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'''2009 H1N1 swine flu genome and protein analysis'''
'''2009 H1N1 swine flu genome and protein analysis'''


This page was created by Michael Strong, other contributers include ...
[[User:Michael_Strong|home]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1|H1N1]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/PB2|PB2]]<font color="blue">•</font> [[User:Michael_Strong/H1N1/PB1|PB1]]<font color="blue">•</font>  [[User:Michael_Strong/H1N1/PA|PA]]  <font color="blue">•</font> [[User:Michael_Strong/H1N1/HA|HA]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NP|NP]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NA|NA]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/MP|MP]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NS|NS]]


[[User:Michael_Strong|home]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1|H1N1]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/PB2|PB2]]<font color="blue">•</font> [[User:Michael_Strong/H1N1/PB1|PB1]]<font color="blue">•</font>  [[User:Michael_Strong/H1N1/PA|PA]]  <font color="blue">•</font> [[User:Michael_Strong/H1N1/HA|HA]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NP|NP]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NA|NA]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/MP|MP]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NS|NS]]


Shown below are Protein Structural Homology Models of the PB2, PA, HA, NP, NA, MP1, MP2, NS1 and NS2 proteins from the 2009 Mexico [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=643780 A/Mexico/InDRE4487/2009] H1N1 Swine flu genome.  Sequence polymorphisms of the PB2, PB1, PA, HA, NP, NA, MP1, MP2, NS1 and NS2 proteins are also indicated, as identified by comparison of subsequently sequenced 2009 H1N1 strains from around the globe.  The "green links" next to the listed amino acids highlight the amino acid polymorphisms in the structural homology models. More detail on each protein, including Multiple Sequence Alignments of newly sequence H1N1 strains, Sequence Polymorphisms, and Related Sequence Homologs are provided on the individual protein pages (links above). 
Genome and protein sequences obtained from: http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html. Multiple sequence alignments of the PB2, PB1, PA, HA, NP, NA, MP, and NS proteins from 2009 H1N1 strains from Mexico, California, Texas, New York, and Canada are also provided below. 


Shown below are Clustal Multiple Sequence Alignmnents of the Protein Sequences from five strains of the recent 2009 H1N1 Swine Influenza Virus, including isolates from Mexico, California, Texas, New York, and Canada.  Protein sequences obtained from: http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html. Multiple sequence alignments of the PB2, PB1, PA, HA, NP, NA, MP, and NS proteins are provided.
== PB2 Protein Structural Homolgy Model ==
== PB2 Protein Structural Homolgy Model ==


<applet load='MPB21.pdb' size='300' frame='true' align='center' caption='PB2 Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009, residues 535-742, 95% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3cw4 3cw4]' scene ='User:Michael_Strong/H1N1/PB2/MSA/1/1' />
<applet load='MPB21.pdb' size='300' frame='true' align='center' caption='PB2 Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998206 A/Mexico/InDRE4487/2009 PB2], residues 535-742, 95% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3cw4 3cw4]' scene ='User:Michael_Strong/H1N1/PB2/MSA/1/1' />


=== PB2 Sequence Polymorphisms ===
=== PB2 Sequence Polymorphisms ===
Line 69: Line 70:
|1
|1
|<scene name='User:Michael_Strong/H1N1/PB2/MSA/2/1'>G698</scene>
|<scene name='User:Michael_Strong/H1N1/PB2/MSA/2/1'>G698</scene>
|----
|}
== PB1 Sequence Polymorphisms ==
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|PB1
|L10V
|gi|229396439_A/New_York/10/200
|1
|----
|PB1
|I12T
|gi|229536040_A/Arizona/02/2009
|1
|----
|PB1
|Q48R
|gi|229783391_A/New_York/1669/2
|1
|----
|PB1
|A157V
|gi|229487525_A/Canada-NS/RV153
|2
|----
|PB1
|A370G
|gi|237624323_A/swine/Alberta/O
|1
|----
|PB1
|F466S
|gi|237624323_A/swine/Alberta/O
|1
|----
|PB1
|V587A
|gi|229487525_A/Canada-NS/RV153
|3
|----
|PB1
|N641S
|gi|229892784_A/Canada-NS/RV153
|1
|----
|PB1
|M646V
|gi|237624323_A/swine/Alberta/O
|1
|----
|PB1
|S665F
|gi|237624323_A/swine/Alberta/O
|1
|----
|PB1
|S678N
|gi|229396395_A/New_York/18/200
|1
|----
|----
|}
|}




== PA Structure ==


<applet load='MSPA1.pdb' size='300' frame='true' align='center' caption='PA Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009, residues 257-716, 97% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3cm8 3cm8]' scene ='User:Michael_Strong/H1N1/PA/MSA/1/1'/>
== PA Protein Structural Homolgy Model ==


=== PA Polymorphisms ===
<applet load='MSPA1.pdb' size='300' frame='true' align='center' caption='PA Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998223 A/Mexico/InDRE4487/2009 PA], residues 257-716, 97% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3cm8 3cm8]' scene ='User:Michael_Strong/H1N1/PA/MSA/1/1'/>
 
=== PA Sequence Polymorphisms ===


{| class="wikitable"
{| class="wikitable"
Line 116: Line 183:
|}
|}


== HA Protein Structural Homolgy Model  ==
<applet load='MSHA2.pdb' size='300' frame='true' align='center' caption='HA Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998208 A/Mexico/InDRE4487/2009 HA], residues 16-341, 83% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3gbn 3gbn]' scene ='User:Michael_Strong/H1N1/HA/MSA/1/1'/>
=== HA Sequence Polymorphisms ===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|HA
|V7I
|gi|237624327_A/swine/Alberta/O
|1
|----
|HA
|L8M
|gi|227831776_A/California/06/2
|5
|----
|HA
|A13T
|gi|229536010_A/Kansas/03/2009
|1
|----
|HA
|N48D
|gi|229536049_A/Arizona/02/2009
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/48/1'>48</scene>
|----
|HA
|L49I
|gi|229535997_A/South_Carolina/
|2
|<scene name='User:Michael_Strong/H1N1/HA/MSA/49/1'>49</scene>
|----
|HA
|I96V
|gi|229598877_A/Ohio/07/2009
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/96/1'>96</scene>
|----
|HA
|S100P
|gi|229535949_A/California/04/2
|5
|<scene name='User:Michael_Strong/H1N1/HA/MSA/100/1'>100</scene>
|----
|HA
|N104K
|gi|229892708_A/Canada-AB/RV153
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/104/1'>104</scene>
|----
|HA
|V125M
|gi|229598896_A/Texas/15/2009
|2
|<scene name='User:Michael_Strong/H1N1/HA/MSA/125/1'>125</scene>
|----
|HA
|V149I
|gi|229536088_A/Indiana/09/2009
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/149/1'>149</scene>
|----
|HA
|A214T
|gi|229535949_A/California/04/2
|2
|<scene name='User:Michael_Strong/H1N1/HA/MSA/214/1'>214</scene>
|----
|HA
|Y215N
|gi|237624327_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/215/1'>215</scene>
|----
|HA
|S220T
|gi|229396494_A/Ohio/07/2009
|21
|<scene name='User:Michael_Strong/H1N1/HA/MSA/220/1'>220</scene>
|----
|HA
|F227L
|gi|229598896_A/Texas/15/2009
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/227/1'>227</scene>
|----
|HA
|D239G
|gi|229892706A/Mexico/InDRE4114
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/239/2'>239</scene>
|----
|HA
|D291E
|gi|229535997_A/South_Carolina/
|2
|<scene name='User:Michael_Strong/H1N1/HA/MSA/291/1'>291</scene>
|----
|HA
|N293D
|gi|229783398_A/New_York/1682/2
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/293/2'>293</scene>
|----
|HA
|V338I
|gi|229535949_A/California/04/2
|5
|<scene name='User:Michael_Strong/H1N1/HA/MSA/338/1'>338</scene>
|----
|HA
|A351V
|gi|237624327_A/swine/Alberta/O
|1
|----
|HA
|I400V
|gi|229484027_A/Canada-NS/RV153
|3
|----
|HA
|V428I
|gi|229598877_A/Ohio/07/2009
|4
|----
|HA
|V444I
|gi|237511819_A/Mexico/4108/200
|1
|----
|HA
|I527F
|gi|229892706A/Mexico/InDRE4114
|1
|----
|}
<scene name='User:Michael_Strong/H1N1/HA/MSA/All/1'>All Polymorphisms</scene>
== NP Protein Structural Homolgy Model  ==
<applet load='MSNP1.pdb' size='300' frame='true' align='center' caption='NP Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998217 A/Mexico/InDRE4487/2009 NP], residues 28-502, 94% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/2q06 2q06]' scene ='User:Michael_Strong/H1N1/NP/MSA/1/1'/>
=== NP Sequence Polymorphisms ===


{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|NP
|G22D
|gi|229598884_A/Texas/15/2009
|1
|----
|NP
|V35A
|gi|237624329_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/35/1'>35</scene>
|----
|NP
|S90N
|gi|229536012_A/Arizona/01/2009
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/90/1'>90</scene>
|----
|NP
|V106I
|gi|229892748_A/Canada-ON/RV152
|28
|<scene name='User:Michael_Strong/H1N1/NP/MSA/106/1'>106</scene>
|----
|NP
|Q128L
|gi|227977162_A/California/07/2
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/128/1'>128</scene>
|----
|NP
|L139I
|gi|229783384_A/New_York/1669/2
|2
|<scene name='User:Michael_Strong/H1N1/NP/MSA/139/1'>139</scene>
|----
|NP
|E198K
|gi|237624329_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/198/1'>198</scene>
|----
|NP
|N208D
|gi|237624329_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/208/1'>208</scene>
|----
|NP
|V223I
|gi|229536102_A/Nebraska/02/200
|2
|<scene name='User:Michael_Strong/H1N1/NP/MSA/223/1'>223</scene>
|----
|NP
|M228T
|gi|237624329_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/228/1'>228</scene>
|----
|NP
|A257T
|gi|229396492_A/Ohio/07/2009
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/257/1'>257</scene>
|----
|NP
|V349I
|gi|229536131_A/Colorado/03/200
|2
|<scene name='User:Michael_Strong/H1N1/NP/MSA/349/1'>349</scene>
|----
|NP
|V358M
|gi|229598873_A/Ohio/07/2009
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/358/1'>358</scene>
|----
|NP
|V369I
|gi|229536077_A/Indiana/09/2009
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/369/1'>369</scene>
|----
|NP
|T379I
|gi|229536102_A/Nebraska/02/200
|18
|<scene name='User:Michael_Strong/H1N1/NP/MSA/379/1'>379</scene>
|----
|NP
|T379V
|gi|229892752_A/Canada-NS/RV153
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/379/1'>379</scene>
|----
|NP
|D381N
|gi|229396423_A/California/08/2
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/381/1'>381</scene>
|----
|NP
|D381Y
|gi|237624329_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/381/1'>381</scene>
|----
|NP
|T402A
|gi|237511901_A/Mexico/4516/200
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/402/1'>402</scene>
|----
|NP
|S456N
|gi|229536077_A/Indiana/09/2009
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/456/1'>456</scene>
|----
|}
<scene name='User:Michael_Strong/H1N1/NP/MSA/All/1'>All Polymorphisms</scene>
== NA Protein Structural Homolgy Model  ==
<applet load='MSNA1.pdb' size='300' frame='true' align='center' caption='NA Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998214 A/Mexico/InDRE4487/2009 NA], residues 83-467, 89% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3b7e 3b7e]' scene ='User:Michael_Strong/H1N1/NA/MSA/1/1'/>
=== NA Sequence Polymorphisms ===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|NA
|H36R
|gi|229892732_A/Mexico/InDRE411
|1
|----
|NA
|E57K
|gi|229536081_A/Indiana/09/2009
|1
|----
|NA
|V83M
|gi|229536111_A/Michigan/02/200
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/83/1'>83</scene>
|----
|NA
|S95G
|gi|228017756_A/California/06/2
|5
|<scene name='User:Michael_Strong/H1N1/NA/MSA/95/2'>95</scene>
|----
|NA
|G96E
|gi|237624331_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/96/2'>96</scene>
|----
|NA
|Y100H
|gi|237624331_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/100/1'>100</scene>
|----
|NA
|V106I
|gi|228481034_A/Auckland/3/2009
|30
|<scene name='User:Michael_Strong/H1N1/NA/MSA/106/1'>106</scene>
|----
|NA
|I108V
|gi|228860931_A/Netherlands/602
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/108/1'>108</scene>
|----
|NA
|P120S
|gi|229892684_A/Catalonia/P48/2
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/120/1'>120</scene>
|----
|NA
|S123L
|gi|237624331_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/123/1'>123</scene>
|----
|NA
|V241I
|gi|229535806_A/Texas/09/2009
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/241/1'>241</scene>
|----
|NA
|N248D
|gi|229396353_A/New_York/12/200
|30
|<scene name='User:Michael_Strong/H1N1/NA/MSA/248/1'>248</scene>
|----
|NA
|N307T
|gi|228481034_A/Auckland/3/2009
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/307/1'>307</scene>
|----
|NA
|S319R
|gi|229892682_A/Korea/01/2009
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/319/1'>319</scene>
|----
|NA
|S334C
|gi|237624331_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/334/1'>334</scene>
|----
|}
<scene name='User:Michael_Strong/H1N1/NA/MSA/All/1'>All Polymorphisms</scene>
==MP1 Protein Structural Homolgy Model  ==
<applet load='MMP21.pdb' size='300' frame='true' align='center' caption='MP2 Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998211 A/Mexico/InDRE4487/2009 MP1], residues 23-60, 82% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/2rlf 2rlf]' scene ='User:Michael_Strong/H1N1/MP/1/2'/>
===MP1 Sequence Polymorphisms===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|MP1
|L3P
|gi|227831763_A/California/05/2
|1
|<scene name='User:Michael_Strong/H1N1/MP/3/2'>3</scene>
|----
|MP1
|H222R
|gi|237624333_A/swine/Alberta/O
|1
|----
|MP1
|A227T
|gi|229484039_A/Canada-ON/RV152
|2
|----
|}
==MP2 Protein Structural Homolgy Model ==
<applet load='MMP21.pdb' size='300' frame='true' align='center' caption='MP2 Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998211 A/Mexico/InDRE4487/2009 MP2], residues 23-60, 82% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/2rlf 2rlf]' scene ='User:Michael_Strong/H1N1/MP2/MSA/1/1'/>
===MP2 Sequence Polymorphisms ===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|MP2
|L3P
|gi|227831764_A/California/05/2
|1
|----
|MP2
|Y52H
|gi|229609551_A/Stockholm/28/20
|1
|<scene name='User:Michael_Strong/H1N1/MP2/MSA/52/1'>52</scene>
|----
|MP2
|T65M
|gi|229536073_A/Texas/07/2009
|1
|----
|MP2
|S82N
|gi|237511788_A/Mexico/4108/200
|1
|----
|}
== NS1 Protein Structural Homolgy Model  ==
<applet load='MNS21.pdb' size='300' frame='true' align='center' caption='NS1 Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998220 A/Mexico/InDRE4487/2009 NS1], residues 5-202, 84% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3f5t 3f5t]' scene ='User:Michael_Strong/H1N1/NS1/MSA/1/1'/>
=== NS1 Sequence Polymorphisms ===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|NS1
|D12E
|gi|229536107_A/Nebraska/02/200
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/12/1'>12</scene>
|----
|NS1
|F32L
|gi|229535811_A/Texas/09/2009
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/32/1'>32</scene>
|----
|NS1
|G45R
|gi|229598886_A/Texas/15/2009
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/45/1'>45</scene>
|----
|NS1
|R88C
|gi|229536033_A/Minnesota/02/20
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/88/1'>88</scene>
|----
|NS1
|E97G
|gi|229892754_A/Canada-NS/RV153
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/97/1'>97</scene>
|----
|NS1
|M104T
|gi|237624336_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/104/1'>104</scene>
|----
|NS1
|I123V
|gi|229892764_A/Canada-AB/RV153
|15
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/123/1'>123</scene>
|----
|NS1
|F134I
|gi|237624336_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/134/1'>134</scene>
|----
|}
<scene name='User:Michael_Strong/H1N1/NS1/MSA/All/2'>All Polymorphisms</scene>
== NS2 Protein Structural Homolgy Model ==
<applet load='MNS22.pdb' size='300' frame='true' align='center' caption='NS2 Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998220 A/Mexico/InDRE4487/2009 NS2], residues 64-116, 94% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/1pd3 1pd3]' scene ='User:Michael_Strong/H1N1/NS2/MSA/1/1'/>
=== NS2 Sequence Polymorphisms ===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|NS2
|E63K
|gi|229783374_A/Korea/01/2009
|1
|----
|NS2
|E67K
|gi|229598887_A/Texas/15/2009
|1
|<scene name='User:Michael_Strong/H1N1/NS2/MSA/67/1'>67</scene>
|----
|NS2
|A89E
|gi|228017754_A/California/06/2
|3
|<scene name='User:Michael_Strong/H1N1/NS2/MSA/89/1'>89</scene>
|----
|NS2
|A115T
|gi|229892755_A/Canada-NS/RV153
|1
|<scene name='User:Michael_Strong/H1N1/NS2/MSA/115/1'>115</scene>
|----
|}
<scene name='User:Michael_Strong/H1N1/NS2/MSA/All/1'>All Polymorphisms</scene>
==Multiple Sequence Alignment of 5 H1N1 Strains==
===multiple sequence alignment of PB2===
===multiple sequence alignment of PB2===


Line 240: Line 859:


--------------------
--------------------
===multiple sequence alignment of PB1===
'''PB1'''
'''PB1'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 359: Line 979:


--------------------
--------------------
===multiple sequence alignment of PA===
'''PA'''
'''PA'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 473: Line 1,094:


--------------------
--------------------
===multiple sequence alignment of HA===
'''HA'''
'''HA'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 563: Line 1,185:


--------------------
--------------------
===multiple sequence alignment of NP===
'''NP'''
'''NP'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 644: Line 1,267:
                             ****
                             ****
</PRE><SPAN class=3Dpsmall>
</PRE><SPAN class=3Dpsmall>


--------------------
--------------------
===multiple sequence alignment of NA===
'''NA'''
'''NA'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 722: Line 1,347:


--------------------
--------------------
===multiple sequence alignment of MP===
'''MP'''
'''MP'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 770: Line 1,396:


--------------------
--------------------
===multiple sequence alignment of NS===
'''NS'''
'''NS'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =

Latest revision as of 23:53, 21 December 2009

2009 H1N1 swine flu genome and protein analysis

home • H1N1 • PB2• PB1• PA • HA • NP • NA • MP • NS


Shown below are Protein Structural Homology Models of the PB2, PA, HA, NP, NA, MP1, MP2, NS1 and NS2 proteins from the 2009 Mexico A/Mexico/InDRE4487/2009 H1N1 Swine flu genome. Sequence polymorphisms of the PB2, PB1, PA, HA, NP, NA, MP1, MP2, NS1 and NS2 proteins are also indicated, as identified by comparison of subsequently sequenced 2009 H1N1 strains from around the globe. The "green links" next to the listed amino acids highlight the amino acid polymorphisms in the structural homology models. More detail on each protein, including Multiple Sequence Alignments of newly sequence H1N1 strains, Sequence Polymorphisms, and Related Sequence Homologs are provided on the individual protein pages (links above).

Genome and protein sequences obtained from: http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html. Multiple sequence alignments of the PB2, PB1, PA, HA, NP, NA, MP, and NS proteins from 2009 H1N1 strains from Mexico, California, Texas, New York, and Canada are also provided below.

PB2 Protein Structural Homolgy ModelPB2 Protein Structural Homolgy Model

PB2 Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009 PB2, residues 535-742, 95% sequence identity to pdp template 3cw4

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PB2 Sequence PolymorphismsPB2 Sequence Polymorphisms

Protein Polymorphism Strain with Polymorphism Number of Strains with Polymorphism
PB2 I30V 229892696_A/Canada-AB/RV153 1
PB2 N82S 229484025_A/Mexico/InDRE448 all others
PB2 H151Q 237624321_A/swine/Alberta/O 1
PB2 D161N 227831783_A/California/06/2 1
PB2 V267I 229783414_A/New_York/1682/2 1
PB2 S324R 237624321_A/swine/Alberta/O 1
PB2 H432Y 237624321_A/swine/Alberta/O 1
PB2 L464M 229892692_A/Mexico/InDRE411 1
PB2 K526R 229892698_A/Canada-NS/RV153 5
PB2 G698D 227831783_A/California/06/2 1

PB1 Sequence PolymorphismsPB1 Sequence Polymorphisms

Protein Polymorphism Strain with Polymorphism Number of Strains with Polymorphism
PB1 L10V 229396439_A/New_York/10/200 1
PB1 I12T 229536040_A/Arizona/02/2009 1
PB1 Q48R 229783391_A/New_York/1669/2 1
PB1 A157V 229487525_A/Canada-NS/RV153 2
PB1 A370G 237624323_A/swine/Alberta/O 1
PB1 F466S 237624323_A/swine/Alberta/O 1
PB1 V587A 229487525_A/Canada-NS/RV153 3
PB1 N641S 229892784_A/Canada-NS/RV153 1
PB1 M646V 237624323_A/swine/Alberta/O 1
PB1 S665F 237624323_A/swine/Alberta/O 1
PB1 S678N 229396395_A/New_York/18/200 1


PA Protein Structural Homolgy ModelPA Protein Structural Homolgy Model

PA Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009 PA, residues 257-716, 97% sequence identity to pdp template 3cm8

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PA Sequence PolymorphismsPA Sequence Polymorphisms

Protein Polymorphism Strain with Polymorphism Number of Strains with Polymorphism
PA S224P 227977170_A/California/07/2 6
PA R269K 229484063_A/Canada-NS/RV153 2
PA L275I 229484065_A/Mexico/InDRE448 all others
PA M581L 237511889_A/Mexico/4108/200 11
PA L702P 237624325_A/swine/Alberta/O 1

HA Protein Structural Homolgy ModelHA Protein Structural Homolgy Model

HA Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009 HA, residues 16-341, 83% sequence identity to pdp template 3gbn

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HA Sequence PolymorphismsHA Sequence Polymorphisms

Protein Polymorphism Strain with Polymorphism Number of Strains with Polymorphism
HA V7I 237624327_A/swine/Alberta/O 1
HA L8M 227831776_A/California/06/2 5
HA A13T 229536010_A/Kansas/03/2009 1
HA N48D 229536049_A/Arizona/02/2009 1
HA L49I 229535997_A/South_Carolina/ 2
HA I96V 229598877_A/Ohio/07/2009 1
HA S100P 229535949_A/California/04/2 5
HA N104K 229892708_A/Canada-AB/RV153 1
HA V125M 229598896_A/Texas/15/2009 2
HA V149I 229536088_A/Indiana/09/2009 1
HA A214T 229535949_A/California/04/2 2
HA Y215N 237624327_A/swine/Alberta/O 1
HA S220T 229396494_A/Ohio/07/2009 21
HA F227L 229598896_A/Texas/15/2009 1
HA D239G 229892706A/Mexico/InDRE4114 1
HA D291E 229535997_A/South_Carolina/ 2
HA N293D 229783398_A/New_York/1682/2 1
HA V338I 229535949_A/California/04/2 5
HA A351V 237624327_A/swine/Alberta/O 1
HA I400V 229484027_A/Canada-NS/RV153 3
HA V428I 229598877_A/Ohio/07/2009 4
HA V444I 237511819_A/Mexico/4108/200 1
HA I527F 229892706A/Mexico/InDRE4114 1

NP Protein Structural Homolgy ModelNP Protein Structural Homolgy Model

NP Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009 NP, residues 28-502, 94% sequence identity to pdp template 2q06

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NP Sequence PolymorphismsNP Sequence Polymorphisms

Protein Polymorphism Strain with Polymorphism Number of Strains with Polymorphism
NP G22D 229598884_A/Texas/15/2009 1
NP V35A 237624329_A/swine/Alberta/O 1
NP S90N 229536012_A/Arizona/01/2009 1
NP V106I 229892748_A/Canada-ON/RV152 28
NP Q128L 227977162_A/California/07/2 1
NP L139I 229783384_A/New_York/1669/2 2
NP E198K 237624329_A/swine/Alberta/O 1
NP N208D 237624329_A/swine/Alberta/O 1
NP V223I 229536102_A/Nebraska/02/200 2
NP M228T 237624329_A/swine/Alberta/O 1
NP A257T 229396492_A/Ohio/07/2009 1
NP V349I 229536131_A/Colorado/03/200 2
NP V358M 229598873_A/Ohio/07/2009 1
NP V369I 229536077_A/Indiana/09/2009 1
NP T379I 229536102_A/Nebraska/02/200 18
NP T379V 229892752_A/Canada-NS/RV153 1
NP D381N 229396423_A/California/08/2 1
NP D381Y 237624329_A/swine/Alberta/O 1
NP T402A 237511901_A/Mexico/4516/200 1
NP S456N 229536077_A/Indiana/09/2009 1

NA Protein Structural Homolgy ModelNA Protein Structural Homolgy Model

NA Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009 NA, residues 83-467, 89% sequence identity to pdp template 3b7e

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NA Sequence PolymorphismsNA Sequence Polymorphisms

Protein Polymorphism Strain with Polymorphism Number of Strains with Polymorphism
NA H36R 229892732_A/Mexico/InDRE411 1
NA E57K 229536081_A/Indiana/09/2009 1
NA V83M 229536111_A/Michigan/02/200 1
NA S95G 228017756_A/California/06/2 5
NA G96E 237624331_A/swine/Alberta/O 1
NA Y100H 237624331_A/swine/Alberta/O 1
NA V106I 228481034_A/Auckland/3/2009 30
NA I108V 228860931_A/Netherlands/602 1
NA P120S 229892684_A/Catalonia/P48/2 1
NA S123L 237624331_A/swine/Alberta/O 1
NA V241I 229535806_A/Texas/09/2009 1
NA N248D 229396353_A/New_York/12/200 30
NA N307T 228481034_A/Auckland/3/2009 1
NA S319R 229892682_A/Korea/01/2009 1
NA S334C 237624331_A/swine/Alberta/O 1

MP1 Protein Structural Homolgy ModelMP1 Protein Structural Homolgy Model

MP2 Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009 MP1, residues 23-60, 82% sequence identity to pdp template 2rlf

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MP1 Sequence PolymorphismsMP1 Sequence Polymorphisms

Protein Polymorphism Strain with Polymorphism Number of Strains with Polymorphism
MP1 L3P 227831763_A/California/05/2 1
MP1 H222R 237624333_A/swine/Alberta/O 1
MP1 A227T 229484039_A/Canada-ON/RV152 2

MP2 Protein Structural Homolgy ModelMP2 Protein Structural Homolgy Model

MP2 Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009 MP2, residues 23-60, 82% sequence identity to pdp template 2rlf

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MP2 Sequence PolymorphismsMP2 Sequence Polymorphisms

Protein Polymorphism Strain with Polymorphism Number of Strains with Polymorphism
MP2 L3P 227831764_A/California/05/2 1
MP2 Y52H 229609551_A/Stockholm/28/20 1
MP2 T65M 229536073_A/Texas/07/2009 1
MP2 S82N 237511788_A/Mexico/4108/200 1

NS1 Protein Structural Homolgy ModelNS1 Protein Structural Homolgy Model

NS1 Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009 NS1, residues 5-202, 84% sequence identity to pdp template 3f5t

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NS1 Sequence PolymorphismsNS1 Sequence Polymorphisms

Protein Polymorphism Strain with Polymorphism Number of Strains with Polymorphism
NS1 D12E 229536107_A/Nebraska/02/200 1
NS1 F32L 229535811_A/Texas/09/2009 1
NS1 G45R 229598886_A/Texas/15/2009 1
NS1 R88C 229536033_A/Minnesota/02/20 1
NS1 E97G 229892754_A/Canada-NS/RV153 1
NS1 M104T 237624336_A/swine/Alberta/O 1
NS1 I123V 229892764_A/Canada-AB/RV153 15
NS1 F134I 237624336_A/swine/Alberta/O 1

NS2 Protein Structural Homolgy ModelNS2 Protein Structural Homolgy Model

NS2 Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009 NS2, residues 64-116, 94% sequence identity to pdp template 1pd3

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NS2 Sequence PolymorphismsNS2 Sequence Polymorphisms

Protein Polymorphism Strain with Polymorphism Number of Strains with Polymorphism
NS2 E63K 229783374_A/Korea/01/2009 1
NS2 E67K 229598887_A/Texas/15/2009 1
NS2 A89E 228017754_A/California/06/2 3
NS2 A115T 229892755_A/Canada-NS/RV153 1


Multiple Sequence Alignment of 5 H1N1 StrainsMultiple Sequence Alignment of 5 H1N1 Strains

multiple sequence alignment of PB2multiple sequence alignment of PB2

CLUSTAL 2.0.10 multiple sequence alignment

PB2 

CLUSTAL 2.0.10 =
multiple sequence alignment of PB2

A/California/04/2009         MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWM 50
A/New_York/18/2009           MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWM 50
A/Canada-ON/RV1527/2009      MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWM 50
A/Texas/09/2009              MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWM 50
A/Mexico/InDRE4487/2009      MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWM 50
                             **************************************************

A/California/04/2009         MAMRYPITADKRIMDMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWN 100
A/New_York/18/2009           MAMRYPITADKRIMDMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWN 100
A/Canada-ON/RV1527/2009      MAMRYPITADKRIMDMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWN 100
A/Texas/09/2009              MAMRYPITADKRIMDMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWN 100
A/Mexico/InDRE4487/2009      MAMRYPITADKRIMDMIPERNEQGQTLWSKTSDAGSDRVMVSPLAVTWWN 100
                             *******************************.******************

A/California/04/2009         RNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPG 150
A/New_York/18/2009           RNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPG 150
A/Canada-ON/RV1527/2009      RNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPG 150
A/Texas/09/2009              RNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPG 150
A/Mexico/InDRE4487/2009      RNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPG 150
                             **************************************************

A/California/04/2009         HADLSAKEAQDVIMEVVFPNEVGARILTSESQLAITKEKKEELQDCKIAP 200
A/New_York/18/2009           HADLSAKEAQDVIMEVVFPNEVGARILTSESQLAITKEKKEELQDCKIAP 200
A/Canada-ON/RV1527/2009      HADLSAKEAQDVIMEVVFPNEVGARILTSESQLAITKEKKEELQDCKIAP 200
A/Texas/09/2009              HADLSAKEAQDVIMEVVFPNEVGARILTSESQLAITKEKKEELQDCKIAP 200
A/Mexico/InDRE4487/2009      HADLSAKEAQDVIMEVVFPNEVGARILTSESQLAITKEKKEELQDCKIAP 200
                             **************************************************

A/California/04/2009         LMVAYMLERELVRKTRFLPVAGGTGSVYIEVLHLTQGTCWEQMYTPGGEV 250
A/New_York/18/2009           LMVAYMLERELVRKTRFLPVAGGTGSVYIEVLHLTQGTCWEQMYTPGGEV 250
A/Canada-ON/RV1527/2009      LMVAYMLERELVRKTRFLPVAGGTGSVYIEVLHLTQGTCWEQMYTPGGEV 250
A/Texas/09/2009              LMVAYMLERELVRKTRFLPVAGGTGSVYIEVLHLTQGTCWEQMYTPGGEV 250
A/Mexico/InDRE4487/2009      LMVAYMLERELVRKTRFLPVAGGTGSVYIEVLHLTQGTCWEQMYTPGGEV 250
                             **************************************************

A/California/04/2009         RNDDVDQSLIIAARNIVRRAAVSADPLASLLEMCHSTQIGGVRMVDILRQ 300
A/New_York/18/2009           RNDDVDQSLIIAARNIVRRAAVSADPLASLLEMCHSTQIGGVRMVDILRQ 300
A/Canada-ON/RV1527/2009      RNDDVDQSLIIAARNIVRRAAVSADPLASLLEMCHSTQIGGVRMVDILRQ 300
A/Texas/09/2009              RNDDVDQSLIIAARNIVRRAAVSADPLASLLEMCHSTQIGGVRMVDILRQ 300
A/Mexico/InDRE4487/2009      RNDDVDQSLIIAARNIVRRAAVSADPLASLLEMCHSTQIGGVRMVDILRQ 300
                             **************************************************

A/California/04/2009         NPTEEQAVDICKAAIGLRISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQ 350
A/New_York/18/2009           NPTEEQAVDICKAAIGLRISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQ 350
A/Canada-ON/RV1527/2009      NPTEEQAVDICKAAIGLRISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQ 350
A/Texas/09/2009              NPTEEQAVDICKAAIGLRISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQ 350
A/Mexico/InDRE4487/2009      NPTEEQAVDICKAAIGLRISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQ 350
                             **************************************************

A/California/04/2009         TLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIV 400
A/New_York/18/2009           TLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIV 400
A/Canada-ON/RV1527/2009      TLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIV 400
A/Texas/09/2009              TLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIV 400
A/Mexico/InDRE4487/2009      TLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIV 400
                             **************************************************

A/California/04/2009         AMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG 450
A/New_York/18/2009           AMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG 450
A/Canada-ON/RV1527/2009      AMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG 450
A/Texas/09/2009              AMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG 450
A/Mexico/InDRE4487/2009      AMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG 450
                             **************************************************

A/California/04/2009         IESIDNVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEYSSTERVVVSIDR 500
A/New_York/18/2009           IESIDNVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEYSSTERVVVSIDR 500
A/Canada-ON/RV1527/2009      IESIDNVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEYSSTERVVVSIDR 500
A/Texas/09/2009              IESIDNVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEYSSTERVVVSIDR 500
A/Mexico/InDRE4487/2009      IESIDNVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEYSSTERVVVSIDR 500
                             **************************************************

A/California/04/2009         FLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTY 550
A/New_York/18/2009           FLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTY 550
A/Canada-ON/RV1527/2009      FLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTY 550
A/Texas/09/2009              FLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTY 550
A/Mexico/InDRE4487/2009      FLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTY 550
                             **************************************************

A/California/04/2009         QWIIRNWEIVKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLF 600
A/New_York/18/2009           QWIIRNWEIVKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLF 600
A/Canada-ON/RV1527/2009      QWIIRNWEIVKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLF 600
A/Texas/09/2009              QWIIRNWEIVKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLF 600
A/Mexico/InDRE4487/2009      QWIIRNWEIVKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLF 600
                             **************************************************

A/California/04/2009         QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVR 650
A/New_York/18/2009           QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVR 650
A/Canada-ON/RV1527/2009      QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVR 650
A/Texas/09/2009              QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVR 650
A/Mexico/InDRE4487/2009      QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVR 650
                             **************************************************

A/California/04/2009         GNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTSGVESAVLRGFLILGKE 700
A/New_York/18/2009           GNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTSGVESAVLRGFLILGKE 700
A/Canada-ON/RV1527/2009      GNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTSGVESAVLRGFLILGKE 700
A/Texas/09/2009              GNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTSGVESAVLRGFLILGKE 700
A/Mexico/InDRE4487/2009      GNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTSGVESAVLRGFLILGKE 700
                             **************************************************

A/California/04/2009         DKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTA 750
A/New_York/18/2009           DKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTA 750
A/Canada-ON/RV1527/2009      DKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTA 750
A/Texas/09/2009              DKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTA 750
A/Mexico/InDRE4487/2009      DKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTA 750
                             **************************************************

A/California/04/2009         TKRIRMAIN 759
A/New_York/18/2009           TKRIRMAIN 759
A/Canada-ON/RV1527/2009      TKRIRMAIN 759
A/Texas/09/2009              TKRIRMAIN 759
A/Mexico/InDRE4487/2009      TKRIRMAIN 759
                             *********

multiple sequence alignment of PB1multiple sequence alignment of PB1

PB1 

CLUSTAL 2.0.10 =
multiple sequence alignment of PB1

A/Canada-ON/RV1527/2009      MDVNPTLLFLKIPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYS 50
A/Texas/09/2009              MDVNPTLLFLKIPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYS 50
A/Mexico/InDRE4487/2009      MDVNPTLLFLKIPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYS 50
A/California/04/2009         MDVNPTLLFLKIPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYS 50
A/New_York/18/2009           MDVNPTLLFLKIPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYS 50
                             **************************************************

A/Canada-ON/RV1527/2009      EKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHP 100
A/Texas/09/2009              EKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHP 100
A/Mexico/InDRE4487/2009      EKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHP 100
A/California/04/2009         EKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHP 100
A/New_York/18/2009           EKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHP 100
                             **************************************************

A/Canada-ON/RV1527/2009      GIFENSCLETMEVVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVF 150
A/Texas/09/2009              GIFENSCLETMEVVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVF 150
A/Mexico/InDRE4487/2009      GIFENSCLETMEVVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVF 150
A/California/04/2009         GIFENSCLETMEVVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVF 150
A/New_York/18/2009           GIFENSCLETMEVVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVF 150
                             **************************************************

A/Canada-ON/RV1527/2009      RSNGLTANESGRLIDFLKDVMESMNKEEIEITTHFQRKRRVRDNMTKKMV 200
A/Texas/09/2009              RSNGLTANESGRLIDFLKDVMESMNKEEIEITTHFQRKRRVRDNMTKKMV 200
A/Mexico/InDRE4487/2009      RSNGLTANESGRLIDFLKDVMESMNKEEIEITTHFQRKRRVRDNMTKKMV 200
A/California/04/2009         RSNGLTANESGRLIDFLKDVMESMNKEEIEITTHFQRKRRVRDNMTKKMV 200
A/New_York/18/2009           RSNGLTANESGRLIDFLKDVMESMNKEEIEITTHFQRKRRVRDNMTKKMV 200
                             **************************************************

A/Canada-ON/RV1527/2009      TQRTIGKKKQRLNKRGYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRG 250
A/Texas/09/2009              TQRTIGKKKQRLNKRGYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRG 250
A/Mexico/InDRE4487/2009      TQRTIGKKKQRLNKRGYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRG 250
A/California/04/2009         TQRTIGKKKQRLNKRGYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRG 250
A/New_York/18/2009           TQRTIGKKKQRLNKRGYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRG 250
                             **************************************************

A/Canada-ON/RV1527/2009      FVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTEISF 300
A/Texas/09/2009              FVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTEISF 300
A/Mexico/InDRE4487/2009      FVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTEISF 300
A/California/04/2009         FVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTEISF 300
A/New_York/18/2009           FVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTEISF 300
                             **************************************************

A/Canada-ON/RV1527/2009      TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNILSMAPIMFSNKMAR 350
A/Texas/09/2009              TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNILSMAPIMFSNKMAR 350
A/Mexico/InDRE4487/2009      TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNILSMAPIMFSNKMAR 350
A/California/04/2009         TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNILSMAPIMFSNKMAR 350
A/New_York/18/2009           TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNILSMAPIMFSNKMAR 350
                             **************************************************

A/Canada-ON/RV1527/2009      LGKGYMFESKRMKIRTQIPAEMLASIDLKYFNESTKKKIEKIRPLLIDGT 400
A/Texas/09/2009              LGKGYMFESKRMKIRTQIPAEMLASIDLKYFNESTKKKIEKIRPLLIDGT 400
A/Mexico/InDRE4487/2009      LGKGYMFESKRMKIRTQIPAEMLASIDLKYFNESTKKKIEKIRPLLIDGT 400
A/California/04/2009         LGKGYMFESKRMKIRTQIPAEMLASIDLKYFNESTKKKIEKIRPLLIDGT 400
A/New_York/18/2009           LGKGYMFESKRMKIRTQIPAEMLASIDLKYFNESTKKKIEKIRPLLIDGT 400
                             **************************************************

A/Canada-ON/RV1527/2009      ASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTIYWWDGLQSSDDFALI 450
A/Texas/09/2009              ASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTIYWWDGLQSSDDFALI 450
A/Mexico/InDRE4487/2009      ASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTIYWWDGLQSSDDFALI 450
A/California/04/2009         ASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTIYWWDGLQSSDDFALI 450
A/New_York/18/2009           ASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTIYWWDGLQSSDDFALI 450
                             **************************************************

A/Canada-ON/RV1527/2009      VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINKTGTFEFTSFFYRYG 500
A/Texas/09/2009              VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINKTGTFEFTSFFYRYG 500
A/Mexico/InDRE4487/2009      VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINKTGTFEFTSFFYRYG 500
A/California/04/2009         VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINKTGTFEFTSFFYRYG 500
A/New_York/18/2009           VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINKTGTFEFTSFFYRYG 500
                             **************************************************

A/Canada-ON/RV1527/2009      FVANFSMELPSFGVSGVNESADMSIGVTVIKNNMINNDLGPATAQMALQL 550
A/Texas/09/2009              FVANFSMELPSFGVSGVNESADMSIGVTVIKNNMINNDLGPATAQMALQL 550
A/Mexico/InDRE4487/2009      FVANFSMELPSFGVSGVNESADMSIGVTVIKNNMINNDLGPATAQMALQL 550
A/California/04/2009         FVANFSMELPSFGVSGVNESADMSIGVTVIKNNMINNDLGPATAQMALQL 550
A/New_York/18/2009           FVANFSMELPSFGVSGVNESADMSIGVTVIKNNMINNDLGPATAQMALQL 550
                             **************************************************

A/Canada-ON/RV1527/2009      FIKDYRYTYRCHRGDTQIQTRRSFELKKLWDQTQSKVGLLVSDGGPNLYN 600
A/Texas/09/2009              FIKDYRYTYRCHRGDTQIQTRRSFELKKLWDQTQSKVGLLVSDGGPNLYN 600
A/Mexico/InDRE4487/2009      FIKDYRYTYRCHRGDTQIQTRRSFELKKLWDQTQSKVGLLVSDGGPNLYN 600
A/California/04/2009         FIKDYRYTYRCHRGDTQIQTRRSFELKKLWDQTQSKVGLLVSDGGPNLYN 600
A/New_York/18/2009           FIKDYRYTYRCHRGDTQIQTRRSFELKKLWDQTQSKVGLLVSDGGPNLYN 600
                             **************************************************

A/Canada-ON/RV1527/2009      IRNLHIPEVCLKWELMDDDYRGRLCNPLNPFVSHKEIDSVNNAVVMPAHG 650
A/Texas/09/2009              IRNLHIPEVCLKWELMDDDYRGRLCNPLNPFVSHKEIDSVNNAVVMPAHG 650
A/Mexico/InDRE4487/2009      IRNLHIPEVCLKWELMDDDYRGRLCNPLNPFVSHKEIDSVNNAVVMPAHG 650
A/California/04/2009         IRNLHIPEVCLKWELMDDDYRGRLCNPLNPFVSHKEIDSVNNAVVMPAHG 650
A/New_York/18/2009           IRNLHIPEVCLKWELMDDDYRGRLCNPLNPFVSHKEIDSVNNAVVMPAHG 650
                             **************************************************

A/Canada-ON/RV1527/2009      PAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFF 700
A/Texas/09/2009              PAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFF 700
A/Mexico/InDRE4487/2009      PAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFF 700
A/California/04/2009         PAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFF 700
A/New_York/18/2009           PAKSMEYDAVATTHSWIPKRNRSILNTNQRGILEDEQMYQKCCNLFEKFF 700
                             ***************************.**********************

A/Canada-ON/RV1527/2009      PSSSYRRPVGISSMVEAMVSRARIDARVDFESGRIKKEEFSEIMKICSTI 750
A/Texas/09/2009              PSSSYRRPVGISSMVEAMVSRARIDARVDFESGRIKKEEFSEIMKICSTI 750
A/Mexico/InDRE4487/2009      PSSSYRRPVGISSMVEAMVSRARIDARVDFESGRIKKEEFSEIMKICSTI 750
A/California/04/2009         PSSSYRRPVGISSMVEAMVSRARIDARVDFESGRIKKEEFSEIMKICSTI 750
A/New_York/18/2009           PSSSYRRPVGISSMVEAMVSRARIDARVDFESGRIKKEEFSEIMKICSTI 750
                             **************************************************

A/Canada-ON/RV1527/2009      EELRRQK 757
A/Texas/09/2009              EELRRQK 757
A/Mexico/InDRE4487/2009      EELRRQK 757
A/California/04/2009         EELRRQK 757
A/New_York/18/2009           EELRRQK 757
                             *******


multiple sequence alignment of PAmultiple sequence alignment of PA

PA 

CLUSTAL 2.0.10 =
multiple sequence alignment of PA

A/Canada-ON/RV1527/2009      MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSD 50
A/Texas/09/2009              MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSD 50
A/Mexico/InDRE4487/2009      MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSD 50
A/New_York/18/2009           MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSD 50
A/California/04/2009         MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSD 50
                             **************************************************

A/Canada-ON/RV1527/2009      FHFIDERGESIIVESGDPNALLKHRFEIIEGRDRIMAWTVVNSICNTTGV 100
A/Texas/09/2009              FHFIDERGESIIVESGDPNALLKHRFEIIEGRDRIMAWTVVNSICNTTGV 100
A/Mexico/InDRE4487/2009      FHFIDERGESIIVESGDPNALLKHRFEIIEGRDRIMAWTVVNSICNTTGV 100
A/New_York/18/2009           FHFIDERGESIIVESGDPNALLKHRFEIIEGRDRIMAWTVVNSICNTTGV 100
A/California/04/2009         FHFIDERGESIIVESGDPNALLKHRFEIIEGRDRIMAWTVVNSICNTTGV 100
                             **************************************************

A/Canada-ON/RV1527/2009      EKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSF 150
A/Texas/09/2009              EKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSF 150
A/Mexico/InDRE4487/2009      EKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSF 150
A/New_York/18/2009           EKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSF 150
A/California/04/2009         EKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSF 150
                             **************************************************

A/Canada-ON/RV1527/2009      TGEEMATKADYTLDEESRARIKTRLFTIRQEMASRSLWDSFRQSERGEET 200
A/Texas/09/2009              TGEEMATKADYTLDEESRARIKTRLFTIRQEMASRSLWDSFRQSERGEET 200
A/Mexico/InDRE4487/2009      TGEEMATKADYTLDEESRARIKTRLFTIRQEMASRSLWDSFRQSERGEET 200
A/New_York/18/2009           TGEEMATKADYTLDEESRARIKTRLFTIRQEMASRSLWDSFRQSERGEET 200
A/California/04/2009         TGEEMATKADYTLDEESRARIKTRLFTIRQEMASRSLWDSFRQSERGEET 200
                             **************************************************

A/Canada-ON/RV1527/2009      IEEKFEITGTMRKLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMS 250
A/Texas/09/2009              IEEKFEITGTMRKLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMS 250
A/Mexico/InDRE4487/2009      IEEKFEITGTMRKLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMS 250
A/New_York/18/2009           IEEKFEITGTMRKLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMS 250
A/California/04/2009         IEEKFEITGTMRKLADQSLPPNFPSLENFRAYVDGFEPNGCIEGKLSQMS 250
                             ***********************.**************************

A/Canada-ON/RV1527/2009      KEVNAKIEPFLRTTPRPLRLPDGPLCHQRSKFLLMDALKLSIEDPSHEGE 300
A/Texas/09/2009              KEVNAKIEPFLRTTPRPLRLPDGPLCHQRSKFLLMDALKLSIEDPSHEGE 300
A/Mexico/InDRE4487/2009      KEVNAKIEPFLRTTPRPLRLPDGPICHQRSKFLLMDALKLSIEDPSHEGE 300
A/New_York/18/2009           KEVNAKIEPFLRTTPRPLRLPDGPLCHQRSKFLLMDALKLSIEDPSHEGE 300
A/California/04/2009         KEVNAKIEPFLRTTPRPLRLPDGPLCHQRSKFLLMDALKLSIEDPSHEGE 300
                             ************************:*************************

A/Canada-ON/RV1527/2009      GIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNYLMAWKQVLAELQDIEN 350
A/Texas/09/2009              GIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNYLMAWKQVLAELQDIEN 350
A/Mexico/InDRE4487/2009      GIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNYLMAWKQVLAELQDIEN 350
A/New_York/18/2009           GIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNYLMAWKQVLAELQDIEN 350
A/California/04/2009         GIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNYLMAWKQVLAELQDIEN 350
                             **************************************************

A/Canada-ON/RV1527/2009      EEKIPRTKNMKRTSQLKWALGENMAPEKVDFDDCKDVGDLKQYDSDEPEP 400
A/Texas/09/2009              EEKIPRTKNMKRTSQLKWALGENMAPEKVDFDDCKDVGDLKQYDSDEPEP 400
A/Mexico/InDRE4487/2009      EEKIPRTKNMKRTSQLKWALGENMAPEKVDFDDCKDVGDLKQYDSDEPEP 400
A/New_York/18/2009           EEKIPRTKNMKRTSQLKWALGENMAPEKVDFDDCKDVGDLKQYDSDEPEP 400
A/California/04/2009         EEKIPRTKNMKRTSQLKWALGENMAPEKVDFDDCKDVGDLKQYDSDEPEP 400
                             **************************************************

A/Canada-ON/RV1527/2009      RSLASWVQNEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEV 450
A/Texas/09/2009              RSLASWVQNEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEV 450
A/Mexico/InDRE4487/2009      RSLASWVQNEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEV 450
A/New_York/18/2009           RSLASWVQNEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEV 450
A/California/04/2009         RSLASWVQNEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEV 450
                             **************************************************

A/Canada-ON/RV1527/2009      SHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNL 500
A/Texas/09/2009              SHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNL 500
A/Mexico/InDRE4487/2009      SHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNL 500
A/New_York/18/2009           SHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNL 500
A/California/04/2009         SHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNL 500
                             **************************************************

A/Canada-ON/RV1527/2009      YGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLL 550
A/Texas/09/2009              YGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLL 550
A/Mexico/InDRE4487/2009      YGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLL 550
A/New_York/18/2009           YGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLL 550
A/California/04/2009         YGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLL 550
                             **************************************************

A/Canada-ON/RV1527/2009      RTAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAES 600
A/Texas/09/2009              RTAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAES 600
A/Mexico/InDRE4487/2009      RTAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAES 600
A/New_York/18/2009           RTAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAES 600
A/California/04/2009         RTAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAES 600
                             **************************************************

A/Canada-ON/RV1527/2009      SVKEKDMTKEFFENKSETWPIGESPRGVEEGSIGKVCRTLLAKSVFNSLY 650
A/Texas/09/2009              SVKEKDMTKEFFENKSETWPIGESPRGVEEGSIGKVCRTLLAKSVFNSLY 650
A/Mexico/InDRE4487/2009      SVKEKDMTKEFFENKSETWPIGESPRGVEEGSIGKVCRTLLAKSVFNSLY 650
A/New_York/18/2009           SVKEKDMTKEFFENKSETWPIGESPRGVEEGSIGKVCRTLLAKSVFNSLY 650
A/California/04/2009         SVKEKDMTKEFFENKSETWPIGESPRGVEEGSIGKVCRTLLAKSVFNSLY 650
                             **************************************************

A/Canada-ON/RV1527/2009      ASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWV 700
A/Texas/09/2009              ASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWV 700
A/Mexico/InDRE4487/2009      ASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWV 700
A/New_York/18/2009           ASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWV 700
A/California/04/2009         ASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWV 700
                             **************************************************

A/Canada-ON/RV1527/2009      LLNASWFNSFLTHALK 716
A/Texas/09/2009              LLNASWFNSFLTHALK 716
A/Mexico/InDRE4487/2009      LLNASWFNSFLTHALK 716
A/New_York/18/2009           LLNASWFNSFLTHALK 716
A/California/04/2009         LLNASWFNSFLTHALK 716
                             ****************


multiple sequence alignment of HAmultiple sequence alignment of HA

HA 

CLUSTAL 2.0.10 =
multiple sequence alignment of HA

A/Texas/04/2009              MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLL 50
A/Mexico/InDRE4487/2009      MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLL 50
A/New_York/18/2009           MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLL 50
A/Canada-ON/RV1527/2009      MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLL 50
A/California/04/2009         MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLL 50
                             **************************************************

A/Texas/04/2009              EDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETS 100
A/Mexico/InDRE4487/2009      EDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETS 100
A/New_York/18/2009           EDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETS 100
A/Canada-ON/RV1527/2009      EDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETS 100
A/California/04/2009         EDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETP 100
                             *************************************************.

A/Texas/04/2009              SSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVT 150
A/Mexico/InDRE4487/2009      SSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVT 150
A/New_York/18/2009           SSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVT 150
A/Canada-ON/RV1527/2009      SSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVT 150
A/California/04/2009         SSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVT 150
                             **************************************************

A/Texas/04/2009              AACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPS 200
A/Mexico/InDRE4487/2009      AACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPS 200
A/New_York/18/2009           AACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPS 200
A/Canada-ON/RV1527/2009      AACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPS 200
A/California/04/2009         AACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPS 200
                             **************************************************

A/Texas/04/2009              TSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTL 250
A/Mexico/InDRE4487/2009      TSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTL 250
A/New_York/18/2009           TSADQQSLYQNADAYVFVGTSRYSKKFKPEIAIRPKVRDQEGRMNYYWTL 250
A/Canada-ON/RV1527/2009      TSADQQSLYQNADAYVFVGTSRYSKKFKPEIAIRPKVRDQEGRMNYYWTL 250
A/California/04/2009         TSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTL 250
                             *************:*****:******************************

A/Texas/04/2009              VEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK 300
A/Mexico/InDRE4487/2009      VEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK 300
A/New_York/18/2009           VEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK 300
A/Canada-ON/RV1527/2009      VEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK 300
A/California/04/2009         VEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK 300
                             **************************************************

A/Texas/04/2009              GAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAI 350
A/Mexico/InDRE4487/2009      GAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAI 350
A/New_York/18/2009           GAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAI 350
A/Canada-ON/RV1527/2009      GAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAI 350
A/California/04/2009         GAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPSIQSRGLFGAI 350
                             *************************************:************

A/Texas/04/2009              AGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVI 400
A/Mexico/InDRE4487/2009      AGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVI 400
A/New_York/18/2009           AGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVI 400
A/Canada-ON/RV1527/2009      AGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVI 400
A/California/04/2009         AGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVI 400
                             **************************************************

A/Texas/04/2009              EKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER 450
A/Mexico/InDRE4487/2009      EKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER 450
A/New_York/18/2009           EKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER 450
A/Canada-ON/RV1527/2009      EKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER 450
A/California/04/2009         EKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER 450
                             **************************************************

A/Texas/04/2009              TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGT 500
A/Mexico/InDRE4487/2009      TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGT 500
A/New_York/18/2009           TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGT 500
A/Canada-ON/RV1527/2009      TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGT 500
A/California/04/2009         TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGT 500
                             **************************************************

A/Texas/04/2009              YDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAI 550
A/Mexico/InDRE4487/2009      YDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAI 550
A/New_York/18/2009           YDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAI 550
A/Canada-ON/RV1527/2009      YDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAI 550
A/California/04/2009         YDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAI 550
                             **************************************************

A/Texas/04/2009              SFWMCSNGSLQCRICI 566
A/Mexico/InDRE4487/2009      SFWMCSNGSLQCRICI 566
A/New_York/18/2009           SFWMCSNGSLQCRICI 566
A/Canada-ON/RV1527/2009      SFWMCSNGSLQCRICI 566
A/California/04/2009         SFWMCSNGSLQCRICI 566
                             ****************

multiple sequence alignment of NPmultiple sequence alignment of NP

NP 

CLUSTAL 2.0.10 =
multiple sequence alignment of NP

A/California/04/2009         ------MASQGTKRSYEQMETGGERQDATEIRASVGRMIGGIGRFYIQMC 44
A/Texas/04/2009              ------MASQGTKRSYEQMETGGERQDATEIRASVGRMIGGIGRFYIQMC 44
A/Mexico/InDRE4487/2009      MSDIEAMASQGTKRSYEQMETGGERQDATEIRASVGRMIGGIGRFYIQMC 50
A/New_York/18/2009           ------MASQGTKRSYEQMETGGERQDATEIRASVGRMIGGIGRFYIQMC 44
A/Canada-ON/RV1527/2009      MSDIEAMASQGTKRSYEQMETGGERQDATEIRASVGRMIGGIGRFYIQMC 50
                                   ********************************************

A/California/04/2009         TELKLSDYDGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGG 94
A/Texas/04/2009              TELKLSDYDGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGG 94
A/Mexico/InDRE4487/2009      TELKLSDYDGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGG 100
A/New_York/18/2009           TELKLSDYDGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGG 94
A/Canada-ON/RV1527/2009      TELKLSDYDGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGG 100
                             **************************************************

A/California/04/2009         PIYRRVDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLN 144
A/Texas/04/2009              PIYRRVDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLN 144
A/Mexico/InDRE4487/2009      PIYRRVDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLN 150
A/New_York/18/2009           PIYRRIDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLN 144
A/Canada-ON/RV1527/2009      PIYRRIDGKWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLN 150
                             *****:********************************************

A/California/04/2009         DATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELI 194
A/Texas/04/2009              DATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELI 194
A/Mexico/InDRE4487/2009      DATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELI 200
A/New_York/18/2009           DATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELI 194
A/Canada-ON/RV1527/2009      DATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELI 200
                             **************************************************

A/California/04/2009         RMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRE 244
A/Texas/04/2009              RMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRE 244
A/Mexico/InDRE4487/2009      RMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRE 250
A/New_York/18/2009           RMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRE 244
A/Canada-ON/RV1527/2009      RMIKRGINDRNFWRGENGRRTRVAYERMCNILKGKFQTAAQRAMMDQVRE 250
                             **************************************************

A/California/04/2009         SRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFERE 294
A/Texas/04/2009              SRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFERE 294
A/Mexico/InDRE4487/2009      SRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFERE 300
A/New_York/18/2009           SRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFERE 294
A/Canada-ON/RV1527/2009      SRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGLAVASGHDFERE 300
                             **************************************************

A/California/04/2009         GYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVS 344
A/Texas/04/2009              GYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVS 344
A/Mexico/InDRE4487/2009      GYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVS 350
A/New_York/18/2009           GYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVS 344
A/Canada-ON/RV1527/2009      GYSLVGIDPFKLLQNSQVVSLMRPNENPAHKSQLVWMACHSAAFEDLRVS 350
                             **************************************************

A/California/04/2009         SFIRGKKVIPRGKLSTRGVQIASNENVETMDSNTLELRSRYWAIRTRSGG 394
A/Texas/04/2009              SFIRGKKVIPRGKLSTRGVQIASNENVETMDSNTLELRSRYWAIRTRSGG 394
A/Mexico/InDRE4487/2009      SFIRGKKVIPRGKLSTRGVQIASNENVETMDSNTLELRSRYWAIRTRSGG 400
A/New_York/18/2009           SFIRGKKVIPRGKLSTRGVQIASNENVETMDSNTLELRSRYWAIRTRSGG 394
A/Canada-ON/RV1527/2009      SFIRGKKVIPRGKLSTRGVQIASNENVETMDSNTLELRSRYWAIRTRSGG 400
                             **************************************************

A/California/04/2009         NTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEV 444
A/Texas/04/2009              NTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEV 444
A/Mexico/InDRE4487/2009      NTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEV 450
A/New_York/18/2009           NTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEV 444
A/Canada-ON/RV1527/2009      NTNQQKASAGQISVQPTFSVQRNLPFERATVMAAFSGNNEGRTSDMRTEV 450
                             **************************************************

A/California/04/2009         IRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFFGDNAE 494
A/Texas/04/2009              IRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFFGDNAE 494
A/Mexico/InDRE4487/2009      IRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFFGDNAE 500
A/New_York/18/2009           IRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFFGDNAE 494
A/Canada-ON/RV1527/2009      IRMMESAKPEDLSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFFGDNAE 500
                             **************************************************

A/California/04/2009         EYDS 498
A/Texas/04/2009              EYDS 498
A/Mexico/InDRE4487/2009      EYDS 504
A/New_York/18/2009           EYDS 498
A/Canada-ON/RV1527/2009      EYDS 504
                             ****


multiple sequence alignment of NAmultiple sequence alignment of NA

NA 

CLUSTAL 2.0.10 =
multiple sequence alignment of NA

A/California/04/2009         MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHSIQLGNQNQIETCN 50
A/Texas/04/2009              MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHSIQLGNQNQIETCN 50
A/Mexico/InDRE4487/2009      MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHSIQLGNQNQIETCN 50
A/New_York/18/2009           MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHSIQLGNQNQIETCN 50
A/Canada-ON/RV1527/2009      MNPNQKIITIGSVCMTIGMANLILQIGNIISIWISHSIQLGNQNQIETCN 50
                             **************************************************

A/California/04/2009         QSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPVSGWAIY 100
A/Texas/04/2009              QSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPVSGWAIY 100
A/Mexico/InDRE4487/2009      QSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPVSGWAIY 100
A/New_York/18/2009           QSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPVSGWAIY 100
A/Canada-ON/RV1527/2009      QSVITYENNTWVNQTYVNISNTNFAAGQSVVSVKLAGNSSLCPVSGWAIY 100
                             **************************************************

A/California/04/2009         SKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIK 150
A/Texas/04/2009              SKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIK 150
A/Mexico/InDRE4487/2009      SKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIK 150
A/New_York/18/2009           SKDNSIRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIK 150
A/Canada-ON/RV1527/2009      SKDNSIRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIK 150
                             *****:********************************************

A/California/04/2009         DRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDN 200
A/Texas/04/2009              DRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDN 200
A/Mexico/InDRE4487/2009      DRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDN 200
A/New_York/18/2009           DRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDN 200
A/Canada-ON/RV1527/2009      DRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDN 200
                             **************************************************

A/California/04/2009         GAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQ 250
A/Texas/04/2009              GAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQ 250
A/Mexico/InDRE4487/2009      GAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQ 250
A/New_York/18/2009           GAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSDGQ 250
A/Canada-ON/RV1527/2009      GAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSDGQ 250
                             ***********************************************:**

A/California/04/2009         ASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSN 300
A/Texas/04/2009              ASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSN 300
A/Mexico/InDRE4487/2009      ASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSN 300
A/New_York/18/2009           ASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSN 300
A/Canada-ON/RV1527/2009      ASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSN 300
                             **************************************************

A/California/04/2009         RPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFS 350
A/Texas/04/2009              RPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFS 350
A/Mexico/InDRE4487/2009      RPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFS 350
A/New_York/18/2009           RPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFS 350
A/Canada-ON/RV1527/2009      RPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFS 350
                             **************************************************

A/California/04/2009         FKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWS 400
A/Texas/04/2009              FKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWS 400
A/Mexico/InDRE4487/2009      FKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWS 400
A/New_York/18/2009           FKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWS 400
A/Canada-ON/RV1527/2009      FKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWS 400
                             **************************************************

A/California/04/2009         GYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNS 450
A/Texas/04/2009              GYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNS 450
A/Mexico/InDRE4487/2009      GYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNS 450
A/New_York/18/2009           GYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNS 450
A/Canada-ON/RV1527/2009      GYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNS 450
                             **************************************************

A/California/04/2009         DTVGWSWPDGAELPFTIDK 469
A/Texas/04/2009              DTVGWSWPDGAELPFTIDK 469
A/Mexico/InDRE4487/2009      DTVGWSWPDGAELPFTIDK 469
A/New_York/18/2009           DTVGWSWPDGAELPFTIDK 469
A/Canada-ON/RV1527/2009      DTVGWSWPDGAELPFTIDK 469
                             *******************

multiple sequence alignment of MPmultiple sequence alignment of MP

MP 

CLUSTAL 2.0.10 =
multiple sequence alignment of MP

A/California/04/2009         ----TEVETYVLSIIPSGPLKAEIAQRLESVFAGKNTDLEALMEWLKTRP 46
A/Texas/04/2009              MSLLTEVETYVLSIIPSGPLKAEIAQRLESVFAGKNTDLEALMEWLKTRP 50
A/New_York/18/2009           MSLLTEVETYVLSIIPSGPLKAEIAQRLESVFAGKNTDLEALMEWLKTRP 50
A/Mexico/InDRE4487/2009      MSLLTEVETYVLSIIPSGPLKAEIAQRLESVFAGKNTDLEALMEWLKTRP 50
A/Canada-ON/RV1527/2009      MSLLTEVETYVLSIIPSGPLKAEIAQRLESVFAGKNTDLEALMEWLKTRP 50
                                 **********************************************

A/California/04/2009         ILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLY 96
A/Texas/04/2009              ILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLY 100
A/New_York/18/2009           ILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLY 100
A/Mexico/InDRE4487/2009      ILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLY 100
A/Canada-ON/RV1527/2009      ILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLY 100
                             **************************************************

A/California/04/2009         KKLKREITFHGAKEVSLSYSTGALASCMGLIYNRMGTVTTEAAFGLVCAT 146
A/Texas/04/2009              KKLKREITFHGAKEVSLSYSTGALASCMGLIYNRMGTVTTEAAFGLVCAT 150
A/New_York/18/2009           KKLKREITFHGAKEVSLSYSTGALASCMGLIYNRMGTVTTEAAFGLVCAT 150
A/Mexico/InDRE4487/2009      KKLKREITFHGAKEVSLSYSTGALASCMGLIYNRMGTVTTEAAFGLVCAT 150
A/Canada-ON/RV1527/2009      KKLKREITFHGAKEVSLSYSTGALASCMGLIYNRMGTVTTEAAFGLVCAT 150
                             **************************************************

A/California/04/2009         CEQIADSQHRSHRQMATTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAA 196
A/Texas/04/2009              CEQIADSQHRSHRQMATTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAA 200
A/New_York/18/2009           CEQIADSQHRSHRQMATTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAA 200
A/Mexico/InDRE4487/2009      CEQIADSQHRSHRQMATTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAA 200
A/Canada-ON/RV1527/2009      CEQIADSQHRSHRQMATTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAA 200
                             **************************************************

A/California/04/2009         EAMEVANQTRQMVHAMRTIGTHPSSSAGLKDDLLENLQAYQKRMGVQMQR 246
A/Texas/04/2009              EAMEVANQTRQMVHAMRTIGTHPSSSAGLKDDLLENLQAYQKRMGVQMQR 250
A/New_York/18/2009           EAMEVANQTRQMVHAMRTIGTHPSSSAGLKDDLLENLQAYQKRMGVQMQR 250
A/Mexico/InDRE4487/2009      EAMEVANQTRQMVHAMRTIGTHPSSSAGLKDDLLENLQAYQKRMGVQMQR 250
A/Canada-ON/RV1527/2009      EAMEVANQTRQMVHAMRTIGTHPSSSTGLKDDLLENLQAYQKRMGVQMQR 250
                             **************************:***********************

A/California/04/2009         FK 248
A/Texas/04/2009              FK 252
A/New_York/18/2009           FK 252
A/Mexico/InDRE4487/2009      FK 252
A/Canada-ON/RV1527/2009      FK 252
                             **

multiple sequence alignment of NSmultiple sequence alignment of NS

NS 

CLUSTAL 2.0.10 =
multiple sequence alignment of NS

A/California/04/2009         MDSNTMSSFQVDCFLWHIRKRFADNGLGDAPFLDRLRRDQKSLKGRGNTL 50
A/Texas/04/2009              MDSNTMSSFQVDCFLWHIRKRFADNGLGDAPFLDRLRRDQKSLKGRGNTL 50
A/Mexico/InDRE4487/2009      MDSNTMSSFQVDCFLWHIRKRFADNGLGDAPFLDRLRRDQKSLKGRGNTL 50
A/New_York/18/2009           MDSNTMSSFQVDCFLWHIRKRFADNGLGDAPFLDRLRRDQKSLKGRGNTL 50
A/Canada-ON/RV1527/2009      MDSNTMSSFQVDCFLWHIRKRFADNGLGDAPFLDRLRRDQKSLKGRGNTL 50
                             **************************************************

A/California/04/2009         GLDIETATLVGKQIVEWILKEESSETLRMTIASVPTSRYLSDMTLEEMSR 100
A/Texas/04/2009              GLDIETATLVGKQIVEWILKEESSETLRMTIASVPTSRYLSDMTLEEMSR 100
A/Mexico/InDRE4487/2009      GLDIETATLVGKQIVEWILKEESSETLRMTIASVPTSRYLSDMTLEEMSR 100
A/New_York/18/2009           GLDIETATLVGKQIVEWILKEESSETLRMTIASVPTSRYLSDMTLEEMSR 100
A/Canada-ON/RV1527/2009      GLDIETATLVGKQIVEWILKEESSETLRMTIASVPTSRYLSDMTLEEMSR 100
                             **************************************************

A/California/04/2009         DWFMLMPRQKIIGPLCVRLDQAIMEKNIVLKANFSVIFNRLETLILLRAF 150
A/Texas/04/2009              DWFMLMPRQKIIGPLCVRLDQAIMEKNIVLKANFSVIFNRLETLILLRAF 150
A/Mexico/InDRE4487/2009      DWFMLMPRQKIIGPLCVRLDQAIMEKNIVLKANFSVIFNRLETLILLRAF 150
A/New_York/18/2009           DWFMLMPRQKIIGPLCVRLDQAVMEKNIVLKANFSVIFNRLETLILLRAF 150
A/Canada-ON/RV1527/2009      DWFMLMPRQKIIGPLCVRLDQAVMEKNIVLKANFSVIFNRLETLILLRAF 150
                             **********************:***************************

A/California/04/2009         TEEGAIVGEISPLPSLPGHTYEDVKNAVGVLIGGLEWNGNTVRVSENIQR 200
A/Texas/04/2009              TEEGAIVGEISPLPSLPGHTYEDVKNAVGVLIGGLEWNGNTVRVSENIQR 200
A/Mexico/InDRE4487/2009      TEEGAIVGEISPLPSLPGHTYEDVKNAVGVLIGGLEWNGNTVRVSENIQR 200
A/New_York/18/2009           TEEGAIVGEISPLPSLPGHTYEDVKNAVGVLIGGLEWNGNTVRVSENIQR 200
A/Canada-ON/RV1527/2009      TEEGAIVGEISPLPSLPGHTYEDVKNAVGVLIGGLEWNGNTVRVSENIQR 200
                             **************************************************

A/California/04/2009         FAWRNCDENGRPSLPPEQK 219
A/Texas/04/2009              FAWRNCDENGRPSLPPEQK 219
A/Mexico/InDRE4487/2009      FAWRNCDENGRPSLPPEQK 219
A/New_York/18/2009           FAWRNCDENGRPSLPPEQK 219
A/Canada-ON/RV1527/2009      FAWRNCDENGRPSLPPEQK 219
                             *******************
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