email: kawaoka@ims.u-tokyo.ac.jp

Received March 7, 2010; Accepted June 28, 2010.

Abstract
Vietnam is one of the countries most affected by highly pathogenic H5N1 influenza A viruses. To evaluate the potential pathogenicity in mammals of H5N1 viruses isolated from humans in Vietnam, we determined the sequences of all eight genes of 22 human isolates collected between 2003 and 2008 and compared their virulence in mice. The isolates were classified into clade 1 and clade 2.3.4 and differed in pathogenicity for mice. Whilst lysine at position 627 of PB2 (PB2-627K) is a critical virulence determinant for clade 2.3.4 viruses, asparagine at position 701 of PB2 and other unknown virulence determinants appear to be involved in the high pathogenicity of clade 1 viruses, warranting further studies to determine the factors responsible for the high virulence of H5N1 viruses in mammals.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3052597/

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Although the above sequence is not public, a human case from 2008, A/Vietnam/HN31432M/2008, is available and was descibed by Kawaoka. In addition, poultry isolates from 2009 are available, and the most closely related poultry sequence is A/chicken/Vietnam/NCVD-281/2009

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Top 100 matches
EPI270268 A/Vietnam/HN31432M/2008 (A/H5N1) segment 4 (HA) 3147.8 0.000000e+00 1704/1704 (100%)
EPI284507 A/muscovy duck/Vietnam/NCVD-079/2008 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1694/1704 (99%)
EPI164293 A/duck/Yunnan/6490/2006 (A/H5N1) segment 4 (HA) 3088.7 0.000000e+00 1692/1702 (99%)
EPI337271 A/environment/Guizhou/2/2009 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI284489 A/chicken/Vietnam/NCVD-035/2008 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1693/1704 (99%)
EPI164373 A/goose/Yunnan/6193/2006 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1694/1705 (99%)
EPI284478 A/chicken/Vietnam/NCVD-081/2008 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI280224 A/environment/Guizhou/2/2009 (A/H5N1) segment 4 (HA) 3079.5 0.000000e+00 1691/1704 (99%)
EPI327223 A/chicken/Viet Nam/TMU007/2008 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI284510 A/muscovy duck/Vietnam/NCVD-038/2008 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI284454 A/chicken/Vietnam/NCVD-281/2009 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI284509 A/muscovy duck/Vietnam/NCVD-034/2008 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1690/1704 (99%)
EPI284455 A/chicken/Vietnam/NCVD-282/2009 (A/H5N1) segment 4 (HA) 3066.6 0.000000e+00 1689/1704 (99%)
EPI284479 A/chicken/Vietnam/NCVD-083/2008 (A/H5N1) segment 4 (HA) 3064.7 0.000000e+00 1689/1704 (99%)
EPI284477 A/chicken/Vietnam/NCVD-080/2008 (A/H5N1) segment 4 (HA) 3064.7 0.000000e+00 1689/1704 (99%)
EPI284456 A/chicken/Vietnam/NCVD-283/2009 (A/H5N1) segment 4 (HA) 3061.0 0.000000e+00 1688/1704 (99%)
EPI284508 A/muscovy duck/Vietnam/NCVD-082/2008 (A/H5N1) segment 4 (HA) 3059.2 0.000000e+00 1688/1704 (99%)
EPI284472 A/chicken/Vietnam/NCVD-296/2009 (A/H5N1) segment 4 (HA) 3059.2 0.000000e+00 1688/1704 (99%)
EPI107759 A/duck/Guangxi/5457/2005 (A/H5N1) segment 4 (HA) 3059.2 0.000000e+00 1682/1695 (99%)
EPI337279 A/environment/Guizhou/4/2009 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1687/1704 (99%)
EPI280232 A/environment/Guizhou/4/2009 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1687/1704 (99%)
EPI284471 A/chicken/Vietnam/NCVD-295/2009 (A/H5N1) segment 4 (HA) 3051.8 0.000000e+00 1686/1704 (98%)
EPI170615 A/chicken/Vietnam/216/2005 (A/H5N1) segment 4 (HA) 3048.1 0.000000e+00 1686/1704 (98%)
EPI170607 A/Muscovy duck/Vietnam/217/2005 (A/H5N1) segment 4 (HA) 3048.1 0.000000e+00 1686/1704 (98%)
EPI170599 A/duck/Vietnam/218/2005 (A/H5N1) segment 4 (HA) 3048.1 0.000000e+00 1686/1704 (98%)
EPI170591 A/duck/Vietnam/219/2005 (A/H5N1) segment 4 (HA) 3048.1 0.000000e+00 1686/1704 (98%)
EPI284545 A/ngan/Vietnam/NCVD-420/2010 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI227371 A/muscovy duck/VietNam/209/2005 (A/H5) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI227010 A/chicken/Ninh Binh/209/2005 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI170742 A/duck/Vietnam/215/2005 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI170741 A/Muscovy duck/Vietnam/213/2005 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI170740 A/chicken/Vietnam/212/2005 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI170739 A/Muscovy duck/Vietnam/211/2005 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI170738 A/duck/Vietnam/210/2005 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI170714 A/chicken/Vietnam/202/2005 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI170690 A/duck/Vietnam/205/2005 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI170674 A/duck/Vietnam/207/2005 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI170658 A/chicken/Vietnam/209/2005 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1685/1704 (98%)
EPI284437 A/chicken/Vietnam/NCVD-383/2009 (A/H5N1) segment 4 (HA) 3037.0 0.000000e+00 1684/1704 (98%)
EPI225081 A/duck/Hai Phong /208/2006 (A/H5N1) segment 4 (HA) 3037.0 0.000000e+00 1684/1704 (98%)
EPI170666 A/duck/Vietnam/208/2005 (A/H5N1) segment 4 (HA) 3037.0 0.000000e+00 1684/1704 (98%)
EPI284531 A/duck/Vietnam/NCVD-391/2009 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI270188 A/Vietnam/UT30850/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1681/1701 (98%)
EPI140703 A/Muscovy duck/Vietnam/39/2007 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1677/1695 (98%)
EPI107765 A/duck/Guangxi/150/2006 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1677/1695 (98%)
EPI337959 A/Guangxi/1/2005 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1682/1704 (98%)
EPI284583 A/muscovy duck/Vietnam/NCVD-401/2010 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1682/1704 (98%)
EPI284506 A/muscovy duck/Vietnam/NCVD-388/2009 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1682/1704 (98%)
EPI284501 A/muscovy duck/Vietnam/NCVD-403/2010 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1682/1704 (98%)
EPI284500 A/muscovy duck/Vietnam/NCVD-402/2010 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1682/1704 (98%)
EPI284483 A/chicken/Vietnam/NCVD-103/2007 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1682/1704 (98%)
EPI164258 A/Guangxi/1/2005 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1682/1704 (98%)
EPI107771 A/chicken/Guangxi/463/2006 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1676/1695 (98%)
EPI224965 A/chicken/Hong Kong/D-06-0947/2006 (A/H5N1) segment 4 (HA) 3020.4 0.000000e+00 1681/1704 (98%)
EPI108329 A/goose/Guangxi/1898/2006 (A/H5N1) segment 4 (HA) 3020.4 0.000000e+00 1675/1695 (98%)
EPI107769 A/duck/Guangxi/288/2006 (A/H5N1) segment 4 (HA) 3020.4 0.000000e+00 1675/1695 (98%)
EPI107755 A/duck/Guangxi/5270/2005 (A/H5N1) segment 4 (HA) 3020.4 0.000000e+00 1675/1695 (98%)
EPI107753 A/duck/Guangxi/5165/2005 (A/H5N1) segment 4 (HA) 3020.4 0.000000e+00 1675/1695 (98%)
EPI107741 A/duck/Guangxi/4428/2005 (A/H5N1) segment 4 (HA) 3020.4 0.000000e+00 1675/1695 (98%)
EPI284505 A/muscovy duck/Vietnam/NCVD-384/2009 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1680/1704 (98%)
EPI280096 A/Hunan/1/2006 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1680/1704 (98%)
EPI275982 A/duck/Hubei/49/2005 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1680/1704 (98%)
EPI275462 A/Guangxi/1/2005 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1680/1704 (98%)
EPI181296 A/Hunan/1/2006 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1680/1704 (98%)
EPI108331 A/goose/Guangxi/1633/2006 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1674/1695 (98%)
EPI107747 A/duck/Guangxi/4830/2005 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1674/1695 (98%)
EPI284438 A/chicken/Vietnam/NCVD-392/2009 (A/H5N1) segment 4 (HA) 3013.0 0.000000e+00 1679/1704 (98%)
EPI337141 A/Anhui/1/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1680/1705 (98%)
EPI280104 A/Guangdong/1/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI280032 A/Anhui/1/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1680/1705 (98%)
EPI279949 A/Zhejiang/1/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI276046 A/goose/Hubei/65/2005 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI275774 A/chicken/Hunan/21/2005 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI181301 A/Guangdong/1/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI181297 A/Zhejiang/1/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI180956 A/duck/Laos/22/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI180951 A/duck/Laos/25/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI108327 A/duck/Guangxi/1830/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1673/1695 (98%)
EPI107743 A/goose/Guangxi/4513/2005 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1673/1695 (98%)
EPI106026 A/China/GD01/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI337128 A/Guangdong/2/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI335220 A/duck/Lao/7/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI335147 A/duck/Lao/962/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI335125 A/duck/Lao/975/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI335109 A/environment/Lao/979/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI335101 A/duck/Lao/980/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI335093 A/duck/Lao/981/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI280025 A/Guangdong/2/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI275386 A/Anhui/2/2005 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI224609 A/China/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI171212 A/guinea fowl/North Okkalarpa/834/2007 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1679/1705 (98%)
EPI164317 A/goose/Yunnan/4389/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI164309 A/goose/Yunnan/4371/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI164277 A/duck/Yunnan/4873/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI126685 A/human/China/GD02/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI107963 A/chicken/Hong Kong/947/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1672/1695 (98%)
EPI107857 A/duck/Hunan/5152/2005 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1672/1695 (98%)
EPI107855 A/duck/Hunan/5106/2005 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1672/1695 (98%)
EPI337107 A/Shanghai/1/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1677/1704 (98%)
EPI335171 A/duck/Lao/670/2010 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1678/1705 (98%)

_________________
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Top 100 matches
EPI284478 A/chicken/Vietnam/NCVD-081/2008 (A/H5N1) segment 4 (HA) 3147.8 0.000000e+00 1704/1704 (100%)
EPI284477 A/chicken/Vietnam/NCVD-080/2008 (A/H5N1) segment 4 (HA) 3131.2 0.000000e+00 1701/1704 (99%)
EPI284507 A/muscovy duck/Vietnam/NCVD-079/2008 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI270268 A/Vietnam/HN31432M/2008 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1692/1704 (99%)
EPI164293 A/duck/Yunnan/6490/2006 (A/H5N1) segment 4 (HA) 3077.6 0.000000e+00 1690/1702 (99%)
EPI337271 A/environment/Guizhou/2/2009 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI284489 A/chicken/Vietnam/NCVD-035/2008 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1691/1704 (99%)
EPI164373 A/goose/Yunnan/6193/2006 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1692/1705 (99%)
EPI280224 A/environment/Guizhou/2/2009 (A/H5N1) segment 4 (HA) 3068.4 0.000000e+00 1689/1704 (99%)
EPI327223 A/chicken/Viet Nam/TMU007/2008 (A/H5N1) segment 4 (HA) 3064.7 0.000000e+00 1689/1704 (99%)
EPI284510 A/muscovy duck/Vietnam/NCVD-038/2008 (A/H5N1) segment 4 (HA) 3064.7 0.000000e+00 1689/1704 (99%)
EPI284509 A/muscovy duck/Vietnam/NCVD-034/2008 (A/H5N1) segment 4 (HA) 3059.2 0.000000e+00 1688/1704 (99%)
EPI337279 A/environment/Guizhou/4/2009 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1687/1704 (99%)
EPI284479 A/chicken/Vietnam/NCVD-083/2008 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1687/1704 (99%)
EPI284454 A/chicken/Vietnam/NCVD-281/2009 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1687/1704 (99%)
EPI280232 A/environment/Guizhou/4/2009 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1687/1704 (99%)
EPI284508 A/muscovy duck/Vietnam/NCVD-082/2008 (A/H5N1) segment 4 (HA) 3048.1 0.000000e+00 1686/1704 (98%)
EPI107759 A/duck/Guangxi/5457/2005 (A/H5N1) segment 4 (HA) 3048.1 0.000000e+00 1680/1695 (99%)
EPI284455 A/chicken/Vietnam/NCVD-282/2009 (A/H5N1) segment 4 (HA) 3044.4 0.000000e+00 1685/1704 (98%)
EPI284456 A/chicken/Vietnam/NCVD-283/2009 (A/H5N1) segment 4 (HA) 3038.9 0.000000e+00 1684/1704 (98%)
EPI284472 A/chicken/Vietnam/NCVD-296/2009 (A/H5N1) segment 4 (HA) 3037.0 0.000000e+00 1684/1704 (98%)
EPI170615 A/chicken/Vietnam/216/2005 (A/H5N1) segment 4 (HA) 3037.0 0.000000e+00 1684/1704 (98%)
EPI170607 A/Muscovy duck/Vietnam/217/2005 (A/H5N1) segment 4 (HA) 3037.0 0.000000e+00 1684/1704 (98%)
EPI170599 A/duck/Vietnam/218/2005 (A/H5N1) segment 4 (HA) 3037.0 0.000000e+00 1684/1704 (98%)
EPI170591 A/duck/Vietnam/219/2005 (A/H5N1) segment 4 (HA) 3037.0 0.000000e+00 1684/1704 (98%)
EPI227371 A/muscovy duck/VietNam/209/2005 (A/H5) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI227010 A/chicken/Ninh Binh/209/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI170742 A/duck/Vietnam/215/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI170741 A/Muscovy duck/Vietnam/213/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI170740 A/chicken/Vietnam/212/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI170739 A/Muscovy duck/Vietnam/211/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI170738 A/duck/Vietnam/210/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI170714 A/chicken/Vietnam/202/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI170690 A/duck/Vietnam/205/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI170674 A/duck/Vietnam/207/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI170658 A/chicken/Vietnam/209/2005 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1683/1704 (98%)
EPI284471 A/chicken/Vietnam/NCVD-295/2009 (A/H5N1) segment 4 (HA) 3029.6 0.000000e+00 1682/1704 (98%)
EPI225081 A/duck/Hai Phong /208/2006 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1682/1704 (98%)
EPI170666 A/duck/Vietnam/208/2005 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1682/1704 (98%)
EPI284545 A/ngan/Vietnam/NCVD-420/2010 (A/H5N1) segment 4 (HA) 3020.4 0.000000e+00 1681/1704 (98%)
EPI270188 A/Vietnam/UT30850/2005 (A/H5N1) segment 4 (HA) 3020.4 0.000000e+00 1679/1701 (98%)
EPI140703 A/Muscovy duck/Vietnam/39/2007 (A/H5N1) segment 4 (HA) 3020.4 0.000000e+00 1675/1695 (98%)
EPI107765 A/duck/Guangxi/150/2006 (A/H5N1) segment 4 (HA) 3020.4 0.000000e+00 1675/1695 (98%)
EPI337959 A/Guangxi/1/2005 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1680/1704 (98%)
EPI284483 A/chicken/Vietnam/NCVD-103/2007 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1680/1704 (98%)
EPI284437 A/chicken/Vietnam/NCVD-383/2009 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1680/1704 (98%)
EPI164258 A/Guangxi/1/2005 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1680/1704 (98%)
EPI107771 A/chicken/Guangxi/463/2006 (A/H5N1) segment 4 (HA) 3014.9 0.000000e+00 1674/1695 (98%)
EPI284531 A/duck/Vietnam/NCVD-391/2009 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI224965 A/chicken/Hong Kong/D-06-0947/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1679/1704 (98%)
EPI108329 A/goose/Guangxi/1898/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1673/1695 (98%)
EPI107769 A/duck/Guangxi/288/2006 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1673/1695 (98%)
EPI107755 A/duck/Guangxi/5270/2005 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1673/1695 (98%)
EPI107753 A/duck/Guangxi/5165/2005 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1673/1695 (98%)
EPI107741 A/duck/Guangxi/4428/2005 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1673/1695 (98%)
EPI335220 A/duck/Lao/7/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1679/1705 (98%)
EPI335147 A/duck/Lao/962/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1679/1705 (98%)
EPI335125 A/duck/Lao/975/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1679/1705 (98%)
EPI335109 A/environment/Lao/979/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1679/1705 (98%)
EPI335101 A/duck/Lao/980/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1679/1705 (98%)
EPI335093 A/duck/Lao/981/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1679/1705 (98%)
EPI284583 A/muscovy duck/Vietnam/NCVD-401/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI284506 A/muscovy duck/Vietnam/NCVD-388/2009 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI284501 A/muscovy duck/Vietnam/NCVD-403/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI284500 A/muscovy duck/Vietnam/NCVD-402/2010 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI280096 A/Hunan/1/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI275462 A/Guangxi/1/2005 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI181296 A/Hunan/1/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1678/1704 (98%)
EPI108331 A/goose/Guangxi/1633/2006 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1672/1695 (98%)
EPI107747 A/duck/Guangxi/4830/2005 (A/H5N1) segment 4 (HA) 3003.8 0.000000e+00 1672/1695 (98%)
EPI337141 A/Anhui/1/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1678/1705 (98%)
EPI335171 A/duck/Lao/670/2010 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1679/1706 (98%)
EPI335163 A/duck/Lao/959/2010 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1679/1706 (98%)
EPI335085 A/duck/Lao/986/2010 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1679/1706 (98%)
EPI280104 A/Guangdong/1/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1677/1704 (98%)
EPI280032 A/Anhui/1/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1678/1705 (98%)
EPI279949 A/Zhejiang/1/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1677/1704 (98%)
EPI276046 A/goose/Hubei/65/2005 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1677/1704 (98%)
EPI275774 A/chicken/Hunan/21/2005 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1677/1704 (98%)
EPI181301 A/Guangdong/1/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1677/1704 (98%)
EPI181297 A/Zhejiang/1/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1677/1704 (98%)
EPI180956 A/duck/Laos/22/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1677/1704 (98%)
EPI180951 A/duck/Laos/25/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1677/1704 (98%)
EPI108333 A/chicken/Guangxi/1951/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1671/1695 (98%)
EPI108327 A/duck/Guangxi/1830/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1671/1695 (98%)
EPI107743 A/goose/Guangxi/4513/2005 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1671/1695 (98%)
EPI106026 A/China/GD01/2006 (A/H5N1) segment 4 (HA) 2998.2 0.000000e+00 1677/1704 (98%)
EPI337128 A/Guangdong/2/2006 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1676/1704 (98%)
EPI335212 A/duck/Lao/9/2010 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1677/1705 (98%)
EPI335117 A/environment/Lao/977/2010 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1678/1706 (98%)
EPI284505 A/muscovy duck/Vietnam/NCVD-384/2009 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1676/1704 (98%)
EPI280025 A/Guangdong/2/2006 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1676/1704 (98%)
EPI275982 A/duck/Hubei/49/2005 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1676/1704 (98%)
EPI275386 A/Anhui/2/2005 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1676/1704 (98%)
EPI224609 A/China/2006 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1676/1704 (98%)
EPI171212 A/guinea fowl/North Okkalarpa/834/2007 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1678/1706 (98%)
EPI164317 A/goose/Yunnan/4389/2006 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1676/1704 (98%)
EPI164309 A/goose/Yunnan/4371/2006 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1676/1704 (98%)
EPI164277 A/duck/Yunnan/4873/2006 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1676/1704 (98%)
EPI126685 A/human/China/GD02/2006 (A/H5N1) segment 4 (HA) 2992.7 0.000000e+00 1676/1704 (98%)

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A/Vietnam/HN31432M/2008 has a number of non-synomous H5 changes, including S133L. RBD changes A188E and T192I and HA cleavage site change R238K. Three of these four changes were also in the recent fatal case in Ghuizhou.

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2012 Guizhou H5N1 Recombination and RBD Changes
Recombinomics Commentary 21:45
February 2, 2012

The WHO Chinese National Influenza Center has released HA, NA, and MP sequences (at GISAID) from the most recent confirmed H5N1 case (39M) from Guizhou Province in China, A/Guizhou/1/2012, representing the first 2012 human H5N1 sequence. The sample was collected on January 22, 2012, the date of the patient’s death, and the center is commended for the rapid release of these important sequences. Like the December case from Shenzhen, China, A/Guangdong-Shenzhen/1/2011, this cases has no reported contact with poultry. However, unlike the earlier case, which was related to clade 2.3.2.1 sequences frequently reported in wild birds in Hong Kong at this time of year, the Guizhou sequence was most closely related to 2009 environmental samples from Guizhou poultry markets which were clade 2.3.4.2. Most human H5N1 cases in China prior to 2008 were clade 2.3.4.

Although this case was from a different sub-clade than the Shenzhen case, it also had a number of receptor binding domain changes flanking position 190 (A188E, A189T, T199I, I202V). In addition the sequence has S133L, which has been found in prior severe and fatal cases in China and southeast Asia (see list here). However, the current HA sequence had a cluster of changes (C434T, A435G, G438A, T445G), which produced S137A in addition to S133L. This cluster of synonymous and non-synonymous was found in clade 2.2.1 F sequences in Egypt, clade 2.1 sequences in Indonesia, and recent sequences in clade 2.3.2.1 and 2.3.4.2 in China and Vietnam (see list here) strongly supporting recombination......
http://www.recombinomics.com/News/02021 ... ation.html

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