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PostPosted: Tue May 03, 2011 5:37 pm 
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The CDC has released another series of 2011 H1N1 isolates (at GISAID), including 3 closely related Chihuahua sub-clade sequences from PA, TX, NJ. PA and TX were also represented in the 5 Chihuahua sequences released earlier.

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PostPosted: Tue May 03, 2011 5:37 pm 
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Newly released sequences with K149N

EPI316451 A/Texas/08/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316424 A/Pennsylvania/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316387 A/New Jersey/05/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618

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PostPosted: Tue May 03, 2011 5:42 pm 
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K149N at GISAID

EPI316451 A/Texas/08/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316424 A/Pennsylvania/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316387 A/New Jersey/05/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI315913 A/Mexico/InDRE2222/2011 (A/H1N1) segment 4 (HA) 27.0 6.37426
EPI315901 A/Mexico/InDRE2200/2011 (A/H1N1) segment 4 (HA) 27.0 6.37426
EPI315898 A/Mexico/InDRE2197/2011 (A/H1N1) segment 4 (HA) 27.0 6.37426
EPI315895 A/Mexico/InDRE2195/2011 (A/H1N1) segment 4 (HA) 27.0 6.37426
EPI315891 A/Mexico/InDRE2192/2011 (A/H1N1) segment 4 (HA) 27.0 6.37426
EPI315840 A/Mexico/InDRE1947/2011 (A/H1N1) segment 4 (HA) 27.0 6.37426
EPI315838 A/Mexico/InDRE1946/2011 (A/H1N1) segment 4 (HA) 27.0 6.37426
EPI315836 A/Mexico/InDRE1945/2011 (A/H1N1) segment 4 (HA) 27.0 6.37426
EPI310133 A/Utah/08/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.31707
EPI310130 A/Texas/07/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.31707
EPI310103 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.31707
EPI310093 A/Oregon/03/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.31707
EPI309970 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA)
EPI266546 A/Boston/115/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI218962 A/Wisconsin/629-D02206/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500

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PostPosted: Tue May 03, 2011 5:46 pm 
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K149N at Genbank

CY089848.1 Influenza A virus (A/Mexico/InDRE2413/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 224 100%
CY089605.1 Influenza A virus (A/Mexico/InDRE2222/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY089593.1 Influenza A virus (A/Mexico/InDRE2200/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY089590.1 Influenza A virus (A/Mexico/InDRE2197/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY089587.1 Influenza A virus (A/Mexico/InDRE2195/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY089583.1 Influenza A virus (A/Mexico/InDRE2192/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY089391.1 Influenza A virus (A/Mexico/InDRE1947/2011(H1N1)) hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY089389.1 Influenza A virus (A/Mexico/InDRE1946/2011(H1N1)) hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY089387.1 Influenza A virus (A/Mexico/InDRE1945/2011(H1N1)) hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY064500.1 Influenza A virus (A/Boston/115/2009(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
CY050420.1 Influenza A virus (A/Wisconsin/629-D02206/2009(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%

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PostPosted: Tue May 03, 2011 5:48 pm 
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Combination of T462A and A489C at GISAID

EPI316451 A/Texas/08/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI316424 A/Pennsylvania/04/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI316387 A/New Jersey/05/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI315913 A/Mexico/InDRE2222/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315901 A/Mexico/InDRE2200/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315898 A/Mexico/InDRE2197/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315895 A/Mexico/InDRE2195/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315891 A/Mexico/InDRE2192/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315840 A/Mexico/InDRE1947/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315838 A/Mexico/InDRE1946/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI315836 A/Mexico/InDRE1945/2011 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI310133 A/Utah/08/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI310130 A/Texas/07/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI310103 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI310093 A/Oregon/03/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI309970 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000

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PostPosted: Tue May 03, 2011 5:53 pm 
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TX/08 was 5M collected March 6
PA/04 was 22M collected March 13
NJ/05 was 3 M collected March 3

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PostPosted: Tue May 03, 2011 6:41 pm 
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35 HA sequences were released (at GISAID). Almost all were 2011 and collected in Feb and Mar. Some were from otherr countries and most sequences (23) had S188T followed by S186P (5).

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PostPosted: Tue May 03, 2011 6:44 pm 
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niman wrote:
35 HA sequences were released (at GISAID). Almost all were 2011 and collected in Feb and Mar. Some were from otehr countries and most sequences had S188T followed by S186P.

Recent sequences with S188T
EPI316490 A/Wisconsin/16/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316478 A/Wisconsin/11/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316471 A/Washington/08/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316460 A/Utah/10/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316448 A/Tennessee/01/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316442 A/Tanzania/42/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316435 A/St. Petersburg/100/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316427 A/Puerto Rico/01/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316421 A/Oregon/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316418 A/Ohio/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316415 A/North Dakota/05/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316402 A/North Carolina/07/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316384 A/Nebraska/10/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316381 A/Montana/06/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316369 A/Kenya/1179/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316366 A/Kentucky/18/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316363 A/Indiana/07/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316360 A/Indiana/05/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316349 A/Florida/12/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316342 A/Delaware/06/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316341 A/Colorado/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316338 A/California/19/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316329 A/Alabama/02/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618

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PostPosted: Tue May 03, 2011 6:46 pm 
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S186P

EPI316493 A/Wisconsin/17/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316475 A/Washington/09/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316378 A/Mississippi/07/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316352 A/Georgia/02/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316335 A/California/17/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618

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PostPosted: Tue May 03, 2011 7:14 pm 
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niman wrote:
Newly released sequences with K149N

EPI316451 A/Texas/08/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316424 A/Pennsylvania/04/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618
EPI316387 A/New Jersey/05/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.39618

The above three HA sequences exactly match each other as well as TX/07, OR/03, MD/04

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