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niman
PostPosted: Fri Jan 21, 2011 8:18 am 
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A1449G

EPI301380 A/Stockholm/12/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI301377 A/Stockholm/11/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294886 A/Anas platyrhynchos/Belgium/04328 pcs17/2010 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI294420 A/DARWIN/165/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294397 A/SYDNEY/517/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294394 A/AUCKLAND/146/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294385 A/DARWIN/55/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294383 A/DARWIN/118/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294379 A/VICTORIA/906/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294369 A/FIJI/27/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294363 A/FIJI/3/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294354 A/DARWIN/156/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294348 A/DARWIN/150/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294336 A/AUCKLAND/56/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294333 A/DARWIN/143/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294330 A/WAIKATO/82/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294327 A/DARWIN/146/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294324 A/WELLINGTON/100/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294303 A/WELLINGTON/94/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294294 A/DARWIN/140/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294285 A/DARWIN/118/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294276 A/DARWIN/92/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294267 A/SOUTH AUSTRALIA/18/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294264 A/VICTORIA/891/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294240 A/DARWIN/95/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294237 A/VICTORIA/880/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294234 A/VICTORIA/881/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294231 A/VICTORIA/866/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294207 A/BRISBANE/107/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294204 A/TOWNSVILLE/10/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294201 A/VICTORIA/858/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294198 A/DARWIN/64/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294174 A/DARWIN/96/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294168 A/DARWIN/84/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294165 A/BRISBANE/76/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294162 A/VICTORIA/571/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294147 A/SOUTH AUCKLAND/20/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294141 A/VICTORIA/848/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI294112 A/DARWIN/55/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279911 A/Stockholm/3/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279211 A/TOWNSVILLE/2/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279162 A/VICTORIA/808/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279155 A/CHRISTCHURCH/5/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279153 A/DARWIN/51A/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279129 A/SOUTH AUCKLAND/10/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279121 A/WAIKATO/5/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279115 A/SOUTH AUCKLAND/2/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279098 A/BRISBANE/20/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279097 A/BRISBANE/19/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279085 A/CHRISTCHURCH/18/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI279059 A/VICTORIA/507/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI271774 A/Singapore/SS012/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI265956 A/Stockholm/3/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI258148 A/Fujian-Yanping/SWL146/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI227124 A/duck/France/05056a/2005 (A/H5N2) segment 4 (HA) 27.0 5.93318
EPI217570 A/Mexico City/011/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI177653 A/swine/Hong Kong/294/2009 (A/H1N2) segment 4 (HA) 27.0 5.93318
EPI172963 A/swine/Ratchaburi/NIAH550/2003 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI110462 A/Philippines/344/2004 (A/H1N2 swl) segment 4 (HA) 27.0 5.93318

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niman
PostPosted: Fri Jan 21, 2011 8:45 am 
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niman wrote:
Swedish Institute for Infectious Disease Control has released three December, 2010 HA sequences (at GISAID) which did not have S186P or S188T. One, A/Jonkoping/1/2010, was from a 10 year old boy who had been vaccinated with 1 dose of Pandemerix.

Swedish sequences are still being added. A/Stockholm/9/2010 is a November 11 isolate and is very closely related to A/Jonkoping/1/2010.

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niman
PostPosted: Fri Jan 21, 2011 9:48 am 
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niman wrote:
niman wrote:
Swedish Institute for Infectious Disease Control has released three December, 2010 HA sequences (at GISAID) which did not have S186P or S188T. One, A/Jonkoping/1/2010, was from a 10 year old boy who had been vaccinated with 1 dose of Pandemerix.

Swedish sequences are still being added. A/Stockholm/9/2010 is a November 11 isolate and is very closely related to A/Jonkoping/1/2010.

Two more sequences added, including A/Stockholm/13/2010, which has S186P and is the most recent (December 13, 2010).

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niman
PostPosted: Fri Jan 21, 2011 9:50 am 
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niman wrote:
C148T pedigree

EPI301383 A/Jonkoping/1/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI300969 A/Indiana/06/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI295737 A/England/124/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI295414 A/Michigan/06/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI276897 A/Pennsylvania/30/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI273013 A/swine/Thailand/CU-CB1/2006 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI257788 A/Jiangsu-Beitang/SWL164/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI248464 A/swine/Ratchaburi/NIAH101942/2008 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI248463 A/swine/Ratchaburi/NIAH101942/2008 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI248462 A/swine/Ratchaburi/NIAH101942/2008 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI245784 A/ENG/93040050/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI245753 A/ENG/92900383/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI237374 A/Wisconsin/629-D00589/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI236511 A/ENG/604/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI218842 A/Wisconsin/629-D01618/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI218802 A/Wisconsin/629-D01262/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI218674 A/Wisconsin/629-D00579/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI214738 A/Wisconsin/629-D02227/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI214410 A/Wisconsin/629-D01092/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI214394 A/Wisconsin/629-D01055/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI211913 A/Catalonia/NS508/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI190629 A/swine/Guangdong/1/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI173663 A/swine/Thailand/HF6/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI172971 A/swine/Chonburi/NIAH9469/2004 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI172939 A/swine/Chachoengsao/NIAH587/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI172931 A/swine/Chonburi/NIAH589/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI172923 A/swine/Chonburi/NIAH977/2004 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI126853 A/swine/Chonburi/06CB2/2006 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI126849 A/swine/Chonburi/05CB1/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI126845 A/swine/Chachoengsao/NIAH587/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI126841 A/swine/Chonburi/NIAH589/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI6767 A/Swine/Wisconsin/464/98 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI6765 A/Swine/Wisconsin/458/98 (A/H1N1) segment 4 (HA) 27.0 5.93318

Update
EPI301392 A/Stockholm/8/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93348
EPI301389 A/Stockholm/9/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93348

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niman
PostPosted: Fri Jan 21, 2011 9:57 am 
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A/Stockholm/13/2010 similar to A/Shahriar/5336/2010.

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niman
PostPosted: Fri Jan 21, 2011 10:00 am 
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Stockholm/8 matches Stockholm/9

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niman
PostPosted: Wed Jan 26, 2011 9:42 am 
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A/Stockholm/15/2010 (collected December 13) has G158E.

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niman
PostPosted: Wed Jan 26, 2011 9:45 am 
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niman wrote:
A/Stockholm/15/2010 (collected December 13) has G158E.

G158E is appended onto background found in A/Jonkoping/1/2010, A/Stockholm/8/2010, A/Stockholm/9/2010, A/Stockholm/14/2010, A/PaisVasco/RR6909/10 .

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Last edited by niman on Wed Jan 26, 2011 10:04 am, edited 2 times in total.

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niman
PostPosted: Wed Jan 26, 2011 9:57 am 
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Location: Pittsburgh, PA USA
niman wrote:
C148T pedigree

EPI301383 A/Jonkoping/1/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI300969 A/Indiana/06/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI295737 A/England/124/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI295414 A/Michigan/06/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI276897 A/Pennsylvania/30/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI273013 A/swine/Thailand/CU-CB1/2006 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI257788 A/Jiangsu-Beitang/SWL164/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI248464 A/swine/Ratchaburi/NIAH101942/2008 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI248463 A/swine/Ratchaburi/NIAH101942/2008 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI248462 A/swine/Ratchaburi/NIAH101942/2008 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI245784 A/ENG/93040050/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI245753 A/ENG/92900383/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI237374 A/Wisconsin/629-D00589/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI236511 A/ENG/604/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI218842 A/Wisconsin/629-D01618/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI218802 A/Wisconsin/629-D01262/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI218674 A/Wisconsin/629-D00579/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI214738 A/Wisconsin/629-D02227/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI214410 A/Wisconsin/629-D01092/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI214394 A/Wisconsin/629-D01055/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI211913 A/Catalonia/NS508/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.93318
EPI190629 A/swine/Guangdong/1/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI173663 A/swine/Thailand/HF6/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI172971 A/swine/Chonburi/NIAH9469/2004 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI172939 A/swine/Chachoengsao/NIAH587/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI172931 A/swine/Chonburi/NIAH589/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI172923 A/swine/Chonburi/NIAH977/2004 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI126853 A/swine/Chonburi/06CB2/2006 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI126849 A/swine/Chonburi/05CB1/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI126845 A/swine/Chachoengsao/NIAH587/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI126841 A/swine/Chonburi/NIAH589/2005 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI6767 A/Swine/Wisconsin/464/98 (A/H1N1) segment 4 (HA) 27.0 5.93318
EPI6765 A/Swine/Wisconsin/458/98 (A/H1N1) segment 4 (HA) 27.0 5.93318

Update
EPI301779 A/Stockholm/14/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI301776 A/Stockholm/15/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI301447 A/PaisVasco/RR6909/10 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI301392 A/Stockholm/8/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI301389 A/Stockholm/9/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029

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niman
PostPosted: Wed Jan 26, 2011 9:58 am 
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Posts: 27555
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A183G
EPI301779 A/Stockholm/14/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI301776 A/Stockholm/15/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI301447 A/PaisVasco/RR6909/10 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI301392 A/Stockholm/8/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI301389 A/Stockholm/9/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI301383 A/Jonkoping/1/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI297193 A/Sendai/TU619/2009 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI278693 A/KOBE/181/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI277566 A/AICHI/116/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI272642 A/YOKOHAMA/67/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI272421 A/SHIZUOKA-C/38/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI258060 A/Guangxi-Fangcheng/SWL1130/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029
EPI257980 A/Guangxi-Yuzhou/SWL125/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.94029

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