Rhiza Labs FluTracker Forum

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

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