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niman
PostPosted: Tue Feb 01, 2011 11:20 am 
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Mill Hill is releasing another series of recent H1N1 sequences (at GISAID), including December, 2010 isolates from Germany, and January, 2011 isolates from Iraq. German isolates have S188T.

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Dingo
PostPosted: Tue Feb 01, 2011 11:26 am 
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So these immune/vaccine escape sequences are now across the northern hemisphere now?
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niman
PostPosted: Tue Feb 01, 2011 11:28 am 
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Dingo wrote:
So these immune/vaccine escape sequences are now across the northern hemisphere now?

No doubt.

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niman
PostPosted: Tue Feb 01, 2011 11:30 am 
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Dingo wrote:
So these immune/vaccine escape sequences are now across the northern hemisphere now?

Two of the four German sequences also have "low reactor" changes at position 157 and 158 (and all 4 have S188T and were from late December, 2010).

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niman
PostPosted: Tue Feb 01, 2011 11:34 am 
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niman wrote:
Dingo wrote:
So these immune/vaccine escape sequences are now across the northern hemisphere now?

Two of the four German sequences also have "low reactor" changes at position 157 and 158 (and all 4 have S188T and were from late December, 2010).

2 of 2 Madagascar sequences (late November) also have S188T and one has "low reactor" change at position 158.

H1N1 clearly knows how to evolve.

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niman
PostPosted: Tue Feb 01, 2011 11:49 am 
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There were a total of six isolates from Germany from three different locations (Nordrhein-Westfalen, Berlin, Baden-Wurttemberg). All six had S188T and five of the six had one or more changes at positions 156, 157, 158.

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niman
PostPosted: Tue Feb 01, 2011 12:00 pm 
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S188T at GISAID

EPI301934 A/Nordrhein-Westfalen/14/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301932 A/Nordrhein-Westfalen/13/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301930 A/Nordrhein-Westfalen/12/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301928 A/Nordrhein-Westfalen/11/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301926 A/Madagascar/7519/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301924 A/Madagascar/7473/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301922 A/Latvia/12-42162/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301908 A/England/143/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301906 A/Egypt/96/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301904 A/Egypt/104/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301902 A/Berlin/12/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301900 A/Baden-Wurttemberg/14/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301876 A/India/Delhi/ND210/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301875 A/India/Delhi/ND221/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301868 A/India/Delhi/ND314/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301845 A/Melilla/RR7085/2011 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301842 A/PaisVasco/RR7060/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301832 A/CastillaLaMancha/RR7050/2011 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301828 A/CastillaLaMancha/RR6918/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301827 A/Madrid/RR6998/2011 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301823 A/LaRioja/RR6970/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301819 A/Madrid/RR6981/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301817 A/Madrid/SO8210/2011 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301809 A/Andalucia/RR6901/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301802 A/Madrid/RR6872/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301801 A/Madrid/SO8034/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301725 A/Delaware/05/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301722 A/California/23/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301719 A/Texas/14/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301713 A/Hawaii/16/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301710 A/Oklahoma/01/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301704 A/Kenya/2708/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301683 A/North Carolina/14/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301674 A/Florida/15/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301444 A/Luxembourg/542/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301442 A/Luxembourg/519/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301441 A/Luxembourg/511/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301440 A/Luxembourg/498/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301439 A/Valladolid/53/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301437 A/Tehran/5858/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301435 A/Tehran/5652/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301425 A/Madrid/SO8034/10 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301421 A/La Reunion/823/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301419 A/La Reunion/815/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301417 A/La Reunion/803/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301409 A/England/151/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301407 A/England/142/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301405 A/England/127/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301403 A/England/119/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI301132 A/NIIGATA/1581/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI300983 A/Kentucky/09/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI300975 A/Utah/05/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI300972 A/Kentucky/08/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI298421 A/Karaj/5327/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI297191 A/Sendai/TU617/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI296641 A/Thailand/SN_0116/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295760 A/England/5040499/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295759 A/England/280/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295758 A/England/4940476/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295757 A/England/4920303/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295756 A/England/4880378/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295755 A/England/142/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295749 A/England/5000135/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295748 A/England/5000125/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295747 A/England/4980078/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295746 A/England/4980074/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295745 A/England/4960201/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295744 A/England/4940126/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295743 A/England/4860049/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295742 A/England/4840022/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295739 A/England/126/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295736 A/England/107/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295734 A/England/106/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295726 A/England/86/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295513 A/Thailand/742/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295498 A/Wisconsin/10/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295495 A/Thailand/594/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295459 A/India/5103/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295417 A/Wisconsin/09/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295411 A/Arizona/08/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI295382 A/KANAGAWA/74/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI294674 A/England/4880374/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI294417 A/VICTORIA/670/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI294405 A/BRUNEI/218/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI294391 A/SYDNEY/217/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI294388 A/SYDNEY/220/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI294297 A/PERTH/198/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI294282 A/BRISBANE/209/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI294195 A/BRISBANE/69/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI294115 A/VICTORIA/833/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI287020 A/Ghana/FS-10-4259/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI287018 A/Ghana/FS-10-4241/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI286992 A/Johannesburg/119/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI286990 A/Johannesburg/115/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI284010 A/Thailand/34-9937/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI284007 A/Thailand/34-9912/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI280311 A/India/8910/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI280289 A/Florida/14/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI279083 A/CHRISTCHURCH/15/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI279064 A/VICTORIA/512/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI278873 A/India/8910/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI278871 A/India/5107/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171
EPI255118 A/swine/Thailand/CU-RA75/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.95171

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niman
PostPosted: Tue Feb 01, 2011 12:13 pm 
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A/Iraq/21-SAK/2011 had D225G (as mixture) as well as D100N, R208K, I219V, V252L, E377K.

H1N1 knows how to evolve.

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niman
PostPosted: Tue Feb 01, 2011 2:23 pm 
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Commentary

http://www.recombinomics.com/News/02011 ... ny_LR.html

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Tex
PostPosted: Tue Feb 01, 2011 4:34 pm 
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If you were choosing the strain for the next influenza vaccine, what strain would you recommend?


Do they choose a couple, and then see which one has the best yield in production and narrow it down?
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