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niman
PostPosted: Wed Aug 17, 2011 2:14 pm 
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CDC has released the HA sequences of a Chihuahua sub-clade isolate, A/Alaska/14/2011. Although it was initially deposited at GISAID in June, it was just "updated". The CDC designated it a LOW REACTOR.

It has a common Chihuahua backbone with N34D, K149N, S165N, A189T, and V275I, but has changes at nucleotide positions 517 and 519, leading to a mixture at postion 159 (N159D and N159E). In the 2009/2010, all US H1N1 isolates designated as low reactors by the CDC had changes at position 159.

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niman
PostPosted: Wed Aug 17, 2011 2:18 pm 
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Location: Pittsburgh, PA USA
niman wrote:
CDC has released the HA sequences of a Chihuahua sub-clade isolate, A/Alaska/14/2011. Although it was initially deposited at GISAID in June, it was just "updated". The CDC designated it a LOW REACTOR.

It has a common Chihuahua backbone with N34D, K149N, S165N, A189T, and V275I, but has changes at nucleotide positions 517 and 519, leading to a mixture at postion 159 (N159D and N159E). In the 2009/2010, all US H1N1 isolates designated as low reactors by the CDC had changes at position 159.

Isolate was collected March 30 from 41M.

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niman
PostPosted: Wed Aug 17, 2011 2:27 pm 
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Location: Pittsburgh, PA USA
Top 100 HA matches

EPI332607 A/Alaska/14/2011 (A/H1N1 swl) segment 4 (HA) 3138.6 0.000000e+00 1701/1701 (100%)
EPI320136 A/Pennsylvania/08/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI316451 A/Texas/08/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI316424 A/Pennsylvania/04/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI316387 A/New Jersey/05/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI310130 A/Texas/07/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI310093 A/Oregon/03/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI309970 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI320039 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA) 3125.7 0.000000e+00 1699/1702 (99%)
EPI319989 A/Alaska/12/2011 (A/H1N1 swl) segment 4 (HA) 3125.7 0.000000e+00 1699/1702 (99%)
EPI315840 A/Mexico/InDRE1947/2011 (A/H1N1) segment 4 (HA) 3125.7 0.000000e+00 1699/1702 (99%)
EPI315838 A/Mexico/InDRE1946/2011 (A/H1N1) segment 4 (HA) 3125.7 0.000000e+00 1699/1702 (99%)
EPI330992 A/Mexico/1946/2011 (A/H1N1 swl) segment 4 (HA) 3120.1 0.000000e+00 1698/1702 (99%)
EPI315836 A/Mexico/InDRE1945/2011 (A/H1N1) segment 4 (HA) 3120.1 0.000000e+00 1698/1702 (99%)
EPI310133 A/Utah/08/2011 (A/H1N1 swl) segment 4 (HA) 3120.1 0.000000e+00 1698/1702 (99%)
EPI310103 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 3120.1 0.000000e+00 1698/1702 (99%)
EPI320121 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 3116.4 0.000000e+00 1697/1702 (99%)
EPI331210 A/Mexico/2208/2011 (A/H1N1 swl) segment 4 (HA) 3114.6 0.000000e+00 1697/1702 (99%)
EPI319994 A/Arizona/02/2011 (A/H1N1 swl) segment 4 (HA) 3110.9 0.000000e+00 1696/1702 (99%)
EPI319430 A/Algeria/G388/2010 (A/H1N1 swl) segment 4 (HA) 3098.0 0.000000e+00 1694/1702 (99%)
EPI319464 A/Estonia/55236/11 (A/H1N1 swl) segment 4 (HA) 3086.9 0.000000e+00 1692/1702 (99%)
EPI295399 A/El Salvador/798/2010 (A/H1N1 swl) segment 4 (HA) 3086.9 0.000000e+00 1692/1702 (99%)
EPI286988 A/CapeTown/29/2010 (A/H1N1 swl) segment 4 (HA) 3086.9 0.000000e+00 1692/1702 (99%)
EPI273662 A/Texas/03/2010 (A/H1N1 swl) segment 4 (HA) 3086.9 0.000000e+00 1692/1702 (99%)
EPI278896 A/Texas/03/2010 (A/H1N1 swl) segment 4 (HA) 3083.2 0.000000e+00 1691/1702 (99%)
EPI320042 A/Massachusetts/09/2011 (A/H1N1 swl) segment 4 (HA) 3081.3 0.000000e+00 1691/1702 (99%)
EPI310173 A/Wisconsin/02/2011 (A/H1N1 swl) segment 4 (HA) 3081.3 0.000000e+00 1691/1702 (99%)
EPI310055 A/New York/02/2011 (A/H1N1 swl) segment 4 (HA) 3081.3 0.000000e+00 1691/1702 (99%)
EPI273656 A/Hawaii/06/2010 (A/H1N1 swl) segment 4 (HA) 3081.3 0.000000e+00 1691/1702 (99%)
EPI273626 A/Arizona/03/2010 (A/H1N1 swl) segment 4 (HA) 3081.3 0.000000e+00 1691/1702 (99%)
EPI320104 A/New York/04/2011 (A/H1N1 swl) segment 4 (HA) 3077.6 0.000000e+00 1690/1702 (99%)
EPI320164 A/Vermont/04/2011 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI310136 A/Vermont/04/2011 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI310049 A/New Jersey/03/2011 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI310002 A/Massachusetts/06/2011 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI309946 A/Maine/03/2011 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI280320 A/Pennsylvania/07/2010 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI278878 A/Mexico/2880/2010 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI273792 A/Wisconsin/03/2010 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI310069 A/North Carolina/03/2011 (A/H1N1 swl) segment 4 (HA) 3070.3 0.000000e+00 1689/1702 (99%)
EPI273838 A/Wisconsin/06/2010 (A/H1N1 swl) segment 4 (HA) 3070.3 0.000000e+00 1689/1702 (99%)
EPI319447 A/Czech Republic/32/2011 (A/H1N1 swl) segment 4 (HA) 3064.7 0.000000e+00 1688/1702 (99%)
EPI273891 A/Dnipropetrovsk/445/2010 (A/H1N1 swl) segment 4 (HA) 3064.7 0.000000e+00 1688/1702 (99%)
EPI273738 A/Minnesota/04/2010 (A/H1N1 swl) segment 4 (HA) 3064.7 0.000000e+00 1688/1702 (99%)
EPI273900 A/California/09/2010 (A/H1N1 swl) segment 4 (HA) 3059.2 0.000000e+00 1687/1702 (99%)
EPI273674 A/Arizona/06/2010 (A/H1N1 swl) segment 4 (HA) 3057.3 0.000000e+00 1686/1702 (99%)
EPI288161 A/Chile/4438/2009 (A/H1N1) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI278380 A/Ghana/FS-09-1345/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI273888 A/Ukraine/220/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI258598 A/California/VRDL97/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI247472 A/Vermont/30/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI247252 A/Colorado/03/2010 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI179301 A/New York/23/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI177415 A/New York/23/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI309892 A/Idaho/04/2011 (A/H1N1 swl) segment 4 (HA) 3049.9 0.000000e+00 1685/1702 (99%)
EPI222975 A/Finland/614/2009 (A/H1N1 swl) segment 4 (HA) 3049.9 0.000000e+00 1685/1702 (99%)
EPI327670 A/mallard/California/1154/2010 (A/H0) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI326493 A/Hong Kong/H090-693-V1 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI326492 A/Hong Kong/H090-693-V2 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324919 A/Montreal/MTL085707/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324896 A/Quebec/QC002461/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324880 A/Quebec/QC148853/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324879 A/Quebec/QC148795/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324878 A/Quebec/QC148621/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324874 A/Quebec/QC146839/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324873 A/Quebec/QC146767/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324871 A/Quebec/QC146618/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324870 A/Quebec/QC146631/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324869 A/Quebec/QC146561/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324868 A/Quebec/QC146496/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324867 A/Quebec/QC146397/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324866 A/Quebec/QC145995/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324864 A/Quebec/QC145783/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324863 A/Quebec/QC145697/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324862 A/Quebec/QC145573/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323576 A/Ireland/4/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323570 A/Ireland/10/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323566 A/Ireland/7/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323550 A/England/393/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323526 A/England/366/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323514 A/Scotland/8/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323486 A/England/346/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323470 A/England/341/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323450 A/England/303/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI320302 A/Australia/38/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI315403 A/Chile/19/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308668 A/Barcelona/INS189/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308445 A/Chicago/WRAIR1691P/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308437 A/Mexico City/WRAIR1691N/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308229 A/San Diego/WRAIR1643P/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308205 A/Virginia/WRAIR1511P/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308165 A/South Carolina/WRAIR1503P/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308101 A/Lima/WRAIR0681F/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308093 A/Lima/WRAIR0672F/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308053 A/Bogota/WRAIR0440T/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI307257 A/Taiwan/7717/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI302563 A/Cambodia/NHRCC00011/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI300637 A/Argentina/HNRG49/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI300555 A/Argentina/HNRG91/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI300553 A/Argentina/HNRG84/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)

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niman
PostPosted: Wed Aug 17, 2011 6:52 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 28253
Location: Pittsburgh, PA USA
niman wrote:
Top 100 HA matches

EPI332607 A/Alaska/14/2011 (A/H1N1 swl) segment 4 (HA) 3138.6 0.000000e+00 1701/1701 (100%)
EPI320136 A/Pennsylvania/08/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI316451 A/Texas/08/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI316424 A/Pennsylvania/04/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI316387 A/New Jersey/05/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI310130 A/Texas/07/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI310093 A/Oregon/03/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI309970 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA) 3131.2 0.000000e+00 1700/1702 (99%)
EPI320039 A/Maryland/04/2011 (A/H1N1 swl) segment 4 (HA) 3125.7 0.000000e+00 1699/1702 (99%)
EPI319989 A/Alaska/12/2011 (A/H1N1 swl) segment 4 (HA) 3125.7 0.000000e+00 1699/1702 (99%)
EPI315840 A/Mexico/InDRE1947/2011 (A/H1N1) segment 4 (HA) 3125.7 0.000000e+00 1699/1702 (99%)
EPI315838 A/Mexico/InDRE1946/2011 (A/H1N1) segment 4 (HA) 3125.7 0.000000e+00 1699/1702 (99%)
EPI330992 A/Mexico/1946/2011 (A/H1N1 swl) segment 4 (HA) 3120.1 0.000000e+00 1698/1702 (99%)
EPI315836 A/Mexico/InDRE1945/2011 (A/H1N1) segment 4 (HA) 3120.1 0.000000e+00 1698/1702 (99%)
EPI310133 A/Utah/08/2011 (A/H1N1 swl) segment 4 (HA) 3120.1 0.000000e+00 1698/1702 (99%)
EPI310103 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 3120.1 0.000000e+00 1698/1702 (99%)
EPI320121 A/Pennsylvania/02/2011 (A/H1N1 swl) segment 4 (HA) 3116.4 0.000000e+00 1697/1702 (99%)
EPI331210 A/Mexico/2208/2011 (A/H1N1 swl) segment 4 (HA) 3114.6 0.000000e+00 1697/1702 (99%)
EPI319994 A/Arizona/02/2011 (A/H1N1 swl) segment 4 (HA) 3110.9 0.000000e+00 1696/1702 (99%)
EPI319430 A/Algeria/G388/2010 (A/H1N1 swl) segment 4 (HA) 3098.0 0.000000e+00 1694/1702 (99%)
EPI319464 A/Estonia/55236/11 (A/H1N1 swl) segment 4 (HA) 3086.9 0.000000e+00 1692/1702 (99%)
EPI295399 A/El Salvador/798/2010 (A/H1N1 swl) segment 4 (HA) 3086.9 0.000000e+00 1692/1702 (99%)
EPI286988 A/CapeTown/29/2010 (A/H1N1 swl) segment 4 (HA) 3086.9 0.000000e+00 1692/1702 (99%)
EPI273662 A/Texas/03/2010 (A/H1N1 swl) segment 4 (HA) 3086.9 0.000000e+00 1692/1702 (99%)
EPI278896 A/Texas/03/2010 (A/H1N1 swl) segment 4 (HA) 3083.2 0.000000e+00 1691/1702 (99%)
EPI320042 A/Massachusetts/09/2011 (A/H1N1 swl) segment 4 (HA) 3081.3 0.000000e+00 1691/1702 (99%)
EPI310173 A/Wisconsin/02/2011 (A/H1N1 swl) segment 4 (HA) 3081.3 0.000000e+00 1691/1702 (99%)
EPI310055 A/New York/02/2011 (A/H1N1 swl) segment 4 (HA) 3081.3 0.000000e+00 1691/1702 (99%)
EPI273656 A/Hawaii/06/2010 (A/H1N1 swl) segment 4 (HA) 3081.3 0.000000e+00 1691/1702 (99%)
EPI273626 A/Arizona/03/2010 (A/H1N1 swl) segment 4 (HA) 3081.3 0.000000e+00 1691/1702 (99%)
EPI320104 A/New York/04/2011 (A/H1N1 swl) segment 4 (HA) 3077.6 0.000000e+00 1690/1702 (99%)
EPI320164 A/Vermont/04/2011 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI310136 A/Vermont/04/2011 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI310049 A/New Jersey/03/2011 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI310002 A/Massachusetts/06/2011 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI309946 A/Maine/03/2011 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI280320 A/Pennsylvania/07/2010 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI278878 A/Mexico/2880/2010 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI273792 A/Wisconsin/03/2010 (A/H1N1 swl) segment 4 (HA) 3075.8 0.000000e+00 1690/1702 (99%)
EPI310069 A/North Carolina/03/2011 (A/H1N1 swl) segment 4 (HA) 3070.3 0.000000e+00 1689/1702 (99%)
EPI273838 A/Wisconsin/06/2010 (A/H1N1 swl) segment 4 (HA) 3070.3 0.000000e+00 1689/1702 (99%)
EPI319447 A/Czech Republic/32/2011 (A/H1N1 swl) segment 4 (HA) 3064.7 0.000000e+00 1688/1702 (99%)
EPI273891 A/Dnipropetrovsk/445/2010 (A/H1N1 swl) segment 4 (HA) 3064.7 0.000000e+00 1688/1702 (99%)
EPI273738 A/Minnesota/04/2010 (A/H1N1 swl) segment 4 (HA) 3064.7 0.000000e+00 1688/1702 (99%)
EPI273900 A/California/09/2010 (A/H1N1 swl) segment 4 (HA) 3059.2 0.000000e+00 1687/1702 (99%)
EPI273674 A/Arizona/06/2010 (A/H1N1 swl) segment 4 (HA) 3057.3 0.000000e+00 1686/1702 (99%)
EPI288161 A/Chile/4438/2009 (A/H1N1) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI278380 A/Ghana/FS-09-1345/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI273888 A/Ukraine/220/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI258598 A/California/VRDL97/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI247472 A/Vermont/30/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI247252 A/Colorado/03/2010 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI179301 A/New York/23/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI177415 A/New York/23/2009 (A/H1N1 swl) segment 4 (HA) 3053.6 0.000000e+00 1686/1702 (99%)
EPI309892 A/Idaho/04/2011 (A/H1N1 swl) segment 4 (HA) 3049.9 0.000000e+00 1685/1702 (99%)
EPI222975 A/Finland/614/2009 (A/H1N1 swl) segment 4 (HA) 3049.9 0.000000e+00 1685/1702 (99%)
EPI327670 A/mallard/California/1154/2010 (A/H0) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI326493 A/Hong Kong/H090-693-V1 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI326492 A/Hong Kong/H090-693-V2 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324919 A/Montreal/MTL085707/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324896 A/Quebec/QC002461/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324880 A/Quebec/QC148853/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324879 A/Quebec/QC148795/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324878 A/Quebec/QC148621/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324874 A/Quebec/QC146839/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324873 A/Quebec/QC146767/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324871 A/Quebec/QC146618/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324870 A/Quebec/QC146631/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324869 A/Quebec/QC146561/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324868 A/Quebec/QC146496/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324867 A/Quebec/QC146397/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324866 A/Quebec/QC145995/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324864 A/Quebec/QC145783/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324863 A/Quebec/QC145697/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI324862 A/Quebec/QC145573/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323576 A/Ireland/4/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323570 A/Ireland/10/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323566 A/Ireland/7/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323550 A/England/393/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323526 A/England/366/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323514 A/Scotland/8/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323486 A/England/346/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323470 A/England/341/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI323450 A/England/303/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI320302 A/Australia/38/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI315403 A/Chile/19/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308668 A/Barcelona/INS189/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308445 A/Chicago/WRAIR1691P/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308437 A/Mexico City/WRAIR1691N/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308229 A/San Diego/WRAIR1643P/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308205 A/Virginia/WRAIR1511P/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308165 A/South Carolina/WRAIR1503P/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308101 A/Lima/WRAIR0681F/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308093 A/Lima/WRAIR0672F/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI308053 A/Bogota/WRAIR0440T/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI307257 A/Taiwan/7717/2009 (A/H1N1 swl) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI302563 A/Cambodia/NHRCC00011/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI300637 A/Argentina/HNRG49/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI300555 A/Argentina/HNRG91/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)
EPI300553 A/Argentina/HNRG84/2009 (A/H1N1) segment 4 (HA) 3048.1 0.000000e+00 1685/1702 (99%)

As seen above, Alaska/14 and Alaska/12 are closely related. They were collected within a week of each other (March 30 and April 5) and were submitted to GISAID on June 21, but the LOW REACTOR sequence was held for almost two months and released two days ago.

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niman
PostPosted: Wed Aug 17, 2011 7:03 pm 
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The collection dates and sequence similarities raise the possibilty that the low reactor sequence A/Alaska/14/2011, was from the father (41M collected March 30) of the second Chihuahua sequence, A/Alaska/12/2011 (12M collected April 5).

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niman
PostPosted: Wed Aug 17, 2011 7:47 pm 
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Commentary

http://www.recombinomics.com/News/08171 ... R_159.html

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