Rhiza Labs FluTracker Forum

The CDC released a series of 50 sets of sequences (at GISAID), almost exclusively from 2011 isolates. D225N was found in four of the HA sequences, including the only HA sequence from Mexico, A/Mexico/1658/2011, which was the S186P sub-clade. The HA sequnece also was a mixture for another novel RBD change, K222N.

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D225N at GISAID

EPI320101 A/New York/03/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI320066 A/Mississippi/07/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI320045 A/Mexico/1658/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI320027 A/Kansas/02/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI319507 A/Netherlands/219/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI318105 A/swine/North Carolina/A01049174/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI318104 A/swine/North Carolina/A01049173/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI317525 A/Constanta/50378/2011 (A/H1N1) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI317491 A/Caras Severin/663/2010 (A/H1N1) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI317485 A/Prahova/2704/2010 (A/H1N1) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI316797 A/Milan/184/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI316366 A/Kentucky/18/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI315836 A/Mexico/InDRE1945/2011 (A/H1N1) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI309661 A/Ireland/6534/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI307492 A/human/Norway/A1s/2009 (A/H1N1) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI301885 A/India/Delhi/VE442/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI301399 A/Alborz/5607/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI295447 A/Kenya/3872/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI280344 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI280341 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI280298 A/Hong Kong/2172/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI278740 A/swine/Germany-NI/R856/10 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI278738 A/swine/Germany-NI/R757/10 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI278734 A/swine/Germany-NI/R299/09 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI278647 A/swine/Germany-NI/R3394/09 (A/H1N1) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI278607 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI269974 A/Perth/431/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI269484 A/Netherlands/2629/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI269476 A/Netherlands/2457b/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI266064 A/Moscow oblast/CRIE-STV/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI266036 A/Ulyanovsk/CRIE-SHTA/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI266016 A/Tambov/CRIE-SPN/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI257276 A/Fujian-Gulou/SWL11951/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI256390 A/Neimenggu-Hangjinhouqi/SWL51/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI255911 A/Ireland/M79556/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI255909 A/Ireland/M79555/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI255841 A/Baden-Wurttemberg/502/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI255234 A/Egypt/N14648/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI254551 A/India/4725/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI254344 A/Nagano/RC1/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI253919 A/Yaroslavl/IIV-198/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI250037 A/South Carolina/47/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI246052 A/YAMAGATA/721/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI244580 A/swine/Italy/7704/2001 (A/H1N1) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI244525 A/swine/Italy/30073/2006 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI244524 A/swine/Italy/30019-2/2007 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI244523 A/swine/Italy/29977/2007 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI244522 A/swine/Italy/29966/2007 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI244521 A/swine/Italy/23255/2006 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI244520 A/swine/Italy/19498/2006 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI244519 A/swine/Italy/19447/2006 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI244382 A/Malaysia/8860/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI240603 A/NIIGATA/1371/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI235513 A/Chernivtsi/844/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI235489 A/Lviv/638/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI235488 A/Lviv/646/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI234526 A/Russia/100/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI233076 A/VICTORIA/2125/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI232951 A/YOKOHAMA/1357/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI230795 A/Ankara/26/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI230387 A/Argentina/HNRG8/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI230277 A/Orenburg/IIV2974/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI227705 A/Michigan/10/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI227701 A/Michigan/10/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI223480 A/Texas/43132503/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI221259 A/Ukraine/02/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI218127 A/New York/4576/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI213223 A/Sao Paulo/53845/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI213222 A/Sao Paulo/53838/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI213073 A/New York/4099/2009 (A/H1N1 swl) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI186629 A/swine/Cotes d'Armor/016007/2005 (A/H1N1) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI181234 A/swine/Granstedt/IDT3475/2004 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI181229 A/swine/Kitzen/IDT6142/2007 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI181228 A/swine/Groitzsch/IDT6016-2/2007 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI181227 A/swine/Groitzsch/IDT6016-1/2007 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI130101 A/Ohio/201/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI130099 A/Ohio/101/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI130097 A/Ohio/101/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI130095 A/Ohio/101/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI130093 A/Ohio/101/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI122229 A/swine/Cloppenburg/IDT4777/2005 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI122211 A/swine/Doetlingen/IDT4735/2005 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI116889 A/Auckland/18/98 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI115331 A/South Africa/214/1999 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI74725 A/Memphis/44/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI58144 A/Chile/1/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI57688 A/Memphis/39/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI56562 A/Memphis/54/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI55313 A/Memphis/53/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI55294 A/Memphis/47/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI55275 A/Memphis/31/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI54971 A/Memphis/51/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI54952 A/Memphis/50/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI54933 A/Memphis/48/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI54914 A/Memphis/46/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI54895 A/Memphis/42/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI54876 A/Memphis/41/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI54857 A/Memphis/40/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI54838 A/Memphis/38/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI49713 A/Memphis/35/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI49694 A/Memphis/25/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48663 A/Memphis/26/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48644 A/Memphis/22/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48625 A/Memphis/21/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48226 A/Memphis/32/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48207 A/Memphis/30/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48188 A/Memphis/29/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48169 A/Memphis/28/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48150 A/Memphis/27/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48131 A/Memphis/24/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48112 A/Memphis/23/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI48093 A/Memphis/20/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI40372 A/Memphis/10/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI38985 A/Memphis/14/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI38018 A/Memphis/2/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI36954 A/Memphis/19/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI35434 A/New York/626/1996 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI34294 A/Memphis/13/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI34275 A/Memphis/11/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI33565 A/Memphis/18/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI33546 A/Memphis/17/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI33527 A/Memphis/16/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI33508 A/Memphis/15/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI33489 A/Memphis/12/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI33470 A/Memphis/8/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI33451 A/Memphis/7/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI33432 A/Memphis/4/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI33413 A/Memphis/3/1983 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI21574 A/sw/Gent/108/01 (A/H1N2) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI15204 A/Ecuador/2625/01 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI563 A/Nagano/6059/1996 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)
EPI285 A/Kamata/69/1996 (A/H1N1 seasonal) segment 4 (HA) 27.0 6.512651e+00 14/14 (100%)

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The increased detection of D225N is inked to more cloning of isolates in eggs. MS/07/11 grown on eggs (EPI320066) has D225N, while the initial sequence did not have D225N.

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I have started a thread on the CDC sequences with D225N and Q226R.

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It is worth noting that the D225N in Mexico/1658 was from a MAMMALIAN isolate. The D225N was not from an egg isolate.

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Commentary

http://www.recombinomics.com/News/06241 ... uahua.html

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