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niman
PostPosted: Fri Jan 07, 2011 9:35 am 
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HPA has release 38 HA sequences (at GISAID) from recent cases in the UK.

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niman
PostPosted: Fri Jan 07, 2011 9:43 am 
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S188T Pedigree

EPI295760 A/England/5040499/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295759 A/England/280/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295758 A/England/4940476/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295757 A/England/4920303/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295756 A/England/4880378/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295755 A/England/142/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295749 A/England/5000135/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295748 A/England/5000125/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295747 A/England/4980078/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295746 A/England/4980074/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295745 A/England/4960201/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295744 A/England/4940126/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295743 A/England/4860049/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295742 A/England/4840022/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295739 A/England/126/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295736 A/England/107/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295734 A/England/106/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295726 A/England/86/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295382 A/KANAGAWA/74/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294674 A/England/4880374/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294417 A/VICTORIA/670/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294405 A/BRUNEI/218/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294391 A/SYDNEY/217/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294388 A/SYDNEY/220/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294297 A/PERTH/198/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294282 A/BRISBANE/209/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294195 A/BRISBANE/69/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294115 A/VICTORIA/833/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI287020 A/Ghana/FS-10-4259/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI287018 A/Ghana/FS-10-4241/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI286992 A/Johannesburg/119/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI286990 A/Johannesburg/115/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI284010 A/Thailand/34-9937/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI284007 A/Thailand/34-9912/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI280311 A/India/8910/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI280289 A/Florida/14/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI279083 A/CHRISTCHURCH/15/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI279064 A/VICTORIA/512/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI278873 A/India/8910/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI278871 A/India/5107/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI255118 A/swine/Thailand/CU-RA75/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494

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niman
PostPosted: Fri Jan 07, 2011 9:48 am 
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Posts: 27439
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S186P Pedigree

EPI295750 A/England/5500192/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295741 A/England/139/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295738 A/England/125/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295733 A/England/99/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295731 A/England/93/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295730 A/England/83/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295729 A/England/91/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295728 A/England/90/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295727 A/England/87/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295725 A/England/85/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295724 A/England/79/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295396 A/SAGA/90/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295385 A/SAGA/85/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI295384 A/CHIBA/23/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294682 A/England/118/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294040 A/NAGANO/2181/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI294029 A/YOKOHAMA/84/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI288179 A/Belgorod/RII4/2009 (A/H1N1) segment 4 (HA) 27.0 5.73494
EPI286652 A/Stockholm/5/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI284314 A/Myanmar/M536/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI280326 A/Wisconsin/08/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI280286 A/Florida/13/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI279208 A/CANBERRA/8/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI279016 A/GOROKA/16/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI278875 A/India/007/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI278516 A/Ukraine/122/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI278514 A/Ukraine/123/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI277042 A/Singapore/478/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI273897 A/India/3725/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI272842 A/Qingdao/492/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI272392 A/CHIBA-C/22/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI272008 A/WELLINGTON/1/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI269839 A/turkey/Ontario/FAV114-17/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI269838 A/turkey/Ontario/FAV117-1C/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI259196 A/swine/NC/19646/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI257748 A/Jiangxi-Donghu/SWL1172/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI256035 A/Thessaloniki/791/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI252354 A/Ontario/25913/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI246200 A/swine/IL/5265-2/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI246197 A/swine/IL/5265-1/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI244054 A/swine/Illinois/02960/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI244053 A/swine/Illinois/02957/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI244041 A/KYOTO/2/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI238359 A/Chernihiv/857/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI237302 A/California/VRDL7/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI230786 A/Ankara/17/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI230497 A/swine/4/Mexico/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI217181 A/Tennessee/17/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI215819 A/DARWIN/2126/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494
EPI210034 A/FUKUOKA-C/2/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.73494

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cpg
PostPosted: Fri Jan 07, 2011 10:30 am 
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This confirms your theories re escape.

No wonder people are dying or getting very Ill , tamiflu probably doesn't work.
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Tex
PostPosted: Fri Jan 07, 2011 10:31 am 
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Is there any indication of whether these sequences are from fatal or severe cases?

Are these the sequences that were on the published phylogenetic tree?
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niman
PostPosted: Fri Jan 07, 2011 10:37 am 
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Tex wrote:
Is there any indication of whether these sequences are from fatal or severe cases?

Are these the sequences that were on the published phylogenetic tree?

These are the sequences on the tree, where severe and fatal cases are marked.
The GISAID sheets give the month collected and for many the location in the UK is given.

However, for the the cases with D225G only the month (December) is given, with a note that the HPA will not give out info that will help identify the patients - which is a VERY bad indication.

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Tex
PostPosted: Fri Jan 07, 2011 10:53 am 
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thanks.
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niman
PostPosted: Fri Jan 07, 2011 11:00 am 
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niman wrote:
Tex wrote:
Is there any indication of whether these sequences are from fatal or severe cases?

Are these the sequences that were on the published phylogenetic tree?

These are the sequences on the tree, where severe and fatal cases are marked.
The GISAID sheets give the month collected and for many the location in the UK is given.

However, for the the cases with D225G only the month (December) is given, with a note that the HPA will not give out info that will help identify the patients - which is a VERY bad indication.

In addition there are three other cases on the same branch which were severe or fatal. They also have the "will not disclose" note, once again confirming that there is a SERIOUS problem.

The two cases on the branch that were not severe/ fatal were from Nottingham and collected in November (as were collection dates for two of the more serious cases).

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cpg
PostPosted: Fri Jan 07, 2011 11:01 am 
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http://www.recombinomics.com/News/01071 ... ences.html

Why do you think they released them so quick. Maybe because after all this is over they can say they did everthing possible to help stop the spread. Geez I'm getting way to sceptical. Not good.
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niman
PostPosted: Fri Jan 07, 2011 11:09 am 
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cpg wrote:
http://www.recombinomics.com/News/01071104/H1N1_HPA_Sequences.html

Why do you think they released them so quick. Maybe because after all this is over they can say they did everthing possible to help stop the spread. Geez I'm getting way to sceptical. Not good.

I believe D225G is a serious problem and they will hide the fact as long as possible.

The "can't reveal identitity" is a VERY big red flag. It is limited to severe/fatal D225G or related cases.

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