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PostPosted: Thu Feb 02, 2012 1:01 pm 
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S133L / S137A combination

EPI352222 A/Guizhou/1/2012 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI348164 A/chicken/Egypt/11VIR4453-18/VRLCU/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI340808 A/quail/Klaten/BBVW-110-II/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI340794 A/chicken/Banjarbaru/BPPVRV-26/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI340166 A/chicken/Egypt/10112SG/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI336996 A/duck/Zhejiang/213/2011 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI336768 A/duck/Nepal/DTS22/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI314032 A/duck/Vietnam/8/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI314030 A/duck/Vietnam/5/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI314027 A/duck/Vietnam/2/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI272182 A/chicken/Jilin/Q23/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI272180 A/chicken/Henan/Q4/2007 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI257059 A/chicken/Egypt/33-1/2008 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI257055 A/chicken/Egypt/37-1/2008 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI246013 A/goose/Egypt/0946smL-NLQP/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI245994 A/chicken/Egypt/096L-NLQP/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI219345 A/peregrine falcon/Hong Kong/810/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI214883 A/chicken/Egypt/09359S-NLQP/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI214878 A/chicken/Egypt/0910QL-NLQP/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)

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PostPosted: Thu Feb 02, 2012 5:26 pm 
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niman wrote:
S133L / S137A combination

EPI352222 A/Guizhou/1/2012 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI348164 A/chicken/Egypt/11VIR4453-18/VRLCU/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI340808 A/quail/Klaten/BBVW-110-II/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI340794 A/chicken/Banjarbaru/BPPVRV-26/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI340166 A/chicken/Egypt/10112SG/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI336996 A/duck/Zhejiang/213/2011 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI336768 A/duck/Nepal/DTS22/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI314032 A/duck/Vietnam/8/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI314030 A/duck/Vietnam/5/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI314027 A/duck/Vietnam/2/2010 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI272182 A/chicken/Jilin/Q23/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI272180 A/chicken/Henan/Q4/2007 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI257059 A/chicken/Egypt/33-1/2008 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI257055 A/chicken/Egypt/37-1/2008 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI246013 A/goose/Egypt/0946smL-NLQP/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI245994 A/chicken/Egypt/096L-NLQP/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI219345 A/peregrine falcon/Hong Kong/810/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI214883 A/chicken/Egypt/09359S-NLQP/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)
EPI214878 A/chicken/Egypt/0910QL-NLQP/2009 (A/H5N1) segment 4 (HA) 27.0 7.523415e+00 14/14 (100%)

The above group shares a cluster of four polymorphisms (of which 2 are nonsynonymous). The above sequences rfepresent multiple sub-clades (2.2.1 F in Egypt, 2.1 in Indonesia, and clades 2.3.4.2 and 2.3.2.1 in China).

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PostPosted: Thu Feb 02, 2012 5:59 pm 
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Commentary

http://www.recombinomics.com/News/02021 ... ation.html

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PostPosted: Fri Feb 03, 2012 1:04 pm 
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niman wrote:
Commentary

http://www.recombinomics.com/News/02021 ... ation.html

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.

A human case of influenza A(H5N1) virus infection was reported in China. The virus belongs to clade 2.3.4.2, and is expected to be sensitive to NAIs and adamantanes by sequencing. Further analysis of the virus including its antigenic relationship with developed candidate reassortant vaccine viruses is being conducted by the WHO Collaborating Centre for Reference and Research on Influenza at the Chinese Center for Disease Control and Prevention.

http://www.who.int/influenza/gisrs_labo ... index.html

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PostPosted: Sat Feb 11, 2012 12:15 pm 
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niman wrote:
HA changes flanking RBD position 190 include A188E, A189T, T199I, I202V.

H5 clade 2.3.4.2 sequence from Vietnam, A/Vietnam/HN31432M/2008. is likely similar to sequence used in Kawaoka paper, has A188E as well as S133L and cleavage site chnage R238K.

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PostPosted: Tue Feb 19, 2013 9:56 pm 
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Closely related to 2013 cases

2013 thread

viewtopic.php?f=5&t=9060

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PostPosted: Tue Feb 19, 2013 10:00 pm 
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niman wrote:
Closely related to 2013 cases

2013 thread

viewtopic.php?f=5&t=9060

T219N adds glycosylation site

EPI420391 A/Guizhou/2/2013 (A/H5N1) segment 4 (HA) 27.0 9.729826e+00 14/14 (100%)
EPI420386 A/Guizhou/1/2013 (A/H5N1) segment 4 (HA) 27.0 9.729826e+00 14/14 (100%)
EPI352222 A/Guizhou/1/2012 (A/H5N1) segment 4 (HA) 27.0 9.729826e+00 14/14 (100%)

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PostPosted: Mon Feb 25, 2013 12:52 pm 
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Pdigree on 2013 sequences at

viewtopic.php?f=5&t=9074

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