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H7n9

Re: H7n9

H7N9 replicated to higher titre in human airway epithelial cells
and in the respiratory tract of ferrets compared to H3N2.
H7N9 had greater infectivity and lethality in mice compared
other H7N9 and H9N2 viruses.
H7N9 was readily transmitted to naive ferrets through direct contact but,
unlike H3N2, did not transmit readily by respiratory droplets.

H7N9 did not cause severe disease in ferrets and did not spread
systemically to the spleen, kidney, liver, or intestinal tract

more lethal illness in mice, replicating in lungs as H3N2
easily infect mice, while H3N2 needs adaption
can pass through the eyes to infect the respiratory tract in mice

20- to 400-fold replication at 2 DPI than seasonal or other H7N9
in human epithelial cells
80000 fold after 24h than H3N2

http://www.cdc.gov/flu/spotlights/h7n9-disease-characteristics.htm
-----------------------------------------------------------------
http://www.cidrap.umn.edu/news-perspective/2013/07/new-studies-h7n9-raise-pandemic-concerns
July,10,2013
Watanabe T, Kiso M, Fukuyama S, et al. Characterization of H7N9 influenza A viruses
isolated from humans, letter. Nature 2013 Jul 10 [Abstract]
Belser JA, Gustin KM, Pearce MB, et al. Pathogenesis and transmission of avian
influenza A (H7N9) virus in ferrets and mice, letter. Nature 2013 Jul 10 [Abstract]

[Kawaoka et.al]: AH/1 transmitted in respiratory droplets in one of three ferret pairs

>The team wrote that since the H5N1 virus requires several mutations for aerosol
> transmission in ferrets, "the pandemic potential of A (H7N9) viruses may be
> greater than that of the highly pathogenic avian H5N1 viruses."

you could also argue, that H7N9 already has these mutations and still didn't
cause a pandemic, while H5N1 still has the chance to acquire these mutations

> In human airway epithelial cells and ferret respiratory tracts, AH/01 and SH/02 replicated
> 20- to 400-fold after 2 days than H3N2 and similar bird strains
> 80,000-fold than H3N2 at 24 hours

> CDC transmission experiments in ferrets showed the virus spread easily through direct contact,
> but did not transmit readily through respiratory droplets,
> The ratio of transmission in ferrets in the CDC study—with two of six ferrets showing infection
> by respiratory droplet—echoed the findings in the Kawaoka study.

but it did transmit in 3/3 ferret pairs in the Chinese study published recently
------------------------------------------------------------------------------------
 
Re: H7n9

updated mutation table:

Code: 
                                                                    00000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111122222222222222222 0000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111122222222 000000000000000000000000000000000000000000111111111111111111111111111111111111112 00000000000000000011111111111111111 0000000000000000000000000000000000011111111111111111 0000000000000001111111 00000000000000000000000000000 000000000000000000000000000 
                                                                    01111222333334444555555555666666778888888889999900111222333444455556666666777777778888888999999900000000011111222 0001112222222333444445555556666677777888888999900000111222223333334455555555556666667777788888899999900111122 001112222222223333334444555677777888889999001111122222233445555566666888888889990 01122335556777788900000000012244456 0001112233333444445556666667788899900000111222222334 0001124568888990011223 00122344444444455666667777888 000001111222333345566677777 
                                                                    70578456124890458222235789145779031222336771336929478077259277923340124779011678890123357122358902344678934569016 2674670133445169238890122991666902567113469137855689012013570147891100234455670233681355906779901445856011912 296780111227990134690134258047888011222569026688912445937460234844677012346770444 87947354887005758216667789961217772 3560468902689034681460445661615946813478128011255054 1471600053469031358370 37088201113336904122591666125 136786779136348973923713346 
                                                                    28642024515706700235975150281080023158144042363098623929362209740123461468103762843540379739969875706762165703295 4321604917362806326787558188369069921394441265706292202320482744924939402514335625530428290080597240657326940 162469014239493878908184352941056249282469231807456297984970408417747857989582143 17409978248344432715681735845930522 3492458868676281206916287035898282218116352056217850 5288939408068969320389 65548721472688879514707069730 262904148384150018264786986 
-codon-position-----------------------------------------------------    2        1    1 1  1 2   1  1  2      1        21  1         1 1    2               1   1                  2      12             1  2   1     1       1           1             1          1          1  1  21 1       1         2 11 1  2  1       1      2 11   1      112  2 1             2  2              2    2 2 121 1    1        2  2 2        1 1                 1   1 21          11   2     1121 21 21  21 1  1    2       1           111111   2122    1 1 2  1121211111 
---Index------------------------------------------------------------TAAGAGTAGCTCCAGCGCAATATACATACACGTCACCGGTGCGATGACACCAGAACTAGACATGCGTAGGTAAATGAATGGTACATCAGTGCATGGAGCTAGGTGATAGTGAG TTTTACAACGGTAGTGCCGTCCATGGGAAGATCATTACCGTGGGTCGAAGGAGGACTCCCCCCAATTTCTGCGCTTTGAACACTGGTGCCCTTGTAAGTCCCCCGAAAT GACCACGCCCCTACACATGTTATTCGTAGTTGACAGTCAATTTGCTAAATAGCCCTTTTGATCCCCAAAAAAAAGTAGCCT CCGATATGCTACTGGAAGGCCATTTCGAAAATGGT AATCAGTAACAATCTCCTCGGCGATGAACATTTACGCTGGGCGGGGGCTAGC GTAGACACGGAGACAAGATAAA CAGAGTATGCTCACGTCTTGTACGACTTT TCGATGCGGAACAAAGAACATTAATTT 
   1 >A/Index/H7N9-China/2013/03/,H7N9                              ................................................................................................................. ............................................................................................................. ................................................................................. ................................... .................................................... ...................... ............................. ...........................        0      0 ,      0      0       1:>A/Index/H7N9-China/2013/03/,H7N9                              
   2 >A/Index_newMP/H7N9-China/2013/03/,H7N9                        ................................................................................................................. ............................................................................................................. ................................................................................. ................................... .................................................... ...................... .G..A.GAAT.TG.ACTCC.CGTCCT..C ...........................       20     20 ,     20     20       2:>A/Index_newMP/H7N9-China/2013/03/,H7N9                        
   3 >A/Index/H7N9-China/2013/01/31,H7N9,China,throat-swab,65m,E1   ................................................................................................................. ............................................................................................................. ................................................................................. ................................... .................................................... ...................... ............................. ...........................        0      0 ,      0      0       3:>A/Index/H7N9-China/2013/01/31,H7N9,China,throat-swab,65m,E1   
   4 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)          .GGA.....T...CA.A.....AG..C.T.TA............C........GG.....T...........C.C.....AGG.G.T..C.A...A..A...A....G.GA.. .G....GG........T...............T..........A....GA..............G........T...A..TG.........C....C...TT..AC... AGT.T..TT...GTGT.A.C..CC..C.AC..G............CG....ATT..C.CA........G.....A.GA..C ................................... ...T....G.....C...TA...GC.G..GCC..TA....A.A....TC... ...................... .G..A.GAA......C.C..C.TTCT..C C..C..TTAC..GT..GG..CC.G...      136    125 ,    136    125       4:>A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)          
   5 >A/chicken/Shanghai/S1358/2013,2013/04/03,China,H7N9           AGGA..CGATC.TCAAA.C.C.AG..AGT.TA..T......A.GCA.TGTTG.GG.CG.CT..A.A.TA...CGCTG..AACG.GC...CAAG.AAGAACG.A.AGCGAGA.. .GCCG.GG.A..G.C.T..C.TGG.AAG...CTGCC.AAAC..ACAAGGA.......TTTTTA.G.C.TCAGATCCAA..T....ACAT.TCCA...T..TT.AACG.. A...T.ATTTA.GT...AA...CCT.C.AC.AG...CT...C..TCGC.C.ATT..C.CA..TTTT..G.G...A.G.T.C ..T...........A.................A.. ....GA...T....C.....A..GC.G...CC..T.T...A......TC... ...A........GTGT...... .G..A.GAAT.TG.ACTCC.CGTCCT..C ...........................      237    226 ,    237    226       5:>A/chicken/Shanghai/S1358/2013,2013/04/03,China,H7N9           
   6 >A/chicken/Jiangsu/SC099/2013,2013/04/16,China,H7N9            AGGA..CGATC.TCAAA.C.C.AG..AGT.TA..T......A.GCA.TGTTG.GG.CG.CT..A.A.TA...CGCTG..AACG.GC...CAAG.AAGAACG.A.AGCGAGA.. .GCCG.GG.A..G.C.T..C.TGG.AAG...CTGCC.AAAC..ACAAGGA.......TTTTTA.G.C.TCAGATCCAA..T....ACAT.TCCA...T..TT.AACG.. ....T.ATTTA.GT...AA...CCT.C.AC.AG...CT...C..TCGC.C.ATT..C.CA..TTTT..G.G...A.G.T.C ..T................................ ..............................C..G.................T ...A........GTGT...... .G..A.GAAT.TG.ACTCC.CGTCCT..C ...........................      214    211 ,    214    211       6:>A/chicken/Jiangsu/SC099/2013,2013/04/16,China,H7N9            
   7 >A/Shanghai/4987T/2013,2013/04/17,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ---------...---------- ----------------------------- ---------------------------      948    465 ,      0      0       7:>A/Shanghai/4987T/2013,2013/04/17,China,H7N9                   
   8 >A/chicken/Shanghai/S1080/2013,2013/04/03,China,H7N9           ................A.......T.....TA............................T........A..C.C....AAGGTG....C............A....G..... .G....GGT....A..T....T..........T..........A....GA..........A...G........T.C.A.GTG....CA.TTC.....T..TT..AC... .GT.........GTGT.A.C..CC..C.AC.....................A.T..C....................A... .T...........A..................... ..............C.T.TAA.AGC.G..GCC..TA.CA.....A..TC... ..................C... ...G...................TT.... ...C......-............G...      171     91 ,    170     90       8:>A/chicken/Shanghai/S1080/2013,2013/04/03,China,H7N9           
   9 >A/Shanghai/4778T/2013,2013/04/10,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ---------....--------- ----------------------------- ---------------------------      946    464 ,      0      0       9:>A/Shanghai/4778T/2013,2013/04/10,China,H7N9                   
  10 >A/Hangzhou/2/2013,2013/04/01,China,H7N9                       ...A..........A.A.....A.AG..................................T...........C...............A..A.C.A..A.............. ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ...G............................... ---------------------------------------------------- ...................... ----------------------------- ---------------------------      580    312 ,     18     14      10:>A/Hangzhou/2/2013,2013/04/01,China,H7N9                       
  11 >A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9,6             ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ...................... ----------------------------- ---------------------------      880    446 ,      0      0      11:>A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9,6             
  12 >A/chicken/Jiangsu/SC537/2013,2013/04/16,China,H7N9            AG.A...GATC.TCAAA.C...AG..AGT.TA..T......A.GCA.TGTT..GG.CG.CT..A.ACTA...CGCTG..AACG.GC...CAAG.AAGA.CG.....CGAGA.. ............................................................................................................. ...................................................C............................. ........T.......................... .................................................... ...................... .G..A.GAAT.TC.AC.C..CGTTCT..C ...........................       91     86 ,     91     86      12:>A/chicken/Jiangsu/SC537/2013,2013/04/16,China,H7N9            
  13 >A/Shanghai/4842T/2013,2013/04/13,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ---------------------------........ ---------------------------------------------------- ---------..A.......--- ----------------------------- ---------------------------      910    451 ,      1      1      13:>A/Shanghai/4842T/2013,2013/04/13,China,H7N9                   
  14 >A/Shanghai/4659T/2013,2013/02/27,China,H7N9                   -----------------------------------.TAAA.........---------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- -------------------AAGAGC.......... ---------------------------------------------------- ---------------------- ----------------------------- ---------------------------      918    448 ,     11     10      14:>A/Shanghai/4659T/2013,2013/02/27,China,H7N9                   
  15 >A/Shanghai/4798T/2013,2013/04/12,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ------........-------- ----------------------------- ---------------------------      932    460 ,      4      0      15:>A/Shanghai/4798T/2013,2013/04/12,China,H7N9                   
  16 >A/duck/Zhejiang/12/2011|2011/06/|China|H7N3|4                 ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- T..G..CA.G..A..G.A..T..A.TA..C....C ---------------------------------------------------- ---------------------- ----------------------------- ---------------------------      902    447 ,     69     14      16:>A/duck/Zhejiang/12/2011|2011/06/|China|H7N3|4                 
  17 >A/chicken/Jiangsu/RD5/2013(H10N9)                             ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ...A.........TG....... ----------------------------- ---------------------------      897    449 ,     17      3      17:>A/chicken/Jiangsu/RD5/2013(H10N9)                             
  18 >A/Shanghai/4655T/2013,2013/02/26,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- -------------------AAGAGC....C.C..C ---------------------------------------------------- ---------------------- ----------------------------- ---------------------------      935    461 ,      9      9      18:>A/Shanghai/4655T/2013,2013/02/26,China,H7N9                   
  19 >A/Shanghai/4665T/2013,2013/03/05,China,H7N9                   -----------------------------------.TAAA.........---------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- -------------------AAGAGC....C.C..C ---------------------------------------------------- ---------------------- ----------------------------- ---------------------------      921    451 ,     13     13      19:>A/Shanghai/4665T/2013,2013/03/05,China,H7N9                   
  20 >A/Shanghai/4821T/2013,2013/04/12,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ---------AG.........-- ----------------------------- ---------------------------      939    459 ,      2      2      20:>A/Shanghai/4821T/2013,2013/04/12,China,H7N9                   
  21 >A/Shanghai/4664T/2013,2013/03/05,China,H7N9                   ........................................................................................A........................ .............................T......................................................................T........ .......................................................................G........C .........................TA........ .................................................... ..G......AG........... .G........................... ...........................       39     11 ,     38     11      21:>A/Shanghai/4664T/2013,2013/03/05,China,H7N9                   
  22 >A/chicken/Zhejiang/SD019/2013,2013/04/11,China,H7N9           .............................................................................................C................... ............................................................................................................. .........................................................C....................... ................................... .................................................... ...................... ..........C....C....C..TC.GCC ...........................       18     10 ,     18     10      22:>A/chicken/Zhejiang/SD019/2013,2013/04/11,China,H7N9           
  23 >A/environment/Shanghai/S1088/2013,2013/04/03,China,H7N9       ................................................................................................................. ............................................................................................................. .................A...G.C................C.....G.................................. ....C.............................. .................................................... ...AG.......GTG.A..... ..........C............TC.GC. ...........................       17     17 ,     17     17      23:>A/environment/Shanghai/S1088/2013,2013/04/03,China,H7N9       
  24 >A/chicken/Shanghai/S1055/2013,2013/04/03,China,H7N9           ...................G.............................................................C............................... ............................................................................................................. ................................................................................. ....C.............................. .................................................... ...AG.......GTG.A..... .............A............... ...........................       13     10 ,     13     10      24:>A/chicken/Shanghai/S1055/2013,2013/04/03,China,H7N9           
  25 >A/chicken/Shanghai/S1053/2013,2013/04/03,China,H7N9           ...................G.............................................................C............................... ..................................................................................................C.......... ................................................................................. ....C.............................. .................................................... ...AG.......GTG.A..... .............A............... ...........................       15     11 ,     15     11      25:>A/chicken/Shanghai/S1053/2013,2013/04/03,China,H7N9           
  26 >A/pigeon/Shanghai/S1421/2013,2013/04/03,China,H7N9            ................................................................................................................. ....................T........................................................................................ ................................................................................. ...........................T....... ......................................A............. AC.....T.............. ..A.......................... ...........................        9      7 ,      9      7      26:>A/pigeon/Shanghai/S1421/2013,2013/04/03,China,H7N9            
  27 >A/chicken/Shanghai/S1413/2013,2013/04/03,China,H7N9           ................................................................................................................. ....................T...........................................................T............................ .............................................CG.C..A............................. ...........................T....... .................................................... AC.....T.............. ..A.......................... ...........................       11     11 ,     11     11      27:>A/chicken/Shanghai/S1413/2013,2013/04/03,China,H7N9           
  28 >A/Anhui/1/2013,H7N9                                           ........................................................................................A........................ ................................................................................T............................ ...A............................................................................. ................................... .................................................... ...................... ............................. ...........................        4      3 ,      4      3      28:>A/Anhui/1/2013,H7N9                                           
  29 >A/Shanghai/02/2013,2013/03/05,China,H7N9                      ..........................................A..................................G..........A........................ .............................T............................................................................... ................................................................................. ..................A................ .................................................... ..G................... ............................. ...........................        7      6 ,      7      6      29:>A/Shanghai/02/2013,2013/03/05,China,H7N9                      
  30 >A/Shanghai/2/2013,H7N9                                        ..........................................A..................................G..........A........................ .............................T............................................................................... ................................................................................. ..................A................ .................................................... ..G................... ............................. ...........................        6      6 ,      6      6      30:>A/Shanghai/2/2013,H7N9                                        
  31 >A/Hangzhou/1/2013,2013/03/24,China,H7N9                       .............................T....................................C....................GA...........G............ ...................................................................A..................................T....G. ..............................C.................................................. ...........A................C...... .................................................... ......C............... ............................. ..........G................       13     13 ,     13     13      31:>A/Hangzhou/1/2013,2013/03/24,China,H7N9                       
  32 >A/Hangzhao/1/2013,2013/03/24,H7N9,China,throat-swab,,         .............................T....................................C....................GA...........G............ ...................................................................A.......................................G. ..............................C.................................................. ...........AA...............C...... .................................................... ......C............... ............................. ..........G................       14     13 ,     14     13      32:>A/Hangzhao/1/2013,2013/03/24,H7N9,China,throat-swab,,         
  33 >A/chicken/Shanghai/S1410/2013,2013/04/03,China,H7N9           .................................T............................................................................... ............................................................................................................. ................................................................................. ............A....A................. ............................................A....... ...................... ............................. ...........................        7      4 ,      7      4      33:>A/chicken/Shanghai/S1410/2013,2013/04/03,China,H7N9           
  34 >A/wild pigeon/Jiangsu/SD001/2013,2013/04/17,China,H7N9        .................................T............................................................................... ..................................................................................................C.......... ................................................................................. ..A.........A...................... .................................................... ...................... ............................. ...........................        8      4 ,      8      4      34:>A/wild pigeon/Jiangsu/SD001/2013,2013/04/17,China,H7N9        
  35 >A/chicken/Zhejiang/DTID-ZJU01/2013,2013/04/,China,H7N9        .................................T............................................................................... ............................................................................................................. -................................................................................ ..A.........A...................... .................................................... .....................G ............................. ...........................       19      5 ,     18      4      35:>A/chicken/Zhejiang/DTID-ZJU01/2013,2013/04/,China,H7N9        
  36 >A/chicken/Guangdong/SD641/2013,2013/05/03,China,H7N9          .................................T............................................................................... ............................................................................................................. ................................................................................. ..................A................ .....................T.............................. ........A............. ............................. ...........................       10      4 ,     10      4      36:>A/chicken/Guangdong/SD641/2013,2013/05/03,China,H7N9          
  37 >A/environment/Fujian/SC337/2013,2013/04/30,China,H7N9         .................................T..........................T.................................................... ............................................................................................................. ................................................................................. ................................... .....................T.............................. ........A............. ............................. ...........................       12      4 ,     12      4      37:>A/environment/Fujian/SC337/2013,2013/04/30,China,H7N9         
  38 >A/chicken/Jiangsu/SC035/2013,2013/04/16,China,H7N9            .................................T...........................G................................................... ............................................................................................................. ................................................................................. ................................... .................................................... ...................... ............................. ..A.A..............G.......       12      5 ,     12      5      38:>A/chicken/Jiangsu/SC035/2013,2013/04/16,China,H7N9            
  39 >A/duck/Anhui/SC702/2013,2013/04/16,China,H7N9                 .................................T............................................................................... ................................................G............................................................ ...............................................................................T. ................................... .................................................... ...................... ............................. ...........................        8      3 ,      8      3      39:>A/duck/Anhui/SC702/2013,2013/04/16,China,H7N9                 
  40 >A/Fujian/1/2013,2013/04/24,China,H7N9                         .................................T......................................................A........................ ....G........................................................................................................ ................................................................................. ................................... .................................................... ...................... ............................. ...........................       27      3 ,     27      3      40:>A/Fujian/1/2013,2013/04/24,China,H7N9                         
  41 >A/Jiangsu/1/2013/03/30,H7N9,China,,45f,E1                     ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ...........A................C...... ---------------------------------------------------- ......C............... ............................. ---------------------------      699    385 ,      5      3      41:>A/Jiangsu/1/2013/03/30,H7N9,China,,45f,E1                     
  42 >A/chicken/Zhejiang/SD033/2013,2013/04/11,China,H7N9           ................................................................................................................. ............................................................................................................. A...TT......GT...A..C.CC...GAC..G.G....G.....CG...GATTTC.CCAGC.....T...G.TAC...TC ................................... .................................................... ...................... ............................. ...........................       37     35 ,     37     35      42:>A/chicken/Zhejiang/SD033/2013,2013/04/11,China,H7N9           
  43 >A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9                        ....................................................T............................................................ ............................................................................................................C A...TT......GT...A..C.CC...GAC..G.G....G.....CG...GATTTC.CCAGC.....T...G.TAC...TC ................................... .................................................... .....................G ............................. ...........................       44     38 ,     44     38      43:>A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9                        
  44 >A/Shanghai/5058T/2013,2013/04/19,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ------......---------- ----------------------------- ---------------------------      933    462 ,      0      0      44:>A/Shanghai/5058T/2013,2013/04/19,China,H7N9                   
  45 >A/chicken/Jiangxi/SD001/2013,2013/05/03,China,H7N9            .GGA.........CA.A.....AG....T..A............................T........AC.C.......A..TG......G......A..A.......GA.. GGCCGTGG.AA.G.C.TTA..T..AA.G...CTG...AAACA.ACA.GGAA..TGA.TT..TAGGCC..C.A.TCCAA..TG...ACATTTCCA...T..TT.AAC... ................................................................................. .T................................. .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ..................C... ...G......................... ...................C.......      137    112 ,    137    112      45:>A/chicken/Jiangxi/SD001/2013,2013/05/03,China,H7N9            
  46 >A/Shanghai/4862T/2013,2013/04/14,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ---------...---------- ----------------------------- ---------------------------      947    465 ,      0      0      46:>A/Shanghai/4862T/2013,2013/04/14,China,H7N9                   
  47 >A/chicken/Zhejiang/SD007/2013,2013/04/22,China,H7N9           .................................T............................................................................... .G.....GT.......................T..C..........A.G.......C.......G........T...A..TG.........C............AC... A...T..TT...TT...A...GCC..C.AC.AG....T..C....CG.C.GATT..C.CA..T.T.......G.A.....C ............A...................... ....GA...T....C.....A..GC.GGT.CC..T.T...A......TC... ...A.........TG....G.. .G..A.GAAT.TG.ACTCC.CGTTCT..C .......TACG..TC..G...C.....      135     99 ,    135     99      47:>A/chicken/Zhejiang/SD007/2013,2013/04/22,China,H7N9           
  48 >A/Shanghai/4701T/2013,2013/04/06,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ---------------------------........ ---------------------------------------------------- ---------...---------- ----------------------------- ---------------------------      922    457 ,      0      0      48:>A/Shanghai/4701T/2013,2013/04/06,China,H7N9                   
  49 >A/Shanghai/4774T/2013,2013/04/10,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ---------.....-------- ----------------------------- ---------------------------      945    463 ,      0      0      49:>A/Shanghai/4774T/2013,2013/04/10,China,H7N9                   
  50 >A/environment/Nanjing/2913/2013,2013/03/29,China,H7N9         .................T....................................................C.......................................... .G.....G...C...A....................G....................................T........T.A..........G...T......... ..........A...........................G...C...................................... ..T..GA............................ ..............................C..G................AT ..............G....... .G..A.GAAT.TG.ACTCC.CGTCCT..C ..A.A......................       45     45 ,     45     45      50:>A/environment/Nanjing/2913/2013,2013/03/29,China,H7N9         
  51 >A/environment-poultry_cage/Nanjing/2913/2013/03/29,H7N9       .................T....................................................C.......................................... .G.....G...C...A....................G....................................T........T.A..........G...T......... ..........A...........................G...C...................................... ..T..GA............................ ..............................C..G................AT ..............G....... .G..A.GAAT.TG.ACTCC.CGTCCT..C ..A.A......................       45     45 ,     45     45      51:>A/environment-poultry_cage/Nanjing/2913/2013/03/29,H7N9       
  52 >A/Hangzhou/3/2013,2013/04/08,China,H7N9                       .................T............................................C.......C.................A......................CA ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ..T..GA...T........................ ---------------------------------------------------- ...A........GTGT.G..G. ----------------------------- ---------------------------      579    315 ,     17     17      52:>A/Hangzhou/3/2013,2013/04/08,China,H7N9                       
  53 >A/Hangzhou/3/2013/04/02,H7N9,m79                              .................T............................................C.......C.................A......................CA ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ..T..GA...T........................ ..............................C..G.................T ...A........GTGT.G..G. ----------------------------- ..A.A..............G.....C.      437    243 ,     24     24      53:>A/Hangzhou/3/2013/04/02,H7N9,m79                              
  54 >A/Zhejiang/HZ1/2013/4/,H7N9                                   .................T............................................C.......C.................A......................CA ............................................................................................................C A...TT......GT...A..C.CC...GAC..G.G....G.....CG...GATTTC.CCAGC.....T...G.TAC...TC ..T..GA...T........................ ..............................C..G.................T ............GTGT.G..G. .G..A.GAAT.TG.ACTCC.CGTCCT..C ..A.A..............G.....C.       80     79 ,     80     79      54:>A/Zhejiang/HZ1/2013/4/,H7N9                                   
  55 >A/Shanghai/4819T/2013,2013/04/12,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ---------...---------- ----------------------------- ---------------------------      947    465 ,      0      0      55:>A/Shanghai/4819T/2013,2013/04/12,China,H7N9                   
  56 >A/Nanjing/1/throat_swab/2013/03/28,H7N9                       .................T....................................................C.......................................... .G.....G...C...A..........A.........G...............A....................T........T.A..........G...T......... ................................................................................. ..T.....T.......................... .........T.T..C..C.....GC.G...CC..T....AA..A...TC... ...A........GTGT...... .G..A.GAAT.TG.ACTCC.CGTCCT..C ...........................       67     56 ,     67     56      56:>A/Nanjing/1/throat_swab/2013/03/28,H7N9                       
  57 >A/Shanghai/4700/2013,2013/04/05,China,H7N9                    ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------------------------- ---------------------------------------------------- ---------...---------- ----------------------------- ---------------------------      947    465 ,      0      0      57:>A/Shanghai/4700/2013,2013/04/05,China,H7N9                    
  58 >A/environment/Shanghai/S1438/2013,2013/04/03,China,H7N9       .G.AG.........A.A.....AG..A.T..A.........A..CA.......GG.....T...........C..T...............A......A..........G... ............................................................................................................. .......TT...TT...A...GCC.AC.AC.AG..A....C....CG.C.GATT..C.CA..T......G....A.G...C .....G........................G.A.. GGGT..CCG.G.CTCA..TA..A.CAGGTGCC..TA.C..AAA..AATCG.. ...................... .G..A.GAAT.TG.ACTCC.CGTCCT..C CT...ATTA..AGCCAGGA.C.G.C..      128    126 ,    128    126      58:>A/environment/Shanghai/S1438/2013,2013/04/03,China,H7N9       
  59 >A/environment/Shanghai/S1436/2013,2013/04/03,China,H7N9       ............................................................T...........C..T...............A......A..........G... ............................................................................................................. A......TT...TT...A....CC..C.AC.AG.......C....CG.C..ATT..C.CA..T.T....G..G.A.G.T.C .....G........................G.... GGGT..CCG.G.CTCA..T...A.CAGGTGCC..TA.C..AAA..AATCG.. ...................... .G..A.GAAT.TG.ACT.C.CGTCCT..C CT.....T....GCC.G...C......       99     99 ,     99     99      59:>A/environment/Shanghai/S1436/2013,2013/04/03,China,H7N9       
  60 >A/Shanghai/5083T/2013,2013/04/20,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- -------------------------.....G.... ---------------------------------------------------- --------...A.......--- ----------------------------- ---------------------------      907    449 ,      2      2      60:>A/Shanghai/5083T/2013,2013/04/20,China,H7N9                   
  61 >A/environment/Shanghai/S1437/2013,2013/04/03,China,H7N9       .G.AG......T..A.A.....AG....T..AC......................A..A.T...T.C.....C..T..C............A......A..A.C.....G... GGCCGTGG.A..G.C.TT...T..AA.....CTG...AAACA.ACA.GGAA..T.A.TT..TAGGCC..C.A.TCCAA..TG...ACAT.TCCA...T..TT.AAC... ...AT..TT...TT...A...GCC.AC.AC.AG..A.T..C....CG.C.GATT..C.......................C .....G........................G.... ..............................Y..................... ...................... .G..A.GAAT.TG.ACT.C.CGTTCT..C CT...ATTAC.AGCCAGGA.CCG.C..      162    157 ,    162    157      61:>A/environment/Shanghai/S1437/2013,2013/04/03,China,H7N9       
  62 >A/Shanghai/5240T/2013,2013/04/25,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------....G.... ---------------------------------------------------- --------...A.......--- ----------------------------- ---------------------------      909    450 ,      2      2      62:>A/Shanghai/5240T/2013,2013/04/25,China,H7N9                   
  63 >A/environment/Shanghai/S1439/2013,2013/04/03,China,H7N9       .G.AG......T..A.A.....AG....T..AC.......A..............A..A.T...T.C.....C..T..C............A......A..A.C.....G... .................................................................................G...............T.......C... .................A...GCC.AC.AC.AG..A.T..C....CG.C................................ .....G........................G.... GGGT..CCG.G.CTCA..TA..A.CAGGTGCC..TA.C..AAA..AATCG.. ...................... .G..A.GAA...G..C.CC.CGTTCT..C ........................C..      104     97 ,    104     97      63:>A/environment/Shanghai/S1439/2013,2013/04/03,China,H7N9       
  64 >A/Shanghai/5180T/2013,2013/04/23,China,H7N9                   ----------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ---------------------------...G.... ---------------------------------------------------- --------...A.......--- ----------------------------- ---------------------------      910    451 ,      2      2      64:>A/Shanghai/5180T/2013,2013/04/23,China,H7N9                   
  65 >A/Taiwan/T02081/2013,2013/04/22,Taiwan,H7N9                   .....................C.............T..........G.................................................................. ............................G.G....................G..........................................C.............. -..........C....G................T................................G.............. .....G..........G.............G.... .................................................... -....A.....A.......... AG..ACGAAT.TG.ACT.C.CGTTCT..C -..........................       52     40 ,     41     37      65:>A/Taiwan/T02081/2013,2013/04/22,Taiwan,H7N9                   
  66 >A/Taiwan/S02076/2013,2013/04/22,Taiwan,H7N9                   .....................C.............T..........G.........................................A........................ ............................G.G....................G..........................................C.............. ...........C....G................T................................G.............. .....G..........G.............G.... .................................................... .....A.....A.......... AG..ACGAAT.TG.ACT.C.CGTTCT..C ...........................       47     38 ,     44     38      66:>A/Taiwan/S02076/2013,2013/04/22,Taiwan,H7N9                   
  67 >A/homing pigeon/Jiangsu/SD184/2013,2013/04/20,China,H7N9      ..............................................G.................................................................. ............................................................................................................. .................................T............................................... .....G......A.................G.... .................................................... ...................... AG..ACGAAT.TG.ACT.C.CGTTCT..C ...........................       31     26 ,     31     26      67:>A/homing pigeon/Jiangsu/SD184/2013,2013/04/20,China,H7N9      
  68 >A/pigeon/Shanghai/S1423/2013,2013/04/03,China,H7N9            ..............................................G.................................................................. ............................................................................................................. .................................T............................................... .....G........A...............G.... .................................................... ...................... AG..ACGAAT.TG.ACT.C.CGTTCT..C ...........................       27     26 ,     27     26      68:>A/pigeon/Shanghai/S1423/2013,2013/04/03,China,H7N9            
  69 >A/chicken/Jiangsu/S002/2013,2013/04/16,China,H7N9             .................................T...........................G................................................... ............................................................................................................. ................................................................................. ..T...A............................ .................................................... ...A........GTGT.G.... .G..A.GAAT.TG.ACTCC.CGTCCT..C ...........................       30     30 ,     30     30      69:>A/chicken/Jiangsu/S002/2013,2013/04/16,China,H7N9             
  70 >A/environment/Hangzhou/34/2013,2013/04/04,China,H7N9          .................................T............................................................................... ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ..A................................ ---------------------------------------------------- ...................... ----------------------------- ---------------------------      564    300 ,      2      2      70:>A/environment/Hangzhou/34/2013,2013/04/04,China,H7N9          
  71 >A/duck/Zhejiang/SC410/2013,2013/04/16,China,H7N9              ................................................................................................................. .G....GGT.......T...............T..........A.A..GA........A.....T........T...A.GTG.........C....C...TTT.AC.G. A...TT......GT...A..C.CC...GAC..G.G....G.....CG...GATTTC.CCAGC.....T...G.TAC...TC ................................... .................................................... ...................... ............................. ...........................       90     60 ,     90     60      71:>A/duck/Zhejiang/SC410/2013,2013/04/16,China,H7N9              
  72 >A/environment/Shandong/SD049/2013,2013/05/03,China,H7N9       .....T...........................T....................................................T.......................... GGCCGTGG.AA.G.C.TTA..T..AA.G...CTG...AAACAAACA.GGAA..TGA.TT..TAGGCC..C.A.TCCAAT.TG.C.ACATTTCCA...T..TT.AAC... ................................................................................. .................................A. .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ..................C... ...G...............A......... ..........................C       99     97 ,     99     97      72:>A/environment/Shandong/SD049/2013,2013/05/03,China,H7N9       
  73 >A/environment/Shandong/SD039/2013,2013/05/03,China,H7N9       .....T...........................T....................................................T.......................... GGCCGTGG.AA.G.C.TTA..T..AA.G...CTG...AAACAAACA.GGAA..TGA.TT..TAGGCC..C.A.TCCAAT.TG.C.ACATTTCCA...T..TT.AAC... ................................................................................. .................................A. .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ..................C... ...G...............A......... ..........................C       97     97 ,     97     97      73:>A/environment/Shandong/SD039/2013,2013/05/03,China,H7N9       
  74 >A/pigeon/Shanghai/S1069/2013,2013/04/02,China,H7N9            .........................G.............................................G......................................... GGCCGTGG.AA.G.C.TTA..T..AA.G...CTG...AAACA.ACA.GGAA..TGA.TT..TAGGCC..C.A.TCCAAT.TG.C.ACATTTCCA...T..TT.AAC... ...........................................A..................................... .T...........A..................... .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ..................C... ...G......................... ...........................       96     95 ,     96     95      74:>A/pigeon/Shanghai/S1069/2013,2013/04/02,China,H7N9            
  75 >A/chicken/Shanghai/S1076/2013,2013/04/03,China,H7N9           .........................G.............................................G......................................... GGCCGTGG.AA.G.C.TTA..T..AA.G...CTG...AAACA.ACA.GGAA..TGA.TT..TAGGCC..C.A.TCCAAT.TG.C.ACATTTCCA...T..TT.AAC... ...........................................A..................................... .T...........A..................... .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ..................C... ...G......................... ...........................       96     95 ,     96     95      75:>A/chicken/Shanghai/S1076/2013,2013/04/03,China,H7N9           
  76 >A/chicken/Shanghai/S1079/2013,2013/04/03,China,H7N9           .........................G.............................................G......................................... GGCCGTGG.AA.G.C.TTA..T..AA.G...CTG...AAACA.ACA.GGAA..TGA.TT..TAGGCC..C.A.TCCAAT.TG.C.ACATTTCCA...T..TT.AAC... ...........................................A..................................... .T...........A..................... .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ..................C... ...G......................... ...........................       96     95 ,     96     95      76:>A/chicken/Shanghai/S1079/2013,2013/04/03,China,H7N9           
  77 >A/chicken/Shanghai/S1078/2013,2013/04/03,China,H7N9           .........................G....................................................................................... GGCCGTGG.AA.G.C.TTA..T..AA.G...CTG...AAACA.ACA.GGAA..TGA.TT..TAGGCC..C.A.TCCAAT.TG.C.ACATTTCCA...T..TT.AAC... ...........................................A..................................... .T...........A..................... .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ..................C... ...G......................... ...........................       94     94 ,     94     94      77:>A/chicken/Shanghai/S1078/2013,2013/04/03,China,H7N9           
  78 >A/chicken/Shanghai/S1077/2013,2013/04/03,China,H7N9           .........................G.............................................G......................................... GGCCGTGG.AA.G.C.TTA..T..AA.G...CTG...AAACA.ACA.GGAA..TGA.TT..TAGGCC..C.A.TCCAAT.TG.C.ACATTTCCA...T..TT.AAC... ................................................................................. .T...........A..................... .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ..................C... ...G......................... ...........................       98     94 ,     98     94      78:>A/chicken/Shanghai/S1077/2013,2013/04/03,China,H7N9           
  79 >A/environment/Henan/SD429/2013,2013/04/24,China,H7N9          .......................................................................G......................................... GGCCGTGG.AA.G.C.TTA..T..AA.G...CTG...AAACA.ACA.GGAA..TGA.TT..TAGGCC..C.A.TCCAA..TG...ACATTTCCA...T..TT.AAC... ................................................................................. .T..........A............T......... .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ..................C... ...G......................... ...........................       99     92 ,     99     92      79:>A/environment/Henan/SD429/2013,2013/04/24,China,H7N9          
  80 >A/environment/Henan/SC232/2013,2013/04/24,China,H7N9          ........................................A..............................G......................................... GGCCGTGG.AA.G.C.TTA..T..AA.G...CTG...AAACA.ACA.GGAA..TGA.TT..TAGGCC..C.A.TCCAA..TG...ACATTTCCA...T..TT.AAC... ................................................................................. .T................................. .........T.T..C.AC.....G..G...CCA.T....AA..A...TC... ..................C... ...G......................... ...........................       96     90 ,     96     90      80:>A/environment/Henan/SC232/2013,2013/04/24,China,H7N9          
  81 >A/Nanchang/1/2013,2013/04/24,China,H7N9                       .......................................................................G................A........................ ------------------------------------------------------------------------------------------------------------- ................................................................................. .T................................. .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ---------------------- ...G......................... ...........................      307    152 ,     23     21      81:>A/Nanchang/1/2013,2013/04/24,China,H7N9                       
  82 >A/environment/Shandong/SD038/2013,2013/05/03,China,H7N9       .......................................................................G......................................... GGCCGTGG.A..GAC.TT...T..AA.G...CTG...AAACA.ACA.GGAAG.T.ACTT..TAGGCC..C.A.TCCAA..TG...ACAT.TCCA...T..TT.AAC... ......A.......................................................................... .T................................. .........T.T..C.AC.....GC.G...CCA.T....AA..A...TC... ..................C... ...G......................... ...........................      102     90 ,    102     90      82:>A/environment/Shandong/SD038/2013,2013/05/03,China,H7N9       
  83 >A/Shanghai/1/2013,H7N9                                        ...A............A.......T...........................T...................C...............A........................ .G.....G...C...A....................G...............A....................T..........A...A......G...T......... ............................A................C................................... T......A.GG.A..G.............C.C..C GGGT..CCG.G.CTCA..TA..A.CAGGTGCC..TA.C..AAA..AATCG.. ...A.......A.TG....G.. .......................T..... ........A..................       82     69 ,     82     69      83:>A/Shanghai/1/2013,H7N9                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
---Index------------------------------------------------------------TAAGAGTAGCTCCAGCGCAATATACATACACGTCACCGGTGCGATGACACCAGAACTAGACATGCGTAGGTAAATGAATGGTACATCAGTGCATGGAGCTAGGTGATAGTGAG TTTTACAACGGTAGTGCCGTCCATGGGAAGATCATTACCGTGGGTCGAAGGAGGACTCCCCCCAATTTCTGCGCTTTGAACACTGGTGCCCTTGTAAGTCCCCCGAAAT GACCACGCCCCTACACATGTTATTCGTAGTTGACAGTCAATTTGCTAAATAGCCCTTTTGATCCCCAAAAAAAAGTAGCCT CCGATATGCTACTGGAAGGCCATTTCGAAAATGGT AATCAGTAACAATCTCCTCGGCGATGAACATTTACGCTGGGCGGGGGCTAGC GTAGACACGGAGACAAGATAAA CAGAGTATGCTCACGTCTTGTACGACTTT TCGATGCGGAACAAAGAACATTAATTT 
-codon-position-----------------------------------------------------    2        1    1 1  1 2   1  1  2      1        21  1         1 1    2               1   1                  2      12             1  2   1     1       1           1             1          1          1  1  21 1       1         2 11 1  2  1       1      2 11   1      112  2 1             2  2              2    2 2 121 1    1        2  2 2        1 1                 1   1 21          11   2     1121 21 21  21 1  1    2       1           111111   2122    1 1 2  1121211111 
                                                                    00000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111122222222222222222 0000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111122222222 000000000000000000000000000000000000000000111111111111111111111111111111111111112 00000000000000000011111111111111111 0000000000000000000000000000000000011111111111111111 0000000000000001111111 00000000000000000000000000000 000000000000000000000000000 
                                                                    01111222333334444555555555666666778888888889999900111222333444455556666666777777778888888999999900000000011111222 0001112222222333444445555556666677777888888999900000111222223333334455555555556666667777788888899999900111122 001112222222223333334444555677777888889999001111122222233445555566666888888889990 01122335556777788900000000012244456 0001112233333444445556666667788899900000111222222334 0001124568888990011223 00122344444444455666667777888 000001111222333345566677777 
                                                                    70578456124890458222235789145779031222336771336929478077259277923340124779011678890123357122358902344678934569016 2674670133445169238890122991666902567113469137855689012013570147891100234455670233681355906779901445856011912 296780111227990134690134258047888011222569026688912445937460234844677012346770444 87947354887005758216667789961217772 3560468902689034681460445661615946813478128011255054 1471600053469031358370 37088201113336904122591666125 136786779136348973923713346 
                                                                    28642024515706700235975150281080023158144042363098623929362209740123461468103762843540379739969875706762165703295 4321604917362806326787558188369069921394441265706292202320482744924939402514335625530428290080597240657326940 162469014239493878908184352941056249282469231807456297984970408417747857989582143 17409978248344432715681735845930522 3492458868676281206916287035898282218116352056217850 5288939408068969320389 65548721472688879514707069730 262904148384150018264786986
 
Re: H7n9

pic.........................


delay


attachment.php
 
Re: H7n9

-----------------------------------

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12515.html
urlhttp://www.nature.com/nature/journal/vaop/ncurrent/full/nature12515.html[/url]


this has many new sequences, which updates the evolution of recent H7N9
forget all previous H7N9-sequence analyseses

> here we show that H7 viruses probably transferred from domestic duck to chicken
> populations in China on at least two independent occasions. We show that the H7
> viruses subsequently reassorted with enzootic H9N2 viruses to generate the H7N9
> outbreak lineage, and a related previously unrecognized H7N7 lineage.
> Guan's team sampled wild birds and poultry markets around Shanghai in April,
> weeks after the H7N9 outbreak began there. The researchers collected throat
> and intestinal swabs from 1,341 birds, including chickens, ducks, geese, pigeons,
> partridges and quails, plus 1,006 water and faecal samples from bird markets.
> About 10% of samples tested positive for an influenza virus; of those, 15% were an H7 virus.

> they found H7N9 and H7N7 to be hybrids of wild Eurasian waterfowl strains, such
> as H7N3 and H11N9. The scientists think that those viruses swapped genes in
> domestic ducks before spreading to chickens,

--------------------------------------

I have not seen any of the H7N7 yet

---------edit-----------------
http://www.ncbi.nlm.nih.gov/nuccore/KF297287

LOCUS KF297287 1683 bp cRNA linear VRL 21-AUG-2013
DEFINITION Influenza A virus (A/chicken/Wenzhou/620b/2013(H7N7)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION KF297287

why did they have to keep it secret until now ?
Presumably the publishing and funding process with the journals.
But they were risking that the data had not been available in time
if H7N9 had gone pandemic

22.Aug.2013 : 624 H7N9 sequences at genbank's flu-page, 447 from 2013



we have big diversity, many subtypes.
It still seems to me that the initial reassortment of the new H7N9 was
in early 2013 and that there was just one introduction
SH1 had just some additional mutations, but this was not
from another introduction

----------edit Aug.25 ---------
now I think the HA,NA introduction happened earlier but the new
H7N9 was formed in early 2013 (Chinese New Year ?) by one dramatic
gain-of-function reassortment or mutation(s),
probably in chickens, and since then it dominated the other variants

--------------------------------------------------------
they give a timeline on page 12 here:
http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12515-s1.pdf


the substitution rates at page 27 look too high to me.
When you compare a virus with one ancester one year later,
you should get 2-5-3 e-3 mutations per site per year.
~30% more in HA
Some mutations arise in the isolates that are not transmitted.

On page 19 they give May 2012 for the emergence of H7 in recent H7N9
and Nov.2011 for N9

so I should check my "early 2013" - estimate
----------------------------------------------------
7484 sequences are mentioned in that paper,
2050 of them are in genbank's update from 2013/08/23
5434 of them are in genbank officially already listed without recent updates (2013/08/24)

I'm planning to include all 7484 in the analysis later and provide them in aligned,computer-readable format,
when they are available in genbank-format (presumably some days)


[-img]http://www.flutrackers.com/forum/attachment.php?attachmentid=16694&d=1377279135[/img]
 

Attachments

  • h7gua01.GIF
    h7gua01.GIF
    90.4 KB · Views: 1
Re: H7n9

5 of the 11 differences in HA of SH1(=A/Shanghai/1/2013/03/04(H7N9))
and 3 of the 8 differences in NA
are shared by the H7N7-lineage,so this looks like a member of a precursor-lineage
of our H7N9, that separated from the poultry strains in 2012, survived into Feb. 2013
but is now (almost) extinct in HA, but still sparsely present in NA.

h7gua4c.gif
h7gua6k.gif


partial mutation tables for segments 1,2,3:
(I printed it with wordpad on two sheets long side = horiz.)

Code: 
==========================================segment 1
 po                                                                                    01001   111211011012120100101210011011012001020010220111110011 
 si                                                                                    07459   503001365150004331748046176937671556913471024999826622 
 ti                                                                                    04605   665900173722809690840775521339189757352007308291279780 
 on                                                                                    67219   957482670732348568873601684624223156371614720987420819 
-codon-position------------------------------------------------------------------------ 1        1  11   2                      1 2   1               
---Index-------------------------------------------------------------------------------ACTAT   AACCACATCAGAGTCCCAGGAGCCAAAAGAAAGGACCGTCCAAAAAACGGATAG 

                                                                                                                                                             
 203 >A/environment/Shanghai/S1438/2013,2013/04/03,China,H7N9                          .....   .................G.A..TT..G.CT.G.....ACAT..G..GTA..CG. 
 204 >A/environment/Shanghai/S1437/2013,2013/04/03,China,H7N9                          .....   ........T........G.A..TT..GGCTTG....TACAT..G..GTAA.CGA 
 205 >A/environment/Shanghai/S1439/2013,2013/04/03,China,H7N9                          .....   ........T........G.A..TT..GGCTTG....TACAT..G..GTAA.CGA 
 206 >A/chicken/Jiangxi/SD001/2013,2013/05/03,China,H7N9                               .....   ......G........T.GAA..TTG.GGCTTG....TAC.T....GGT.A.CGA 
 207 >A/Hangzhou/2/2013,2013/04/01,China,H7N9                                          ....C   ...................A..T...GGCTTGTA..TACAT..G...TAAGCGA 
 208 >A/environment/Shanghai/S1436/2013,2013/04/03,China,H7N9                          .....   ......................T...GGCTTG.AT.TACATG.GG.GTAAGCGA 
 209 >A/environment/Fujian/SC337/2013,2013/04/30,China,H7N9                            .....   ......................T...GGCTTGTATATACATGCGGCGTAAGCGA 
 210 >A/chicken/Zhejiang/DTID-ZJU01/2013,2013/04/,China,H7N9                           .....   ..........................GGCTTGTATATACATGCGGCGTAAGCGA 
                                                                                                                                                             
 264 >A/chicken/Shanghai/S1413/2013,2013/04/03,China,H7N9                              .....   ..........................GGCTTGTATATACATGCGGCGTAAGCGA 
 265 >A/Index/H7N9-China/2013/01/31,H7N9,China,throat-swab,65m,E1                      .....   ..........................GGCTTGTATATACATGCGGCGTAAGCGA 
 266 >A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9                                           .....   ..........................GGCTTGTATATACATGCGGCGTAAGCGA 
                                                                                                                                                             
 267 >A/Shanghai/1/2013,H7N9                                                           .....   ..........................GGCTTGTAT.TACAT.CG.CGTAAGCGA 
 268 >A/chicken/Shanghai/S1080/2013,2013/04/03,China,H7N9                              .....   ..................A.GAT...GGCGT.TAT.T.CA.GCG.CG..A..GA 


 269 >A/chicken/Hong Kong/FL96/2010(H9N2)) segment1 polymerase PB2 (PB2) gene          .....   .................GAAGATTGGGGCTTG..........C......A..G. 
 270 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)                             .....   .................GAAGATTGGGGTGCG....................G. 

 271 >A/chicken/Rizhao/811/2013(H9N2)) segment1 polymerase PB2 (PB2) gene              .....   GGTATAGCT....CTTTGA.GATTG.GGTGCGA..................... 
 272 >A/chicken/Rizhao/249/2013(H9N2)) segment1 polymerase PB2 (PB2) gene              .....   GGTATAGCT....CTTTGA.GATTG.GGTGCGA..................... 
                                                                                                                                                             
 309 >A/chicken/Wenzhou/690/2013(H7N7)) segment1 polymerase PB2 (PB2) gene             .....   GGTATAGCTGACACTTTGAAGATTGGGGTGCG...................... 


============================segment 2
 po                                                              2011010111121000012111101001111021020111100111001001011021101
 si                                                              0061628372719007420121841226558409719036904128544930045617210
 ti                                                              6359318933519517755339115103477258011683169170283898810610155
 on                                                              8667985240889122748291815945530356622292732089867763149464296
-codon-position-----------------------------------------------   1           1  1   1         11   1                  1 11    
---Index------------------------------------------------------   CGCCCATTGCGGATTCACACCATGAGGGTACTTTTAAAGTCAAATTAAAAACTCCCATTAG
                                                                                                                              
 146 >A/duck/Jiangxi/11278/2009(H11N9)) segment2 polymerase PB   ......................C..AAA..........A..................CCGA
 147 >A/duck/Jiangxi/22620/2012(H11N9)) segment2 polymerase PB   .T................G.....GAA......CC.....T.....G.G...C..TC.CG.
 149 >A/duck/Guangdong/4323/2007(H11N9)) segment2 polymerase P   .TT...............G......A.......CC.....T....CG.G...C..TC..G.
 151 >A/duck/Guangdong/455/2000(H3N9)) segment2 polymerase PB1   .T................G.....GA........C.....T......GG...C..TC...A
 152 >A/chicken/Wenzhou/614/2013(H9N2)) segment2 polymerase PB   .............C..GA......................AGC.CCGGGGGTC.T.C....
 153 >A/chicken/Rizhao/1339/2013(H9N2)) segment2 polymerase PB   ........ATA......T......................AGCG.CGGG.GTC...C....
 157 >A/chicken/Jiangsu/SC099/2013,2013/04/16,China,H7N9         ........ATA......T.........A............AGCG.CGGG.GTC...C....
 173 >A/environment/Shandong/SD038/2013,2013/05/03,China,H7N9    .......CATA......T......................AGCTCC.GGGGTC...C.C..
 174 >A/environment/Shanghai/S1437/2013,2013/04/03,China,H7N9    .......CATA......T......................AGCTCC.GGGGTC...C....
 175 >A/chicken/Shanghai/S1080/2013,2013/04/03,China,H7N9        ..........A.............................AGCGC.GGGGGTCTT.C....
 176 >A/chicken/Hong Kong/NT266/2012(H9N2)) segment2 polymeras   .....GCCA..........TTGC..................GCGCCGGGG.TCTTTC...A
 190 >A/chicken/Hong Kong/YO151W/2011(H9N2)) segment2 polymera   .....GCCA...........TGC..................GC.CCG.GGGTC.TTC....
 191 >A/chicken/Hong Kong/NT305W/2011(H9N2)) segment2 polymera   .....GCCA...........TGC..................GC.CCG.GGGTC.TTC....
 211 >A/chicken/Hong Kong/CSW445W/2011(H9N2)) segment2 polymer   .....GC.A..........TTGC..................GCGCC.GGGGT.TTTC...A
 212 >A/chicken/Hong Kong/YU219/2010(H9N2)) segment2 polymeras   .........................................GCGCCGGGGGTCTTTC....
 213 >A/chicken/Hong Kong/YU214/2010(H9N2)) segment2 polymeras   .........................................GCGCCGGGGGTCTTTC....
 214 >A/chicken/Hong Kong/YU218/2010(H9N2)) segment2 polymeras   .........................................GCGCCGGGGGTCTTTC....
 215 >A/chicken/Hong Kong/HH8/2010(H9N2)) segment2 polymerase    .........................................GCGCCGGGGGTCTTTC....
 216 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)       .........................................GCGCCGGGGGTCTT.C....
 217 >A/chicken/Hong Kong/FL96/2010(H9N2)) segment2 polymerase   ..........................A.C..C........AGCGCCGGGGGTCTT.C....
 218 >A/environment/Shanghai/S1439/2013,2013/04/03,China,H7N9    .........................AA.CGTCCCCGGGACATCGCCGGGGGTCTT.C...A
                                                                                                                              
 226 >A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9                     .........................AAACGTCCCCGGGACATCGCCGGGGGTCTT.....A
                                                                                                                              
 258 >A/environment/Shanghai/S1088/2013,2013/04/03,China,H7N9    .........................AAACGTCCCCGGGACATCGCCGGGGGTCTT.....A
 259 >A/environment-poultry_cage/Nanjing/2913/2013/03/29,H7N9    ..........................AA.GTCCCCGGGACAGCGCCGGGG.TCTT.....A
 260 >A/environment/Nanjing/2913/2013,2013/03/29,China,H7N9      ..........................AA.GTCCCCGGGACAGCGCCGGGG.TCTT.....A
 261 >A/Nanjing/1/throat_swab/2013/03/28,H7N9                    ..........................AA.GTCCCCGGGACAGCGCCGGGG.TCTT.....A
 262 >A/environment/Wuxi/1/2013,2013/04/02,H7N9                  ..........................AA.GTCCCCGGGACAGCGCCGGGG.TCTT.....A
 263 >A/Shanghai/1/2013,H7N9                                     ..........................AA.GTCCCCGGGACAGCGCCGGGG.TCTT.....A
 264 >A/chicken/Wenzhou/606/2013(H9N2)) segment2 polymerase PB   ..........................A..GTCCC..GGACAGCGCCGGGGGTCTT.C.C..
 265 >A/silkie chicken/Wenzhou/812/2013(H9N2)) segment2 polyme   ..........................A..GTCCC..GGACAGCGCCGGGGGTCTT.C.C..
 266 >A/chicken/Wenzhou/598/2013(H9N2)) segment2 polymerase PB   ..........................A..GTCCC..GGACAGTGCCGGGGGTCTT.C.C..
 267 >A/chicken/Zhejiang/SD007/2013,2013/04/22,China,H7N9        ......C...................A....CCC..GG..AGCGCCGGG.GTCTT.C.C..

=========================================segment 3
 po                                                              11100102101110101101110010110111000110101110001100010101220111001111011000021100010001100001001101 
 si                                                              08294581285843141931487253429299118068559409225231834172104612814063222147404125299412450372301938 
 ti                                                              61961461049947321014277906320324707209313991018168139682418379966677944834446618193965159085428596 
 on                                                              25361812034302706286581406719014120384035450904593482356530829121774929684437812439854026367810909 
-codon-position-----------------------------------------------             1                   1            12     1  222    2    2  2 1      11 11            1    
---Index------------------------------------------------------   TATTACTACATTTGGCGGCGAATAGGCCGACCAAAGAATCAAACCATCAAGCTGAGGACAGTTTCAGCTATTCACCCCTCTTAGTAGTGGGTAAGACA 
   1 >A/chicken/Hong Kong/TSTA7W/2009(H9N2)) segment3 polymera                                                                                                      
 211 >A/chicken/Hong Kong/YU214/2010(H9N2)) segment3 polymeras   .................ATAGGCGAA............C......GCTGCATC.GAAGTGACC.................CCGACTCC.......... 

 212 >A/chicken/Shanghai/S1080/2013,2013/04/03,China,H7N9        .................AT...CG.....................GCTGTATCAGAAGTGACC.TGA...CA...TTTC.CCGACTCC..A..GAG.G 
 213 >A/Wuxi/2/2013,2013/03/31,H7N9                              .................A...........................GCTGTATCAGAAGTGAC.CTGATCGCATGTTTTCTCCGACTCCAAACTGAGTG 
 214 >A/Wuxi/1/2013,2013/04/02,H7N9                              .............................................GCTGTATCAGAAGTGACCCTGATCGCATGTTTTCTCCGACTCCAAACTGAGTG 
 215 >A/chicken/Zhejiang/SD019/2013,2013/04/11,China,H7N9        .............................................GCTGTATCAGAAGTGACCCTGATCGCATGTTTTCTCCGACTCCAAACTGAGTG 
 216 >A/wild pigeon/Jiangsu/SD001/2013,2013/04/17,China,H7N9     .............................................GCTGTATCAGAAGTGACCCTGATCGCATGTTTTCTCCGACTCCAAACTGAGTG 

 262 >A/Shanghai/02/2013,2013/03/05,China,H7N9                   .............................................GCTGTATCAGAAGTGACCCTGATCGCATGTTTTCTCCGACTCCAAACTGAGTG 
 263 >A/Shanghai/1/2013,H7N9                                     .............................................GCTGTATCAGAAGTGACCCTGATCGCAT.TTT.CTCCGACTCCAAACTGAGTG 
 264 >A/chicken/Shanghai/S1413/2013,2013/04/03,China,H7N9        .............................................GCTGTATCAGAAGTGACCCTGATC.CATGTTT.CTCCGACTCCAAACTG.GTG 
 265 >A/environment/Shanghai/S1088/2013,2013/04/03,China,H7N9    ...CG........................................GCTGTATCAGAAGTGACCCTGATCGCATG.TTTCTCCGACTCCAAAC.G.GTG 
 266 >A/environment/Shanghai/S1439/2013,2013/04/03,China,H7N9    ...CG.................C......................GCTGTATCA.AAGTGACCCTGATCGCA...TT.C.CCTACTCCAA.C.G.GTG 
 267 >A/environment/Shanghai/S1437/2013,2013/04/03,China,H7N9    ...CG.................CT.....................GCTGTATCA..AGTGACCCTGA.........T....CGACTCCAA...G.GTG 
 268 >A/environment/Shanghai/S1438/2013,2013/04/03,China,H7N9    ...CGT...............GCTA....................GCTGTATCA..AGTGACCCTGA....A.........CGACTCCAA...G.GT. 
 269 >A/chicken/Rizhao/55/2013(H9N2)) segment3 polymerase PA (   ...CGT...............GCTA....................GCTGTATCA..AGTGACCCTGA..............CTACTCCAA.....GT. 
 270 >A/silkie chicken/Wenzhou/812/2013(H9N2)) segment3 polyme   ...CGT...............GCTA...................TGCTGTATCA..AGTGACCCTGA..............CGACTCCAA....AGT. 
 271 >A/chicken/Wenzhou/666/2013(H7N7)) segment3 polymerase PA   ...CGT...............GCTA....................GCTGTATCAG.AGTGACCCTGA..............CGACTCCAA.....GT. 
 272 >A/chicken/Wenzhou/614/2013(H9N2)) segment3 polymerase PA   ...CGT...............GCTA....................GCTGTATCAG.AGTGACCCTGA..............CGACTCCAA.....GT. 
 273 >A/chicken/Wenzhou/606/2013(H9N2)) segment3 polymerase PA   ...CGT...............GCTA....................GCTGTATCAG.AGTGACCCTGA..............CGACTCCAA.....GT. 
 274 >A/chicken/Zhejiang/SD007/2013,2013/04/22,China,H7N9        ...CGT................CTA....................GCTGTATCA..AGTGACCCTGA..............CGACTCCAA.....GT. 
 275 >A/environment/Shanghai/S1436/2013,2013/04/03,China,H7N9    ...C.T...............GCTA....................GCTGTATCA.AAGTGACCCTGA....A.........CGACTCCAA.....GT. 
 276 >A/chicken/Rizhao/853/2013(H9N2)) segment3 polymerase PA    .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA.....GT. 
 277 >A/chicken/Rizhao/1363/2013(H9N2)) segment3 polymerase PA   .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA.....GT. 
 278 >A/chicken/Rizhao/811/2013(H9N2)) segment3 polymerase PA    .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA.....GT. 
 279 >A/chicken/Rizhao/1436/2013(H9N2)) segment3 polymerase PA   .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA.....GT. 
 280 >A/chicken/Shanghai/S1358/2013,2013/04/03,China,H7N9        .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA.....GT. 
 281 >A/chicken/Jiangsu/SC099/2013,2013/04/16,China,H7N9         .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA...G.GT. 
 282 >A/chicken/Wenzhou/642/2013(H9N2)) segment3 polymerase PA   ......................CGA............GC.....TGC.GT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA...G.GT. 
 283 >A/chicken/Wenzhou/598/2013(H9N2)) segment3 polymerase PA   ......................CGA............GC.....TGC.GT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA...G.GT. 
 284 >A/chicken/Wenzhou/253/2013(H9N2)) segment3 polymerase PA   ......................CGA............GC.....TGCTGT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA...G.GT. 
 285 >A/chicken/Zhejiang/SD033/2013,2013/04/11,China,H7N9        ......................CGA......T......C.....TGCTGT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA.....GT. 
 286 >A/duck/Zhejiang/SC410/2013,2013/04/16,China,H7N9           ......................CGA......T......C.....TGCTGT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA.....GT. 
 287 >A/Zhejiang/HZ1/2013/4/,H7N9                                ......................CGA......T......C.....TGCTGT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA.....GT. 
 288 >A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9                     ......................CGA......T......C.....TGCTGT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA.....GT.
 

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Re: H7n9

segment 6,NA , selected interesting sequences
to demonstrate H7N9,2013 ancestry


Code: 
                                             000000000000000000111111111 
differences  at                              000112235678888999001112223 
the positions                                379015531970257125353560490 
                                             920580156977580341462571839 
-codon-position------------------------------    1122       1  2 1  1  1 
---Index-------------------------------------TTAGGAAGCATTGACACAAATAAGAAA 
>A/Index/H7N9-China/2013/01/31,H7N9          ...........................
>A/Ck/Zhejiang/SD007/2013,2013/04/22,H7N9    C...A...........TG...G..G.G
>A/Hangzhou/3/2013,2013/04/08,China,H7N9     ....A..........GTGT...G..G.
>A/northern shoveler/HK/MPL133/2010//,H2N9   .AG.AGG.TGC.....TG.GC..AG..
>A/Ck/Jiangsu/RD5/2013(H10N9)                ..GTAGGATGCCAGT.TG.G...A...

number of differences

Code: 
                                                 1   2   3   4   5
--------------------------------------------------------------------
1 A/Index/H7N9-China/2013/01/31,H7N9             0   7  17   7  14
2 A/Ck/Zhejiang/SD007/2013,2013/04/22            7   0  18   8  13
3 A/Ck/Jiangsu/RD5/2013(H10N9)                  17  18   0  18   9
4 A/Hangzhou/3/2013,2013/04/08,China,H7N9        7   8  18   0  15
5 A/northern shoveler/HK/MPL133/2010//,H2N9     14  13   9  15   0


9 differences in NA in ~3 years from the H2N9-shoveler
from 2010 in Hong Kong to the H10N9 chicken in 2013
That should indicate an almost direct ancestry,
a most recent common ancestor in 2010.


we might create a pre-index which had 118A,924T,951G and the deletion

It had 11 differences from the shoveler
3 differences from my H7N9-index(Jan.2013)
4 differences from Ck/Zhej./2013/04/22
4 differences from Hangzhou/3/2013/04/08
14 differences from the Jingsu-chicken/2013

so, that could be dated somewhere in late 2011 or early 2012 then.
But the most recent ancester with Jiangsu chicken were in ~2010-2011

So the deletion would already have happened in 2010-2011
since then it would be evolving at low levels in poultry
in life markets. No domestic ducks are needed here, but of
course there might haven been and it was evolving in the ducks
until recently - it's another possibility.
And, remember, this is just for segment 6 = NA.
 
Re: H7n9

sorry, I have to repost this edited post above, so google finds it
(can be deleted later)

can someone post a link to this flutrackers-page
as a comment to the "nature" article website ?
someone who has read and accepted their terms and conditions already

-----------------------------------

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12515.html
urlhttp://www.nature.com/nature/journal/vaop/ncurrent/full/nature12515.html[/url]

The genesis and source of the H7N9 influenza viruses causing human infections in China


this has many new sequences, which updates the evolution of recent H7N9
forget all previous H7N9-sequence analyseses

> here we show that H7 viruses probably transferred from domestic duck to chicken
> populations in China on at least two independent occasions. We show that the H7
> viruses subsequently reassorted with enzootic H9N2 viruses to generate the H7N9
> outbreak lineage, and a related previously unrecognized H7N7 lineage.
> Guan's team sampled wild birds and poultry markets around Shanghai in April,
> weeks after the H7N9 outbreak began there. The researchers collected throat
> and intestinal swabs from 1,341 birds, including chickens, ducks, geese, pigeons,
> partridges and quails, plus 1,006 water and faecal samples from bird markets.
> About 10% of samples tested positive for an influenza virus; of those, 15% were an H7 virus.

> they found H7N9 and H7N7 to be hybrids of wild Eurasian waterfowl strains, such
> as H7N3 and H11N9. The scientists think that those viruses swapped genes in
> domestic ducks before spreading to chickens,

--------------------------------------

I have not seen any of the H7N7 yet

---------edit-----------------
http://www.ncbi.nlm.nih.gov/nuccore/KF297287

LOCUS KF297287 1683 bp cRNA linear VRL 21-AUG-2013
DEFINITION Influenza A virus (A/chicken/Wenzhou/620b/2013(H7N7)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION KF297287

why did they have to keep it secret until now ?
Presumably the publishing and funding process with the journals.
But they were risking that the data had not been available in time
if H7N9 had gone pandemic

22.Aug.2013 : 624 H7N9 sequences at genbank's flu-page, 447 from 2013



we have big diversity, many subtypes.
It still seems to me that the initial reassortment of the new H7N9 was
in early 2013 and that there was just one introduction
SH1 had just some additional mutations, but this was not
from another introduction

----------edit Aug.25 ---------
now I think the HA,NA introduction happened earlier but the new
H7N9 was formed in early 2013 (Chinese New Year ?) by one dramatic
gain-of-function reassortment or mutation(s),
probably in chickens, and since then it dominated the other variants

--------------------------------------------------------
they give a timeline on page 12 here:
http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12515-s1.pdf


the substitution rates at page 27 look too high to me.
When you compare a virus with one ancester one year later,
you should get 2-5-3 e-3 mutations per site per year.
~30% more in HA
Some mutations arise in the isolates that are not transmitted.

On page 19 they give May 2012 for the emergence of H7 in recent H7N9
and Nov.2011 for N9

so I should check my "early 2013" - estimate
----------------------------------------------------
7484 sequences are mentioned in that paper,
2050 of them are in genbank's update from 2013/08/23
5434 of them are in genbank officially already listed without recent updates (2013/08/24)

I'm planning to include all 7484 in the analysis later and provide them in aligned,computer-readable format,
when they are available in genbank-format (presumably some days)


[-img]http://www.flutrackers.com/forum/attachment.php?attachmentid=16694&d=1377279135[/img]
 
Re: H7n9

examining the ancestry in all 8 segments
(sequences from Friday)

so, it seems that these reassortments, that I previosly thought
were subsequent to the initial H7N9 reassortment may well
have happened before that or inbetween:
It was probably not one H7N9 introduction but
N9 first (H10N9,H11N9) and then H7.

Code: 
 po                                                                                    01001   111211011012120100101210011011012001020010220111110011 
 si                                                                                    07459   503001365150004331748046176937671556913471024999826622 
 ti                  segment 1                                                         04605   665900173722809690840775521339189757352007308291279780 
 on                                                                                    67219   957482670732348568873601684624223156371614720987420819 
-codon-position------------------------------------------------------------------------ 1        1  11   2                      1 2   1               
---Index-------------------------------------------------------------------------------ACTAT   AACCACATCAGAGTCCCAGGAGCCAAAAGAAAGGACCGTCCAAAAAACGGATAG 

                                                                                                                                                             
 203 >A/environment/Shanghai/S1438/2013,2013/04/03,China,H7N9                          .....   .................G.A..TT..G.CT.G.....ACAT..G..GTA..CG. 
 204 >A/environment/Shanghai/S1437/2013,2013/04/03,China,H7N9                          .....   ........T........G.A..TT..GGCTTG....TACAT..G..GTAA.CGA 
 205 >A/environment/Shanghai/S1439/2013,2013/04/03,China,H7N9                          .....   ........T........G.A..TT..GGCTTG....TACAT..G..GTAA.CGA 
 206 >A/chicken/Jiangxi/SD001/2013,2013/05/03,China,H7N9                               .....   ......G........T.GAA..TTG.GGCTTG....TAC.T....GGT.A.CGA 
 207 >A/Hangzhou/2/2013,2013/04/01,China,H7N9                                          ....C   ...................A..T...GGCTTGTA..TACAT..G...TAAGCGA 
 208 >A/environment/Shanghai/S1436/2013,2013/04/03,China,H7N9                          .....   ......................T...GGCTTG.AT.TACATG.GG.GTAAGCGA 
 209 >A/environment/Fujian/SC337/2013,2013/04/30,China,H7N9                            .....   ......................T...GGCTTGTATATACATGCGGCGTAAGCGA 
 210 >A/chicken/Zhejiang/DTID-ZJU01/2013,2013/04/,China,H7N9                           .....   ..........................GGCTTGTATATACATGCGGCGTAAGCGA 
                                                                                                                                                             
 264 >A/chicken/Shanghai/S1413/2013,2013/04/03,China,H7N9                              .....   ..........................GGCTTGTATATACATGCGGCGTAAGCGA 
 265 >A/Index/H7N9-China/2013/01/31,H7N9,China,throat-swab,65m,E1                      .....   ..........................GGCTTGTATATACATGCGGCGTAAGCGA 
 266 >A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9                                           .....   ..........................GGCTTGTATATACATGCGGCGTAAGCGA 
                                                                                                                                                             
 267 >A/Shanghai/1/2013,H7N9                                                           .....   ..........................GGCTTGTAT.TACAT.CG.CGTAAGCGA 
 268 >A/chicken/Shanghai/S1080/2013,2013/04/03,China,H7N9                              .....   ..................A.GAT...GGCGT.TAT.T.CA.GCG.CG..A..GA 



 269 >A/chicken/Hong Kong/FL96/2010(H9N2)) segment1 polymerase PB2 (PB2) gene          .....   .................GAAGATTGGGGCTTG..........C......A..G. 
 270 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)                             .....   .................GAAGATTGGGGTGCG....................G. 



 271 >A/chicken/Rizhao/811/2013(H9N2)) segment1 polymerase PB2 (PB2) gene              .....   GGTATAGCT....CTTTGA.GATTG.GGTGCGA..................... 
 272 >A/chicken/Rizhao/249/2013(H9N2)) segment1 polymerase PB2 (PB2) gene              .....   GGTATAGCT....CTTTGA.GATTG.GGTGCGA..................... 
                                                                                                                                                             
 309 >A/chicken/Wenzhou/690/2013(H7N7)) segment1 polymerase PB2 (PB2) gene             .....   GGTATAGCTGACACTTTGAAGATTGGGGTGCG...................... 



 po                                                              2011010111121000012111101001111021020111100111001001011021101
 si                                                              0061628372719007420121841226558409719036904128544930045617210
 ti         segment 2                                            6359318933519517755339115103477258011683169170283898810610155
 on                                                              8667985240889122748291815945530356622292732089867763149464296
-codon-position-----------------------------------------------   1           1  1   1         11   1                  1 11    
---Index------------------------------------------------------   CGCCCATTGCGGATTCACACCATGAGGGTACTTTTAAAGTCAAATTAAAAACTCCCATTAG
                                                                                                                              
 146 >A/duck/Jiangxi/11278/2009(H11N9)) segment2 polymerase PB   ......................C..AAA..........A..................CCGA
 147 >A/duck/Jiangxi/22620/2012(H11N9)) segment2 polymerase PB   .T................G.....GAA......CC.....T.....G.G...C..TC.CG.
 149 >A/duck/Guangdong/4323/2007(H11N9)) segment2 polymerase P   .TT...............G......A.......CC.....T....CG.G...C..TC..G.
 151 >A/duck/Guangdong/455/2000(H3N9)) segment2 polymerase PB1   .T................G.....GA........C.....T......GG...C..TC...A
 152 >A/chicken/Wenzhou/614/2013(H9N2)) segment2 polymerase PB   .............C..GA......................AGC.CCGGGGGTC.T.C....
 153 >A/chicken/Rizhao/1339/2013(H9N2)) segment2 polymerase PB   ........ATA......T......................AGCG.CGGG.GTC...C....
 157 >A/chicken/Jiangsu/SC099/2013,2013/04/16,China,H7N9         ........ATA......T.........A............AGCG.CGGG.GTC...C....
 173 >A/environment/Shandong/SD038/2013,2013/05/03,China,H7N9    .......CATA......T......................AGCTCC.GGGGTC...C.C..
 174 >A/environment/Shanghai/S1437/2013,2013/04/03,China,H7N9    .......CATA......T......................AGCTCC.GGGGTC...C....
 175 >A/chicken/Shanghai/S1080/2013,2013/04/03,China,H7N9        ..........A.............................AGCGC.GGGGGTCTT.C....
 176 >A/chicken/Hong Kong/NT266/2012(H9N2)) segment2 polymeras   .....GCCA..........TTGC..................GCGCCGGGG.TCTTTC...A
 190 >A/chicken/Hong Kong/YO151W/2011(H9N2)) segment2 polymera   .....GCCA...........TGC..................GC.CCG.GGGTC.TTC....
 191 >A/chicken/Hong Kong/NT305W/2011(H9N2)) segment2 polymera   .....GCCA...........TGC..................GC.CCG.GGGTC.TTC....
 211 >A/chicken/Hong Kong/CSW445W/2011(H9N2)) segment2 polymer   .....GC.A..........TTGC..................GCGCC.GGGGT.TTTC...A
 212 >A/chicken/Hong Kong/YU219/2010(H9N2)) segment2 polymeras   .........................................GCGCCGGGGGTCTTTC....
 213 >A/chicken/Hong Kong/YU214/2010(H9N2)) segment2 polymeras   .........................................GCGCCGGGGGTCTTTC....
 214 >A/chicken/Hong Kong/YU218/2010(H9N2)) segment2 polymeras   .........................................GCGCCGGGGGTCTTTC....
 215 >A/chicken/Hong Kong/HH8/2010(H9N2)) segment2 polymerase    .........................................GCGCCGGGGGTCTTTC....
 216 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)       .........................................GCGCCGGGGGTCTT.C....
 217 >A/chicken/Hong Kong/FL96/2010(H9N2)) segment2 polymerase   ..........................A.C..C........AGCGCCGGGGGTCTT.C....
 218 >A/environment/Shanghai/S1439/2013,2013/04/03,China,H7N9    .........................AA.CGTCCCCGGGACATCGCCGGGGGTCTT.C...A
                                                                                                                              
 226 >A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9                     .........................AAACGTCCCCGGGACATCGCCGGGGGTCTT.....A
                                                                                                                              
 258 >A/environment/Shanghai/S1088/2013,2013/04/03,China,H7N9    .........................AAACGTCCCCGGGACATCGCCGGGGGTCTT.....A
 259 >A/environment-poultry_cage/Nanjing/2913/2013/03/29,H7N9    ..........................AA.GTCCCCGGGACAGCGCCGGGG.TCTT.....A
 260 >A/environment/Nanjing/2913/2013,2013/03/29,China,H7N9      ..........................AA.GTCCCCGGGACAGCGCCGGGG.TCTT.....A
 261 >A/Nanjing/1/throat_swab/2013/03/28,H7N9                    ..........................AA.GTCCCCGGGACAGCGCCGGGG.TCTT.....A
 262 >A/environment/Wuxi/1/2013,2013/04/02,H7N9                  ..........................AA.GTCCCCGGGACAGCGCCGGGG.TCTT.....A
 263 >A/Shanghai/1/2013,H7N9                                     ..........................AA.GTCCCCGGGACAGCGCCGGGG.TCTT.....A
 264 >A/chicken/Wenzhou/606/2013(H9N2)) segment2 polymerase PB   ..........................A..GTCCC..GGACAGCGCCGGGGGTCTT.C.C..
 265 >A/silkie chicken/Wenzhou/812/2013(H9N2)) segment2 polyme   ..........................A..GTCCC..GGACAGCGCCGGGGGTCTT.C.C..
 266 >A/chicken/Wenzhou/598/2013(H9N2)) segment2 polymerase PB   ..........................A..GTCCC..GGACAGTGCCGGGGGTCTT.C.C..
 267 >A/chicken/Zhejiang/SD007/2013,2013/04/22,China,H7N9        ......C...................A....CCC..GG..AGCGCCGGG.GTCTT.C.C..


 po                                                              11100102101110101101110010110111000110101110001100010101220111001111011000021100010001100001001101 
 si                                                              08294581285843141931487253429299118068559409225231834172104612814063222147404125299412450372301938 
 ti         segment 3                                            61961461049947321014277906320324707209313991018168139682418379966677944834446618193965159085428596 
 on                                                              25361812034302706286581406719014120384035450904593482356530829121774929684437812439854026367810909 
-codon-position-----------------------------------------------             1                   1            12     1  222    2    2  2 1      11 11            1    
---Index------------------------------------------------------   TATTACTACATTTGGCGGCGAATAGGCCGACCAAAGAATCAAACCATCAAGCTGAGGACAGTTTCAGCTATTCACCCCTCTTAGTAGTGGGTAAGACA 
   1 >A/chicken/Hong Kong/TSTA7W/2009(H9N2)) segment3 polymera                                                                                                      
 211 >A/chicken/Hong Kong/YU214/2010(H9N2)) segment3 polymeras   .................ATAGGCGAA............C......GCTGCATC.GAAGTGACC.................CCGACTCC.......... 

 212 >A/chicken/Shanghai/S1080/2013,2013/04/03,China,H7N9        .................AT...CG.....................GCTGTATCAGAAGTGACC.TGA...CA...TTTC.CCGACTCC..A..GAG.G 
 213 >A/Wuxi/2/2013,2013/03/31,H7N9                              .................A...........................GCTGTATCAGAAGTGAC.CTGATCGCATGTTTTCTCCGACTCCAAACTGAGTG 
 214 >A/Wuxi/1/2013,2013/04/02,H7N9                              .............................................GCTGTATCAGAAGTGACCCTGATCGCATGTTTTCTCCGACTCCAAACTGAGTG 
 215 >A/chicken/Zhejiang/SD019/2013,2013/04/11,China,H7N9        .............................................GCTGTATCAGAAGTGACCCTGATCGCATGTTTTCTCCGACTCCAAACTGAGTG 
 216 >A/wild pigeon/Jiangsu/SD001/2013,2013/04/17,China,H7N9     .............................................GCTGTATCAGAAGTGACCCTGATCGCATGTTTTCTCCGACTCCAAACTGAGTG 

 262 >A/Shanghai/02/2013,2013/03/05,China,H7N9                   .............................................GCTGTATCAGAAGTGACCCTGATCGCATGTTTTCTCCGACTCCAAACTGAGTG 
 263 >A/Shanghai/1/2013,H7N9                                     .............................................GCTGTATCAGAAGTGACCCTGATCGCAT.TTT.CTCCGACTCCAAACTGAGTG 
 264 >A/chicken/Shanghai/S1413/2013,2013/04/03,China,H7N9        .............................................GCTGTATCAGAAGTGACCCTGATC.CATGTTT.CTCCGACTCCAAACTG.GTG 
 265 >A/environment/Shanghai/S1088/2013,2013/04/03,China,H7N9    ...CG........................................GCTGTATCAGAAGTGACCCTGATCGCATG.TTTCTCCGACTCCAAAC.G.GTG 
 266 >A/environment/Shanghai/S1439/2013,2013/04/03,China,H7N9    ...CG.................C......................GCTGTATCA.AAGTGACCCTGATCGCA...TT.C.CCTACTCCAA.C.G.GTG 
 267 >A/environment/Shanghai/S1437/2013,2013/04/03,China,H7N9    ...CG.................CT.....................GCTGTATCA..AGTGACCCTGA.........T....CGACTCCAA...G.GTG 
 268 >A/environment/Shanghai/S1438/2013,2013/04/03,China,H7N9    ...CGT...............GCTA....................GCTGTATCA..AGTGACCCTGA....A.........CGACTCCAA...G.GT. 
 269 >A/chicken/Rizhao/55/2013(H9N2)) segment3 polymerase PA (   ...CGT...............GCTA....................GCTGTATCA..AGTGACCCTGA..............CTACTCCAA.....GT. 
 270 >A/silkie chicken/Wenzhou/812/2013(H9N2)) segment3 polyme   ...CGT...............GCTA...................TGCTGTATCA..AGTGACCCTGA..............CGACTCCAA....AGT. 
 271 >A/chicken/Wenzhou/666/2013(H7N7)) segment3 polymerase PA   ...CGT...............GCTA....................GCTGTATCAG.AGTGACCCTGA..............CGACTCCAA.....GT. 
 272 >A/chicken/Wenzhou/614/2013(H9N2)) segment3 polymerase PA   ...CGT...............GCTA....................GCTGTATCAG.AGTGACCCTGA..............CGACTCCAA.....GT. 
 273 >A/chicken/Wenzhou/606/2013(H9N2)) segment3 polymerase PA   ...CGT...............GCTA....................GCTGTATCAG.AGTGACCCTGA..............CGACTCCAA.....GT. 
 274 >A/chicken/Zhejiang/SD007/2013,2013/04/22,China,H7N9        ...CGT................CTA....................GCTGTATCA..AGTGACCCTGA..............CGACTCCAA.....GT. 
 275 >A/environment/Shanghai/S1436/2013,2013/04/03,China,H7N9    ...C.T...............GCTA....................GCTGTATCA.AAGTGACCCTGA....A.........CGACTCCAA.....GT. 
 276 >A/chicken/Rizhao/853/2013(H9N2)) segment3 polymerase PA    .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA.....GT. 
 277 >A/chicken/Rizhao/1363/2013(H9N2)) segment3 polymerase PA   .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA.....GT. 
 278 >A/chicken/Rizhao/811/2013(H9N2)) segment3 polymerase PA    .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA.....GT. 
 279 >A/chicken/Rizhao/1436/2013(H9N2)) segment3 polymerase PA   .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA.....GT. 
 280 >A/chicken/Shanghai/S1358/2013,2013/04/03,China,H7N9        .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA.....GT. 
 281 >A/chicken/Jiangsu/SC099/2013,2013/04/16,China,H7N9         .G...T...............GCGA........................TATCA.AAGTGACCCTG...............CGACTCCAA...G.GT. 
 282 >A/chicken/Wenzhou/642/2013(H9N2)) segment3 polymerase PA   ......................CGA............GC.....TGC.GT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA...G.GT. 
 283 >A/chicken/Wenzhou/598/2013(H9N2)) segment3 polymerase PA   ......................CGA............GC.....TGC.GT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA...G.GT. 
 284 >A/chicken/Wenzhou/253/2013(H9N2)) segment3 polymerase PA   ......................CGA............GC.....TGCTGT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA...G.GT. 
 285 >A/chicken/Zhejiang/SD033/2013,2013/04/11,China,H7N9        ......................CGA......T......C.....TGCTGT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA.....GT. 
 286 >A/duck/Zhejiang/SC410/2013,2013/04/16,China,H7N9           ......................CGA......T......C.....TGCTGT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA.....GT. 
 287 >A/Zhejiang/HZ1/2013/4/,H7N9                                ......................CGA......T......C.....TGCTGT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA.....GT. 
 288 >A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9                     ......................CGA......T......C.....TGCTGT..CAG.AGTGA.CCTGAT..........CTCCGACTCCAA.....GT. 
                                                                                                                                                                    

 po                                                  1000000000111111111000001000100010000111000101001000  
 si                                                  4498464533455655311683000143517535459662576200922931  
 ti            segment 4                             5984591153154076374788545126690664003422816787644066  
 on                                                  5843691079319520866800216486644237873729449517208034  
-codon-position-----------------------------------               1       1212  2  22111    222     2    2  
---Index------------------------------------------   TTGGTTACTAAACCGCACGAGAGTATCAAGAAAGCTAGCCGGGCTGAGTTGG  
  47 >A/duck/Wenzhou/47/2013(H7N7)) segment4 hemag   ............T...................................CC.A  
  48 >A/pigeon/Wenzhou/559/2013(H7N7)) segment4 he   ............T...................................CC.A  
  49 >A/duck/Wenzhou/771/2013(H7N3)) segment4 hema   ................................................CC.A  
  50 >A/duck/Wenzhou/775/2013(H7N2)) segment4 hema   ................................................CC.A  
  51 >A/goose/Guangdong/7472/2012(H7N7)) segment4    ................................................CC.A  
  55 >A/duck/Fujian/6390/2010(H7N3)) segment4 hema   ...............AG.............................GAC..A  
  56 >A/duck/Fujian/6380/2010(H7N3)) segment4 hema   ...............AG.............................GAC..A  
  57 >A/duck/Fujian/6388/2010(H7N3)) segment4 hema   ...............AG.............................GAC..A  
  58 >A/duck/Fujian/6326/2010(H7N3)) segment4 hema   ...............AG.............................GAC..A  

  53 >A/chicken/Rizhao/719b/2013(H7N9)) segment4 h   ...........--..-........G.....TGGATATATATAATCTGACCAA  
  60 >A/Shanghai/1/2013,H7N9                         ...................G...........GGATATA...AAT.TGACCAA  
  61 >A/environment/Henan/SD429/2013,2013/04/24,Ch   ...............................GGATATATATAATCTGACCAA  
  62 >A/chicken/Shanghai/S1077/2013,2013/04/03,Chi   ..............................TGGATATATATAATCTGACCAA  
 117 >A/environment-poultry_cage/Nanjing/2913/2013   ........AG...................TTGGATATATATAATCTGACCAA  
 118 >A/environment/Wuxi/1/2013,2013/04/02,H7N9      ........AG...................TTGGATATATATAATCTGACCAA  
 119 >A/Shanghai/5083T/2013,2013/04/20,China,H7N9    .---------G........---------.---G----ATA---T----C---  
 120 >A/homing pigeon/Jiangsu/SD184/2013,2013/04/2   .........GG....................GGATATATATAATCTGACCAA  
 121 >A/Shanghai/5180T/2013,2013/04/23,China,H7N9    .---------G........---------.---G----ATA---T----C---  
 126 >A/environment/Shanghai/S1436/2013,2013/04/03   .........GG...................TGGATATATATAATCTGACCAA  
 127 >A/environment/Shanghai/S1437/2013,2013/04/03   .........GG...................TGGATATATATAATCTGACCAA  
 128 >A/pigeon/Shanghai/S1423/2013,2013/04/03,Chin   .........GG...................TGGATATATATAATCTGACCAA  
 129 >A/Shanghai/5240T/2013,2013/04/25,China,H7N9    .---------G........---------.---G----ATA---T----C---  
 130 >A/chicken/Zhejiang/DTID-ZJU01/2013,2013/04/,   .............................A.GGATATATATAATCTGACCAA  
 131 >A/Shanghai/4842T/2013,2013/04/13,China,H7N9    .---------.........---------.---G----ATA---T----C---  
 132 >A/Shanghai/4664T/2013,2013/03/05,China,H7N9    ..............................TGGATATATATAATCTGACCAA  
 133 >A/Shanghai/4701T/2013,2013/04/06,China,H7N9    .---------.........---------.---G----ATA---T----C---  
 134 >A/Shanghai/4659T/2013,2013/02/27,China,H7N9    .---------.........---------.---G----ATA---T-.--C---  
 135 >A/Shanghai/4665T/2013,2013/03/05,China,H7N9    .---------.........---------.---G----A..---T-.--C---  
 136 >A/Shanghai/4655T/2013,2013/02/26,China,H7N9    .---------.........---------.---G----A..---T-.--C---  


 po                                                  000100001111001101000010110001000110000101010  
 si                                                  884328432042150151662117204882961008536173820  
 ti          segment 5                               332561228899907911565730123955840411404862855  
 on                                                  146516977663575763738118668287282119962286511  
-codon-position-----------------------------------      2      2   1         1  1  1                
---Index------------------------------------------   TTCGGTGCTGGAAATGCGTAGCCAAACCCCTGTCAGAGAACTGTA  

   1 >A/chicken/Wenzhou/642/2013(H9N2)) segment5 n   A............GGATAC....GGGA...........GTTC...  
   2 >A/chicken/Wenzhou/634/2013(H7N7)) segment5 n   A............GGATAC....GGGA...........GTTC...  
   3 >A/chicken/Wenzhou/645/2013(H7N7)) segment5 n   A............GGATAC....GGGA...........GTTC...  
  33 >A/chicken/Wenzhou/323/2013(H7N7)) segment5 n   A............GGATAC....GGGA...........GTTC...  
  34 >A/chicken/Hong Kong/NT266/2012(H9N2)) segmen   ...........G.GGATACGA.TGG.A.................G  
  35 >A/chicken/Hong Kong/TSTB32W/2011(H9N2)) segm   ...........G.GGATACGA.TGG.A.................G  
  36 >A/chicken/Hong Kong/YU551W/2011(H9N2)) segme   ...........G.GGATACGA.TGG.A.................G  
  37 >A/chicken/Hong Kong/CSW530/2011(H9N2)) segme   ...........G.GGATACGA.TGG.A.................G  
  38 >A/chicken/Hong Kong/CSW533/2011(H9N2)) segme   ...........G.GGATACGA.TGG.A.................G  
  39 >A/chicken/Hong Kong/FY64W/2010(H9N2)) segmen   ...........G.GGATACGATTGGGA..................  
  40 >A/chicken/Hong Kong/JV75/2011(H9N2)) segment   ...........G.GGATACGATTGGGA.....C............  
  41 >A/chicken/Hong Kong/YU158/2011(H9N2)) segmen   ...........G.GGATACGATTGGGA.....C............  
  42 >A/chicken/Hong Kong/YO151W/2011(H9N2)) segme   ...........G.GGATACGATTGGGA................C.  
  43 >A/chicken/Hong Kong/JV17/2012(H9N2)) segment   ...........G.GGATACGATTGGGA..A...........C.C.  
  44 >A/silkie chicken/Hong Kong/YU595W/2011(H9N2)   ...........G.GGATACGATTGGGA..A...........C...  
  50 >A/chicken/Hong Kong/YO6/2012(H9N2)) segment5   ....A......G.GGATACGATTGGGA....A.........C...  
  51 >A/chicken/Hong Kong/FY6W/2012(H9N2)) segment   ....A......G.GGATACGATTGGGA....A.........C...  
  52 >A/chicken/Hong Kong/WF1W/2012(H9N2)) segment   ....A......G.GGATACGATTGGGA....A.........C...  
  53 >A/chicken/Hong Kong/WF3/2012(H9N2)) segment5   ....A......G.GGATACGATTGGGA....A.........C...  
  54 >A/chicken/Hong Kong/TC18/2011(H9N2)) segment   ......T....GGGGATACGATTGGGA....A.........C...  
  55 >A/chicken/Hong Kong/YU148/2012(H9N2)) segmen   ......CT...GGGGATACGATTGGGA....A.........C...  

  61 >A/chicken/Hong Kong/YU262W/2012(H9N2)) segme   ......CT...GGGGATAC.ATTGGGA....A.........C...  
  62 >A/chicken/Hong Kong/HH117/2012(H9N2)) segmen   ......CT...GGGGATAC.ATTGGGA....A.........C...  
  63 >A/chicken/Hong Kong/CSW445W/2011(H9N2)) segm   ..........AG.GGATACGATTGGGA....A........T...G  

  64 >A/environment/Shanghai/S1438/2013,2013/04/03   .............G..TACGATTG.G.....A........T...G  
  65 >A/Shanghai/1/2013,H7N9                         ................TACGATTG.G.....A........T...G  
  66 >A/environment/Shanghai/S1439/2013,2013/04/03   ................TACGATTG.G.....A........T...G  
  67 >A/environment/Shanghai/S1436/2013,2013/04/03   ................TACGATTG.G.....A....G...T...G  
  68 >A/poultry/index/East-China/2010,2009//,H9N2    ..........A.....TACGATTGGG.......T....G.....G  
  69 >A/chicken/Hong Kong/HH8/2010(H9N2)) segment5   ................TACGATTGGG..................G  
  70 >A/chicken/Hong Kong/FL96/2010(H9N2)) segment   ................TACGATTGGG..................G  
  71 >A/chicken/Hong Kong/YU218/2010(H9N2)) segmen   .......A........TACGATTGGG.....A..........A.G  
  72 >A/chicken/Hong Kong/YU214/2010(H9N2)) segmen   .......A........TACGATTGGG.....A..........A.G  
  73 >A/chicken/Hong Kong/YU219/2010(H9N2)) segmen   .......A........TACGATTGGG.....A..........A.G  
  74 >A/chicken/Hong Kong/TC8/2012(H9N2)) segment5   ................TACGAT.GGG................A.G  
  75 >A/chicken/Shanghai/S1080/2013,2013/04/03,Chi   ........C.......T.CGAT.GGG......C....A.G....G  

  76 >A/pigeon/Shanghai/S1421/2013,2013/04/03,Chin   ....................ATTGGGTTTTCACTGAGAGG...CG  
  77 >A/Index_newMP/H7N9-China/2013/03/,H7N9         ....................ATTGGGTTTTCACTGAGAGG...CG  

 112 >A/Wuxi/1/2013,2013/04/02,H7N9                  ....................ATTGGGTTTTCACTGAGAGG...CG  
 113 >A/Index/H7N9-China/2013/03/,H7N9               ....................ATTGGGTTTTCACTGAGAGG...CG  
 114 >A/environment/Shanghai/S1437/2013,2013/04/03   ....................ATTGGGTTYTCACTGAGAGG...CG  
 115 >A/Hangzhou/3/2013/04/02,H7N9,m79               ....................ATTGGGTT.TCACTGAGAGG...CG  
 116 >A/environment/Wuxi/1/2013,2013/04/02,H7N9      ....................ATTGGGTT.TCACTGAGAGG...CG  
 117 >A/chicken/Jiangsu/SC099/2013,2013/04/16,Chin   ....................ATTGGGTT.TCACTGAGAGG...CG  
 118 >A/environment/Nanjing/2913/2013,2013/03/29,C   ...A................ATTGGGTT.TCACTGAGAGG...CG  
 119 >A/environment-poultry_cage/Nanjing/2913/2013   ...A................ATTGGGTT.TCACTGAGAGG...CG  
 120 >A/Zhejiang/HZ1/2013/4/,H7N9                    ....................ATTGGGTT.TCACTGAGAGG...CG  

 121 >A/environment/Henan/SC232/2013,2013/04/24,Ch   .........A.......A.GATTGGG......CTGAGAGG....G  
 122 >A/Nanchang/1/2013,2013/04/24,China,H7N9        .........A.......ACGATTGGG......CTGAGAGG....G  
 123 >A/environment/Henan/SD429/2013,2013/04/24,Ch   .........A.......ACGATTGGG......CTGAGAGG....G  
 124 >A/chicken/Shanghai/S1077/2013,2013/04/03,Chi   .........A.......ACGATTGGG......CTGAGAGG....G  
 134 >A/Nanjing/1/throat_swab/2013/03/28,H7N9        .........A.......ACGATTGGG......CTGAGAGG....G  

 135 >A/chicken/Rizhao/811/2013(H9N2)) segment5 nu   ..T..............ACGATTGGG......CTGAGAGGT...G  
 136 >A/chicken/Rizhao/55/2013(H9N2)) segment5 nuc   ..T..............ACGATTGGG......CTGAGAGGT...G  
 145 >A/chicken/Rizhao/1436/2013(H9N2)) segment5 n   ......A...A......ACGATTGGG......CTGAGAGG..T.G  
 146 >A/chicken/Hong Kong/NT180W/2011(H9N2)) segme   .....CA.....GG...ACGA..............AG....C...  
 147 >A/chicken/Hong Kong/YU250W/2011(H9N2)) segme   .....CA.....GG...ACGA..............AG....C...  
 148 >A/chicken/Hong Kong/NT148W/2011(H9N2)) segme   .....CA.....GG...ACGA..............AG...TC...  
 149 >A/chicken/Hong Kong/NT149W/2011(H9N2)) segme   .....CA.....GG...ACGA..............AG...TC...  
 150 >A/chicken/Hong Kong/NT305W/2011(H9N2)) segme   .....CA......G...ACGA..............AG...TC...  
 151 >A/pigeon/Hong Kong/CSW1121/2008(H9N2)) segme   .....C...........ACGA..............A.........  
 152 >A/chukkar/Hong Kong/CSW948/2008(H9N2)) segme   .....C...........ACGA..............A.........  
 153 >A/pheasant/Hong Kong/HH225/2008(H9N2)) segme   .....C...........ACGA..............A.........  
 154 >A/chicken/Rizhao/85/2013(H9N2)) segment5 nuc   ............G.....CGA.........CAC......T..A..  
 155 >A/chicken/Rizhao/15/2013(H9N2)) segment5 nuc   ............G.....CGA.........CAC......T..A..  
 156 >A/chicken/Rizhao/437/2013(H9N2)) segment5 nu   ............G.....CGA.........CAC......T..A..  
                                                                                                    

 po                                                  10000101010000001110001001000011000011000011100010000001100001010000000  
 si                                                  11020271002729710028581390700301240910924821054202967993095651929912222  
 ti               segment 6                          94859073755141897070181335354312269426164918966374168817761969742511000  
 on                                                  18410172260112686354020903256575583228547728575749798785736945284183748  
-codon-position-----------------------------------    1 2 1 1  1 1   21         112                    2 2  1     1    1   1  
---Index------------------------------------------   TACAAGTTTAACAGGCCATGGGCGAGCGAGTCCTGCAGTAACTAGAGGGGACAAGATTCACTTACAGTACA  
   5 >A/chicken/Rizhao/867/2013(H7N9)) segment6 ne   ..............................................................AC...----  
   6 >A/chicken/Rizhao/715/2013(H7N9)) segment6 ne   ..............................................................AC...----  
   7 >A/chicken/Rizhao/719b/2013(H7N9)) segment6 n   ..............................................................AC...----  
  12 >A/chicken/Rizhao/515/2013(H7N9)) segment6 ne   .............................A.................................C...----  
  42 >A/Index/H7N9-China/2013/03/,H7N9               ...................................................................----  
  43 >A/chicken/Zhejiang/SD019/2013,2013/04/11,Chi   ...................................................................----  
  44 >A/pigeon/Shanghai/S1423/2013,2013/04/03,Chin   ...................................................................----  
  45 >A/environment/Shandong/SD038/2013,2013/05/03   .............................................................C.....----  
  46 >A/Nanchang/1/2013(H7N9)) segment6 neuraminid   .............................................................C.....----  
  47 >A/chicken/Shanghai/S1078/2013,2013/04/03,Chi   .............................................................C.....----  
  59 >A/environment-poultry_cage/Nanjing/2913/2013   .................................................................G.----  
  60 >A/environment/Nanjing/2913/2013,2013/03/29,C   .................................................................G.----  
  61 >A/chicken/Shanghai/S1055/2013,2013/04/03,Chi   ................................................................TGA----  
  62 >A/environment/Shanghai/S1088/2013,2013/04/03   ................................................................TGA----  
  63 >A/chicken/Shanghai/S1053/2013,2013/04/03,Chi   ................................................................TGA----  
  64 >A/chicken/Jiangsu/SC099/2013,2013/04/16,Chin   ................................................................TGA----  
  65 >A/Nanjing/1/throat_swab/2013/03/28,H7N9        ................................................................TGA----  
  66 >A/chicken/Shanghai/S1358/2013,2013/04/03,Chi   ................................................................TGA----  
  67 >A/chicken/Jiangsu/S002/2013,2013/04/16,China   ................................................................TGA----  
  68 >A/Hangzhou/3/2013/04/02,H7N9,m79               ................................................................TGA----  
  69 >A/Hangzhou/3/2013,2013/04/08,China,H7N9        ................................................................TGA----  
  70 >A/Zhejiang/HZ1/2013/4/,H7N9                    ................................................................TG.----  
  71 >A/environment/Wuxi/1/2013,2013/04/02,H7N9      ................................................................TGA----  
  74 >A/Shanghai/1/2013,H7N9                         ...............................................................GTGA----  
  75 >A/chicken/Zhejiang/SD007/2013,2013/04/22,Chi   ...............................................................GTGA----  
  76 >A/chicken/Jiangsu/RD5/2013(H10N9)              ...GGAC..GG..................A............................TG....TGA----  
  77 >A/common teal/Hong Kong/MPL1075/2011(H11N9))   ..TGGACCAGGTGAA......................................GA....GT..GTGA....  
  78 >A/wild waterfowl/Hong Kong/MPL1060/2011(H11N   ..TGGACCAGGTGAA......................................GA....GT..GTGA....  
  79 >A/duck/Guizhou/1078/2011(H11N9)) segment6 ne   ..TGGACCAGGTGAA.........................................C..GT..GTGA....  

  85 >A/northern shoveler/Hong Kong/MPL961/2011(H2   ...GGACCAGG...............................................TG...GTGA....  
  86 >A/northern shoveler/Hong Kong/MPL133/2010(H2   ...GGACCAGG...............................................TG...GTGA....  
  87 >A/duck/Jiangxi/21714/2011(H11N9)) segment6 n   ...GGACCAGG.........................................G.....TG...GTGA....  
  88 >A/wild waterfowl/Hong Kong/MPP1311/2013(H2N9   ...GGACCAGG.........................................G.....TG...GTGA....  

 po                                                  00000000000000000000000000000000000000000000 
 si                                                  72530645235676454647855466747814397208775441 
 ti         segment 7                                53934874262729343293315151117900076875660108 
 on                                                  04135481501530698185702775748098670850967123 
-codon-position-----------------------------------         11  2   1             121  21  111     
---Index------------------------------------------   GGAATTCCGAGCGACCATGAGCTCTTCGAGAAGGTAGCTCCAGG 
   1 >A/chicken/Shanghai/S1080/2013,2013/04/03,Chi   A..........T................TAGGAA.GATCTTTA. 
   2 >A/environment/Henan/SC232/2013,2013/04/24,Ch   ............................TAGGAAGGATCATTA. 
   3 >A/chicken/Shanghai/S1079/2013,2013/04/03,Chi   ............................TAGGAAGGATCATTAA 
  20 >A/Jiangsu/1/2013/03/30,H7N9,China,,45f,E1      ............................TAGGA.GGATCATTA. 
  21 >A/Wuxi/1/2013,2013/04/02,H7N9                  ............................TAGGAAGGATCATTA. 
  22 >A/Shanghai/4664T/2013,2013/03/05,China,H7N9    ............................TAGGAAGG.TCATTA. 
  35 >A/Index/H7N9-China/2013/03/,H7N9               ............................TAGGAAGGATCATTA. index
                                                                                                  
  43 >A/Fujian/1/2013,2013/04/24,China,H7N9          ............................TAGGAAGGATCATTA. 
  44 >A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9         ............................TAGGAAGGATCATTA. 
  45 >A/Shanghai/1/2013,H7N9                         ............................TAGGAA.GATCATTA. 
  46 >A/environment/Shanghai/S1088/2013,2013/04/03   ............................TAGGAA.GATC.TTA. 
  47 >A/chicken/Zhejiang/SD019/2013,2013/04/11,Chi   ........................C...TAGGAA.GA.C..TA. 
  48 >A/chicken/Wenzhou/598/2013(H9N2)) segment7 m   ........................CCTATAGGAA........A. 
  49 >A/silkie chicken/Wenzhou/812/2013(H9N2)) seg   ........................CCTATAGGAA........A. 
  50 >A/chicken/Rizhao/811/2013(H9N2)) segment7 ma   .TG.........AG...........CTATAGGAA.......... 
  51 >A/chicken/Rizhao/55/2013(H9N2)) segment7 mat   .TG.........AG...........CTATAGGAA.......... 
  52 >A/chicken/Rizhao/15/2013(H9N2)) segment7 mat   .TG.........AG...........CTATAGGAA.......... 
  53 >A/chicken/Rizhao/249/2013(H9N2)) segment7 ma   .TG.........AG...........CTATAGGAA.......... 
  54 >A/chicken/Rizhao/723/2013(H9N2)) segment7 ma   .TG.........AG...........CTATAGGAA.......... 
  55 >A/chicken/Rizhao/1313/2013(H9N2)) segment7 m   .TG.........AG...........CTATAGGAA.......... 
  56 >A/chicken/Rizhao/437/2013(H9N2)) segment7 ma   .TG.........AG...........CTATAGGAA.......... 
  57 >A/chicken/Rizhao/85/2013(H9N2)) segment7 mat   .TG.........AG...........CTATAGGAA.......... 
  58 >A/chicken/Rizhao/651/2013(H9N2)) segment7 ma   .TG.........AG...........CTATAGGAA.......... 
  59 >A/chicken/Wenzhou/89/2013(H7N7)) segment7 ma   .TGGACAAACATAG........C.CCTATAGGAA.......... 
  86 >A/chicken/Wenzhou/275/2013(H7N7)) segment7 m   .TGGACAAACATAG..........CCTATAGGAA....C..... 
  87 >A/chicken/Wenzhou/610/2013(H7N7)) segment7 m   .TGGACAAAC.TAG..........CCTATAGGAA.......... 
  88 >A/silkie chicken/Wenzhou/816/2013(H7N7)) seg   .TGGACAAAC.TAG..........CCTATAGGAA.......... 
  89 >A/chicken/Wenzhou/606/2013(H9N2)) segment7 m   .TGGAC.AA..TAGT.........CCTATAGGA........... 
  90 >A/chicken/Hong Kong/YU158/2011(H9N2)) segmen   .T...........G..........CCTATAGGA........... 
  91 >A/chicken/Hong Kong/JV75/2011(H9N2)) segment   .T...........G..........CCTATAGGA........... 
  92 >A/chicken/Hong Kong/FL96/2010(H9N2)) segment   .T...........G..........CCTATAGGA........... 
  93 >A/environment/Shanghai/S1439/2013,2013/04/03   .........C...G..GC......CCTATAGGAA.......... 
  94 >A/chicken/Zhejiang/SD007/2013,2013/04/22,Chi   .............GTTGCA..T.TCCTATAGGAA.......... 
  97 >A/chicken/Wenzhou/678/2013(H7N7)) segment7 m   .............GTTGCA....TCCTATAGGAA.......... 
  98 >A/chicken/Wenzhou/642/2013(H9N2)) segment7 m   ....-........GTTGCA....TCCTATAGGAA.......... 
  99 >A/Taiwan/S02076/2013,2013/04/22,Taiwan,H7N9    .............GTTGCA....TC.TATAGGAA.......... 
 100 >A/Taiwan/T02081/2013,2013/04/22,Taiwan,H7N9    .............GTTGCA....TC.TATAGGA-.......... 
 101 >A/homing pigeon/Jiangsu/SD184/2013,2013/04/2   .............GTTGCA....TC.TATAGGAA.......... 
 104 >A/environment/Shanghai/S1436/2013,2013/04/03   .............GTTGCA....TC.TATAGGAAC......... 
 105 >A/Zhejiang/HZ1/2013/4/,H7N9                    .............GTTGCA....TCCTATAGGAAC......... 
 113 >A/Index_newMP/H7N9-China/2013/03/,H7N9         .............GTTGCA....TCCTATAGGAAC......... index

 114 >A/chicken/Jiangsu/SC099/2013,2013/04/16,Chin   .............GTTGCA....TCCTATAGGAAC......... 
 118 >A/chicken/Rizhao/1339/2013(H9N2)) segment7 m   .............GTTGCA.A..TCCTATAGGAAC......... 
 119 >A/chicken/Jiangsu/SC537/2013,2013/04/16,Chin   .............GT.C.A....TCCTATAGGAA.......... 
 120 >A/poultry/index/East-China/2010,2009//,H9N2    ........................CCTATAGGAA.......... 
 121 >A/chicken/Hong Kong/YU218/2010(H9N2)) segmen   ........................CCTAG............... 
 122 >A/chicken/Hong Kong/YU219/2010(H9N2)) segmen   ........................CCTAG............... 
 123 >A/chicken/Hong Kong/YU214/2010(H9N2)) segmen   ........................CCTAG............... 
 124 >A/chicken/Hong Kong/HH8/2010(H9N2)) segment7   ....................A...CCTA................ 
 125 >A/chicken/Hong Kong/TSTB32W/2011(H9N2)) segm   T.G...............ATAT..CCTA................ 
 126 >A/chicken/Hong Kong/CSW533/2011(H9N2)) segme   T.................ATAT..CCTA............T... 
 127 >A/chicken/Hong Kong/CSW530/2011(H9N2)) segme   T.................ATAT..CCTA............T... 
 128 >A/chicken/Hong Kong/YU551W/2011(H9N2)) segme   T.................ATAT..CCTA................ 
 129 >A/chicken/Hong Kong/FY64W/2010(H9N2)) segmen   T..................TAT..CCTA................ 
 130 >A/chicken/Hong Kong/TC18/2011(H9N2)) segment   T................C.TATC.CCTA................ 
 131 >A/chicken/Hong Kong/CRA45W/2010(H9N2)) segme   T..................TATCACC.A................ 
 132 >A/chicken/Hong Kong/CRA45/2010(H9N2)) segmen   T..................TATCACC.A................ 
 133 >A/chicken/Hong Kong/YO28/2011(H9N2)) segment   T..................TATCACC.A................ 
 134 >A/chicken/Hong Kong/YO117W/2012(H9N2)) segme   T..................TATCACC.A.....A......T... 
 156 >A/chicken/Hong Kong/NT305W/2011(H9N2)) segme   T..................TATCACC.A.....A.......... 
 157 >A/chicken/Hong Kong/CSW445W/2011(H9N2)) segm   T..................TATCACC.A.....A.......... 
 158 >A/chicken/Hong Kong/TC8/2012(H9N2)) segment7   T..................TAT..CC.A.....A.......... 
 159 >A/chicken/Hong Kong/NT155/2008(H9N2)) segmen   A......T.................CT......A.......... 
 160 >A/chicken/Hong Kong/YU471W/2008(H9N2)) segme   A........................CT......A.......... 
 182 >A/chicken/Hong Kong/YU797/2007(H9N2)) segmen   .......................TCCT......A.......... 
 183 >A/chicken/Hong Kong/HH181/2007(H9N2)) segmen   .......................TACT......A.......... 
 184 >A/pheasant/Hong Kong/HH185/2007(H9N2)) segme   .......................TACT......A.......... 

 po                                                  0000000000000000000000000000000000000000000000000000000000000  
 si                                                  4701644227341614231442476206671760123252766403731536044888871  
 ti    segment 8                                     2292156313662792581560235265126430727330547273437343173344436  
 on                                                  7167092739733781604681005231345816190967766393214854212901268  
-codon-position-----------------------------------   11 11    111 2 112     11   11 11  1122 111 1 11 1 1   2 121   
---Index------------------------------------------   GATCAAAGATAGGTGCGAAATGGAATAGAAATATTCACGGACAGCGAGTGTCCGATGATAT  
  60 >A/chicken/Rizhao/853/2013(H9N2)) segment8 nu   .................CGTAAAGGC......G.ATG......................G.  
  61 >A/chicken/Rizhao/1436/2013(H9N2)) segment8 n   .................CGTAAAGGC......G.ATG.....................-G.  
  62 >A/chicken/Rizhao/1363/2013(H9N2)) segment8 n   .................CGTAAAGGC......G.ATG......................G.  
  66 >A/chicken/Hong Kong/HH8/2010(H9N2)) segment8   ..................GTAAAGGCG.......ATG............A.........GC  
  67 >A/chicken/Hong Kong/YU219/2010(H9N2)) segmen   ..................GTAAAGGCG.......ATG......................GC  
  68 >A/chicken/Hong Kong/YU214/2010(H9N2)) segmen   ..................GTAAAGGCG.......ATG......................GC  
 112 >A/chicken/Hong Kong/YO151W/2011(H9N2)) segme   ...................TATAGGCG.....G.ATG........A.........C...G.  
 113 >A/chicken/Hong Kong/NT305W/2011(H9N2)) segme   ...................TATAGGCG.....G.ATG........A.........C...G.  
 114 >A/chicken/Shanghai/S1080/2013,2013/04/03,Chi   A......-............A...G.G.......CTG-AAG..T.AGAGAATTAG----G.  
 115 >A/Hangzhao/1/2013,2013/03/24,H7N9,China,thro   ..................................CTGGAAGAGTAAGAGAATTAG----..  
 129 >A/Taiwan/T02081/2013,2013/04/22,Taiwan,H7N9    .................................-CTGGAAGAGTAAGAGAAT-AG----..  
 147 >A/Index/H7N9-China/2013/03/,H7N9               ..................................CTGGAAGAGTAAGAGAATTAG----.. index 

 158 >A/chicken/Rizhao/515/2013(H7N9)) segment8 nu   ..................................CTGGAAGAGTAAGAGAATTAG...A..  
 165 >A/chicken/Rizhao/871/2013(H7N9)) segment8 nu   ..................................ATGGAAGAGTAAGAGAATTAG......  
 166 >A/chicken/Rizhao/875/2013(H7N9)) segment8 nu   ..................................ATGGAAGAGTAAGAGAATTAG......  
 175 >A/chicken/Zhejiang/SD019/2013,2013/04/11,Chi   ..................................CTGGAAGAGTAAGAGAATTAG----..  
 176 >A/environment/Shanghai/S1436/2013,2013/04/03   .................C................CTGGAAGAGTAAG..AC...G----..  
 177 >A/environment/Shanghai/S1438/2013,2013/04/03   .........C....A..C.................TGGAAGAGTAAG...C...G----..  
 178 >A/environment/Shanghai/S1437/2013,2013/04/03   ........CC...CA..C.................TGGAAGAGTAAG...C...G----..  
 179 >A/chicken/Wenzhou/598/2013(H9N2)) segment8 n   T.......CC...CA..C.................TGGAAGAGTAAG...C...G......  
 180 >A/silkie chicken/Wenzhou/812/2013(H9N2)) seg   T.......CC...CA..C.................TGGAAGAGTAAG...C...G......  
 181 >A/chicken/Wenzhou/662/2013(H7N7)) segment8 n   ..CTGGGACCGTACAATC..................GGAAGAGTAAG..A...........  
 182 >A/chicken/Wenzhou/602/2013(H7N7)) segment8 n   ..CTGGGACCGTACAATC.........A........GGAAGAGTAAG..............  
 183 >A/chicken/Wenzhou/698/2013(H7N7)) segment8 n   ..CTGGGACCGTACAATC.........A........GGAAGAGTAAG...........A..  
 212 >A/chicken/Zhejiang/SD007/2013,2013/04/22,Chi   ........C....CA..C................CTGGAAGAGTAAGA...TTAG----..  
 213 >A/poultry/index/East-China/2010,2009//,H9N2    ........C....CA.......A............TGGAAGAGT..G.......G----G.  PI


-----------------------------------------

file lamg1 (2013/09/01):
sg=8 , m= 171 n=:2282 2279 2153 1817 1499 1534 984 840
names:33-81
s=1: lengths:2282-2282 letters:2280-2280(2280)
s=2: lengths:2279-2279 letters:2274-2277(2276)
s=3: lengths:2153-2153 letters:2151-2151(2151)
s=4: lengths:1817-1817 letters:1683-1701(1684)
s=5: lengths:1499-1499 letters:1497-1497(1497)
s=6: lengths:1534-1534 letters:1356-1416(1401)
s=7: lengths:984-984 letters:982-982(982)
s=8: lengths:840-840 letters:838-838(838)
----------------------------------
lama1 m= 942 n=:2380 names:37-73
s=1: lengths:2380-2380 letters:2009-2350(2285)

lama2 m= 934 n=:2392 names:37-72
s=1: lengths:2392-2392 letters:2007-2350(2281)

lama3 m= 949 n=:2273 names:37-72
s=1: lengths:2273-2273 letters:1901-2262(2167)

lama5 m= 920 n=:1622 names:38-72
s=1: lengths:1622-1622 letters:1428-1594(1509)

lama47 m= 386 n=:1756 names:40-69
s=1: lengths:1756-1756 letters:1561-1745(1688)

lama49 m= 139 n=:1685 names:44-62
s=1: lengths:1685-1685 letters:1569-1683(1671)

------------------------------------------------------------
 
Re: H7n9

we have 2 new genomes at genbank from late 2013
with quite a different H7N9 now:

it has segments 4,6,7 (and 3) from our known H7N9
but the other segments from poultry viruses that
separated in ~2007 and evolved away from my East-China-Index(2009)
I haven't yet checked the closest relatives .... maybe it's
similar to some of the viruses from the Lam et.al. paper
above, let's see ...



1 >A/Index/H7N9-China/2013/03/,H7N9
2 >A/Index_newMP/H7N9-China/2013/03/,H7N9
3 >A/Huizhou/01/2013,2013/08/08,H7N9
4 >A/Guangdong/02/2013,2013/11/04,H7N9
5 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)

#differences:

3 >A/Huizhou/01/2013,2013/08/08,H7N9
1: 85, 64, 8, 4, 50, 0, 0, 28, -
2: 85, 64, 8, 4, 50, 0, 20, 28, -
4: 6, 3, 82, 1, 7, 4, 1, 6, -
5: 57, 50, 43, 4, 40, 0, 13, 24, -

4 >A/Guangdong/02/2013,2013/11/04,H7N9
1: 87, 63, 76, 3, 55, 4, 1, 30, -
2: 87, 63, 76, 3, 55, 4, 21, 30, -
3: 6, 3, 82, 1, 7, 4, 1, 6, -
5: 59, 49, 45, 3, 43, 4, 14, 26, -

----------------------------------------------------------------------------------
Code: 
 closest relatives in the 8 segments of   A/Huizhou/01/2013,2013/08/08,H7N9
(neig79 7914n 4)

----------segment 1------------- 
 118   27 2280 9291 >KF260868,A/chicken/Hong Kong/TC18/2011,2011//,Hong Kong,H9N2
 153   35 2280 9305 >KF260882,A/chicken/Hong Kong/YO173W/2011,2011//,Hong Kong,H9N2
 157   36 2280 9304 >KF260881,A/silkie chicken/Hong Kong/YU595W/2011,2011//,Hong Kong,H9N2
 162   37 2280 9314 >KF260891,A/chicken/Hong Kong/JV17/2012,2012//,Hong Kong,H9N2
 166   38 2280 9322 >KF260899,A/chicken/Hong Kong/NT266/2012,2012//,Hong Kong,H9N2
...
 271   62 2280 8245 >KC768062,A/duck/Shanghai/C164/2009,2009/11/04,China,H9N2
 271   62 2280 9064 >AB841269,A/muscovy duck/Vietnam/LBM417/2013,2013/05/07,Viet Nam,H9N2
...
 342   78 2280 7602 >KC464595,A/brambling/Beijing/16/2012,2012/11/07,China,H9N2
 346   79 2280 7374 >KC417067,A/chicken/Shanghai/C1/2012,2012/01/,China,H9N2
 350   80 2280 7376 >KC417069,A/chicken/Shanghai/C3/2012,2012/01/,China,H9N2
 359   82 2280 7375 >KC417068,A/chicken/Shanghai/C2/2012,2012/01/,China,H9N2
 364   80 2193 4960 >JF519810,A/chicken/Shanghai/Q0704/2007,2007/04/,China,H9N2
 364   83 2280 9326 >KF260903,A/chicken/Wenzhou/189/2013,2013//,China,H7N7
 364   83 2280 9342 >KF260919,A/chicken/Wenzhou/645/2013,2013//,China,H7N7
 364   83 2280 9349 >KF260926,A/chicken/Wenzhou/698/2013,2013//,China,H7N7
 368   84 2280 6003 >JQ356885,A/chicken/Zhejiang/607/2011,2011/06/,China,H9N2
 368   84 2280 9333 >KF260910,A/chicken/Wenzhou/279/2013,2013//,China,H7N7
 372   85 2280    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 2------------- 
 136   31 2274 9108 >AB824277,A/duck/Quanh Ninh/21/2013,2013/04/10,Viet Nam,H5N1
 145   33 2274 9173 >AB841270,A/muscovy duck/Vietnam/LBM417/2013,2013/05/07,Viet Nam,H9N2
 153   35 2274 9168 >AB836737,A/chicken/Quanh Ninh/26/2013,2013/04/10,Viet Nam,H9N2
 180   41 2274 9369 >KF260611,A/chicken/Hong Kong/FY64W/2010,2010//,Hong Kong,H9N2
 193   44 2274 9395 >KF260637,A/silkie chicken/Hong Kong/YU595W/2011,2011//,Hong Kong,H9N2
...
 250   57 2274 5727 >JN869529,A/chicken/Jiangsu/Q3/2010,2010/02/,China,H9N2
 250   57 2274 8354 >KC768059,A/duck/Shanghai/C164/2009,2009/11/04,China,H9N2
 281   64 2274    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 3------------- 
  37    8 2130 8501 >KC899668,A/chicken/Zhejiang/DTID-ZJU01/2013,2013/04/,China,H7N9
  37    8 2151    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
----------segment 4------------- 
  23    4 1683    2 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 5------------- 
 207   31 1497 9364 >KF259909,A/chicken/Hong Kong/TC8/2012,2012//,Hong Kong,H9N2
 253   38 1497 9335 >KF259880,A/chicken/Hong Kong/HH8/2010,2010//,Hong Kong,H9N2
 260   39 1497 5639 >JN869524,A/chicken/Zhejiang/Q1D4/2010,2010/02/,China,H9N2
 273   41 1497 6075 >JQ356880,A/chicken/Zhejiang/611/2011,2011/06/,China,H9N2
...
 334   50 1497    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 6------------- 
   0    0 1398    2 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 7------------- 
   0    0  982    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 8------------- 
  71    6  838 3624 >JN869534,A/chicken/Jiangsu/Q3/2010,2010/02/,China,H9N2
  83    7  838 6151 >AB836743,A/chicken/Quanh Ninh/26/2013,2013/04/10,Viet Nam,H9N2
  83    7  838 6156 >AB841276,A/muscovy duck/Vietnam/LBM417/2013,2013/05/07,Viet Nam,H9N2
  83    7  838 6323 >KF260123,A/chicken/Hong Kong/FY64W/2010,2010//,Hong Kong,H9N2
  83    7  838 6324 >KF260124,A/chicken/Hong Kong/HH8/2010,2010//,Hong Kong,H9N2
  83    7  838 6338 >KF260138,A/chicken/Hong Kong/YU158/2011,2011//,Hong Kong,H9N2
  83    7  838 6354 >KF260154,A/chicken/Hong Kong/FY6W/2012,2012//,Hong Kong,H9N2
  83    7  838 6355 >KF260155,A/chicken/Hong Kong/YO6/2012,2012//,Hong Kong,H9N2
  83    7  838 6356 >KF260156,A/chicken/Hong Kong/WF3/2012,2012//,Hong Kong,H9N2
  83    7  838 6357 >KF260157,A/chicken/Hong Kong/WF1W/2012,2012//,Hong Kong,H9N2
  88    7  795 4758 >AB769248,A/chicken/Vietnam/OIE-2468/2012,2012/08/13,Viet Nam,H9N2
...
 107    9  838 3279 >JF795090,A/chicken/Shandong/BD/2010,2010/05/,China,H9N2
 107    9  838 3923 >JN653680,A/chicken/Wuxi/7/2010,2010/07/10,China,H9N2
 107    9  838 3928 >JN653675,A/chicken/Jiawang/2/2011,2011/02/15,China,H9N2
 107    9  838 4255 >JN653671,A/chicken/Yongcheng/1/2011,2011/01/31,China,H9N2
 107    9  838 5749 >KC951126,A/chicken/Guangdong/LG1/2013,2013/01/,China,H9N2
 107    9  838 6336 >KF260136,A/chicken/Hong Kong/TC18/2011,2011//,Hong Kong,H9N2
 107    9  838 6347 >KF260147,A/chicken/Hong Kong/CSW445W/2011,2011//,Hong Kong,H9N2
 107    9  838 6410 >KF260210,A/chicken/Rizhao/85/2013,2013//,China,H9N2
... 
 238   20  838 1579 >EU753278,A/chicken/Shanghai/2/1999,1999//,China,H9N2
...
 286   24  838  950 >AB256670,A/chicken/Osaka/aq48/97,1997//,Japan,H9N2
...



Code: 
closest neighbors in the 8 segments of  A/Guangdong/02/2013,2013/11/04,H7N9
(neig79 7914n 5)

----------segment 1------------- 
 127   29 2280 9291 >KF260868,A/chicken/Hong Kong/TC18/2011,2011//,Hong Kong,H9N2
 162   37 2280 9305 >KF260882,A/chicken/Hong Kong/YO173W/2011,2011//,Hong Kong,H9N2
 166   38 2280 9304 >KF260881,A/silkie chicken/Hong Kong/YU595W/2011,2011//,Hong Kong,H9N2
 171   39 2280 9314 >KF260891,A/chicken/Hong Kong/JV17/2012,2012//,Hong Kong,H9N2
 175   40 2280 9322 >KF260899,A/chicken/Hong Kong/NT266/2012,2012//,Hong Kong,H9N2
 188   43 2280 9288 >KF260865,A/chicken/Hong Kong/CRA45/2010,2010//,Hong Kong,H9N2
 188   43 2280 9289 >KF260866,A/chicken/Hong Kong/CRA45W/2010,2010//,Hong Kong,H9N2
 210   48 2280 5555 >JN869543,A/chicken/Guangdong/ZCY/2011,2011/07/,China,H9N2
...
 350   80 2280 7602 >KC464595,A/brambling/Beijing/16/2012,2012/11/07,China,H9N2
 355   81 2280 7374 >KC417067,A/chicken/Shanghai/C1/2012,2012/01/,China,H9N2
...
 381   87 2280    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 2------------- 
 131   30 2274 9108 >AB824277,A/duck/Quanh Ninh/21/2013,2013/04/10,Viet Nam,H5N1
 140   32 2274 9173 >AB841270,A/muscovy duck/Vietnam/LBM417/2013,2013/05/07,Viet Nam,H9N2
 149   34 2274 9168 >AB836737,A/chicken/Quanh Ninh/26/2013,2013/04/10,Viet Nam,H9N2
 175   40 2274 9369 >KF260611,A/chicken/Hong Kong/FY64W/2010,2010//,Hong Kong,H9N2
 189   43 2274 9395 >KF260637,A/silkie chicken/Hong Kong/YU595W/2011,2011//,Hong Kong,H9N2
...
 277   63 2274    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 3------------- 
 204   44 2151 9456 >KF260367,A/chicken/Hong Kong/FY64W/2010,2010//,Hong Kong,H9N2
 204   44 2151 9476 >KF260387,A/chicken/Hong Kong/NT180W/2011,2011//,Hong Kong,H9N2
 213   46 2151 9466 >KF260377,A/chicken/Hong Kong/CRA45/2010,2010//,Hong Kong,H9N2
...
 255   55 2151 5553 >JN869523,A/chicken/Zhejiang/Q1D4/2010,2010/02/,China,H9N2
...
 320   69 2151 9534 >KF260445,A/chicken/Wenzhou/606/2013,2013//,China,H9N2
 325   70 2151 7767 >KC464597,A/brambling/Beijing/16/2012,2012/11/07,China,H9N2
...
 353   76 2151    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 4------------- 
  18    3 1663    2 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 5------------- 
 227   34 1497 9364 >KF259909,A/chicken/Hong Kong/TC8/2012,2012//,Hong Kong,H9N2
 273   41 1497 9335 >KF259880,A/chicken/Hong Kong/HH8/2010,2010//,Hong Kong,H9N2
 280   42 1497 5639 >JN869524,A/chicken/Zhejiang/Q1D4/2010,2010/02/,China,H9N2
...
 367   55 1497    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 6------------- 
  30    4 1324    2 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
 ...
----------segment 7------------- 
  10    1  982    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9
...
----------segment 8------------- 
 119   10  838 3624 >JN869534,A/chicken/Jiangsu/Q3/2010,2010/02/,China,H9N2
 119   10  838 6333 >KF260133,A/chicken/Hong Kong/CRA45/2010,2010//,Hong Kong,H9N2
 119   10  838 6334 >KF260134,A/chicken/Hong Kong/CRA45W/2010,2010//,Hong Kong,H9N2
 131   11  838 6151 >AB836743,A/chicken/Quanh Ninh/26/2013,2013/04/10,Viet Nam,H9N2
 131   11  838 6156 >AB841276,A/muscovy duck/Vietnam/LBM417/2013,2013/05/07,Viet Nam,H9N2
 131   11  838 6323 >KF260123,A/chicken/Hong Kong/FY64W/2010,2010//,Hong Kong,H9N2
...
 262   22  838 1579 >EU753278,A/chicken/Shanghai/2/1999,1999//,China,H9N2


Code: 
 >A/Zhejiang/DTID-ZJU10/2013,2013/10/14,China,H7N9

----------segment 1------------- 
  57   13 2268 7602 >KC464595,A/brambling/Beijing/16/2012,2012/11/07,China,H9N2
  79   18 2268 9082 >CY146985,A/chicken/Shanghai/S1078/2013,2013/04/03,China,H7N9
  79   18 2268 9089 >CY147041,A/chicken/Zhejiang/SD019/2013,2013/04/11,China,H7N9
  83   19 2268    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 2------------- 
  41    9 2177    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 3------------- 
  37    8 2130    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 4------------- 
  24    4 1649    2 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 5------------- 
  13    2 1497    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 6------------- 
  57    8 1398    2 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 7------------- 
  10    1  982    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 8------------- 
  47    4  838    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

Code: 
   0    0 2280    1 >KF662944,A/Guangdong/1/2013,2013/08/10,China,H7N9

----------segment 1------------- 
 118   27 2280 9291 >KF260868,A/chicken/Hong Kong/TC18/2011,2011//,Hong Kong,H9N2

----------segment 2------------- 
 140   32 2274 9108 >AB824277,A/duck/Quanh Ninh/21/2013,2013/04/10,Viet Nam,H5N1
 149   34 2274 9173 >AB841270,A/muscovy duck/Vietnam/LBM417/2013,2013/05/07,Viet Nam,H9N2
 158   36 2274 9168 >AB836737,A/chicken/Quanh Ninh/26/2013,2013/04/10,Viet Nam,H9N2
 175   40 2274 9369 >KF260611,A/chicken/Hong Kong/FY64W/2010,2010//,Hong Kong,H9N2

----------segment 3------------- 
  32    7 2151    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 4------------- 
  23    4 1683    2 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 5------------- 
 200   30 1497 9364 >KF259909,A/chicken/Hong Kong/TC8/2012,2012//,Hong Kong,H9N2

----------segment 6------------- 
   0    0 1398    2 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 7------------- 
   0    0  982    3 >A/Index/H7N9-China/2013,2013/01/01,China,H7N9

----------segment 8------------- 
  83    7  838 3624 >JN869534,A/chicken/Jiangsu/Q3/2010,2010/02/,China,H9N2


so, it reassorted with Hongkong-like H9N2.

only 3,4,1 differences to our H7N9 index in segments 4,6,7 until Nov.2013
only 8,4,0,0 differences to our H7N9 index in segments 3,4,6,7 until Aug.2013

it's not soo unusual, but it could (still weakly) indicate prolonged survival in the environment
or in some immunity protected places in animals without replicating.
Or NA,MP are especially stable (unusual)

===========update===========
Code: 
   0    0 2280    1 >A/Index/H7N9-China/2013/03/,H7N9
------------------segment 1------------------
 372   85 2280    9 >A/Guangdong/1/2013,2013/08/10,China,H7N9
 372   85 2280   10 >A/Huizhou/01/2013,2013/08/08,China,H7N9
 381   87 2280   11 >A/Guangdong/02/2013,2013/11/,China,H7N9
 412   94 2280   14 >A/Guangdong/05/2013,2013/12/17,H7N9
---------------------segment 2----------------------
 277   63 2274    9 >A/Guangdong/1/2013,2013/08/10,China,H7N9
 281   64 2274   10 >A/Huizhou/01/2013,2013/08/08,China,H7N9
 277   63 2274   11 >A/Guangdong/02/2013,2013/11/,China,H7N9
 277   63 2270   13 >A/Guangdong/04/2013,2013/12/16,H7N9
 290   66 2270   14 >A/Guangdong/05/2013,2013/12/17,H7N9
---------------------segment 3-----------------------
  32    7 2151    9 >A/Guangdong/1/2013,2013/08/10,China,H7N9
  37    8 2151   10 >A/Huizhou/01/2013,2013/08/08,China,H7N9
 353   76 2151   11 >A/Guangdong/02/2013,2013/11/,China,H7N9
 371   80 2151   13 >A/Guangdong/04/2013,2013/12/16,H7N9
 371   80 2151   14 >A/Guangdong/05/2013,2013/12/17,H7N9
-----------------------segment 4---------------------------
  23    4 1683    9 >A/Guangdong/1/2013,2013/08/10,China,H7N9
  23    4 1683   10 >A/Huizhou/01/2013,2013/08/08,China,H7N9
  18    3 1663   11 >A/Guangdong/02/2013,2013/11/,China,H7N9
  41    7 1683   12 >A/Guangdong/03/2013,2013/12/15,H7N9
  23    4 1683   13 >A/Guangdong/04/2013,2013/12/16,H7N9
  23    4 1683   14 >A/Guangdong/05/2013,2013/12/17,H7N9
------------------segment 5--------------------
 340   51 1497    9 >A/Guangdong/1/2013,2013/08/10,China,H7N9
 334   50 1497   10 >A/Huizhou/01/2013,2013/08/08,China,H7N9
 367   55 1497   11 >A/Guangdong/02/2013,2013/11/,China,H7N9
 394   59 1497   12 >A/Guangdong/03/2013,2013/12/15,H7N9
 367   55 1497   13 >A/Guangdong/04/2013,2013/12/16,H7N9
 374   56 1497   14 >A/Guangdong/05/2013,2013/12/17,H7N9
----------------------segment 6-----------------------
   0    0 1398    9 >A/Guangdong/1/2013,2013/08/10,China,H7N9
   0    0 1398   10 >A/Huizhou/01/2013,2013/08/08,China,H7N9
  30    4 1324   11 >A/Guangdong/02/2013,2013/11/,China,H7N9
   7    1 1398   12 >A/Guangdong/03/2013,2013/12/15,H7N9
  42    6 1398   13 >A/Guangdong/04/2013,2013/12/16,H7N9
  35    5 1398   14 >A/Guangdong/05/2013,2013/12/17,H7N9
---------------------segment 7------------------------
   0    0  982    9 >A/Guangdong/1/2013,2013/08/10,China,H7N9
   0    0  982   10 >A/Huizhou/01/2013,2013/08/08,China,H7N9
  10    1  982   11 >A/Guangdong/02/2013,2013/11/,China,H7N9
  50    5  982   12 >A/Guangdong/03/2013,2013/12/15,H7N9
   0    0  982   13 >A/Guangdong/04/2013,2013/12/16,H7N9
  10    1  982   14 >A/Guangdong/05/2013,2013/12/17,H7N9
----------------------segment 8---------------------------
 322   27  838    9 >A/Guangdong/1/2013,2013/08/10,China,H7N9
 334   28  838   10 >A/Huizhou/01/2013,2013/08/08,China,H7N9
 357   30  838   11 >A/Guangdong/02/2013,2013/11/,China,H7N9
 393   33  838   12 >A/Guangdong/03/2013,2013/12/15,H7N9
 369   31  838   13 >A/Guangdong/04/2013,2013/12/16,H7N9
 369   31  838   14 >A/Guangdong/05/2013,2013/12/17,H7N9

85,63,7-76,4,50,0,0,27 differences to old H7N9 in the 8 segments
mrcad in ~ 2006,2008,2013-2007,2013,2007,2013,2013,2008
mrcad=most recent common ancestor date

compare it with the re-emerging H5N1 in 2000 after it had been eradicated
in HK in 1997 : that one had ~200 differences to the old H5N1 in the
polymerase segments, 2-3 times more than the 2 H7N9 variants

GD2 has 1879G->627E while GD1,GD5,HZ1 have 1879A->627K , GD3,GD4 not available

the new GD-strain shares G194A(4),A418G(4),G516A(4) with
A/environment/Shenzhen/1/2013,2013/10/,H7N9
of which we only have the HA.
 
Re: H7n9

A/Hong Kong/470129/2013,2013/11/,H7N9
today at genbank

close to normal H7N9 in segments 4,6,7
close to A/Guangdong/1/2013,2013/08/10,H7N9 in segments 1,8
but different to other (to me) known H7N9 in segments 2,3,5
closer to my East-China poultry index
so a completely new reassortant

best H9N2 matches:
Code: 
   0    0 2280    1 >A/Hong Kong/470129/2013,2013/11/11,H7N9
----------segment 1------------- 
 236   54 2280 6828 >A/chicken/Guangdong/ZCY/2011,2011/07/,H9N2
----------segment 2------------- 
 145   33 2274 6854 >A/chicken/Guangdong/ZCY/2011,2011/07/,H9N2
----------segment 3------------- 
 160   17 1059 8281 >A/duck/Vietnam/OIE-2749/2012,2012/08/14,H9N8
 213   46 2151 6597 >A/chicken/Guangdong/ZHJ/2011,2011/06/,H9N2
----------segment 5------------- 
 213   32 1497 6682 >A/chicken/Guangdong/ZHJ/2011,2011/06/,H9N2
 220   33 1497 6679 >A/chicken/Zhejiang/Q1D4/2010,2010/02/,H9N2
----------segment 8------------- 
  96    8  827 5693 >A/chicken/Jiangsu/Q3/2010,2010/02/,H9N2
 114    9  784 6871 >A/chicken/Vietnam/OIE-2468/2012,2012/08/13,H9N2
 120   10  827 5181 >A/chicken/Shandong/03/2010,2010/05/,H9N2
 120   10  827 5602 >A/chicken/Tongshan/1/2011,2011/01/31,H9N2
 120   10  827 5696 >A/chicken/Guangdong/ZCY/2011,2011/07/,H9N2
 121    8  660 3415 >A/chicken/Shanghai/Y2/2008,2008//,H9N2


http://www.ncbi.nlm.nih.gov/pubmed/24576826
 
Re: H7n9

Infection with Possible Precursor of Avian Influenza A(H7N9) Virus

http://wwwnc.cdc.gov/eid/article/20/8/14-0325-t1

A/Shanghai/JS01/2013/04/03,H7N9



to me it looks like it's the domestic ducks in China where the virus
evolves and developes new strains, dangerous for humans.
Wild mallards as well as chickens can contribute new segments that
are then reassorted in domestic ducks and are maintained and can
further evolve and develope mutations and deletions/insertions.
The improved new strains then go to chickens who are often
in proximity of domestic ducks in China.


the decisive moment in the emergence of H7N9 seems to have been the
deletion in NA in early 2013. That new strain had some new characteristics
which made it dangerous to humans.
These deletions are rare in nature, somehow harder to achieve than single
mutations, but we could easily test some other such deletions in the lab
so to gain the function of other circulating strains ...


---------------------------------------------------------
http://www.ncbi.nlm.nih.gov/nuccore/CY146657
A/duck/Hunan/S4111/2011(H9N2

Deng,G., Tan,D., Shi,J., Cui,P., Jiang,Y., Liu,L., Tian,G.,
Kawaoka,Y., Li,C. and Chen,H.
TITLE Complex reassortment of multiple subtypes of avian influenza
viruses in domestic ducks at the Dongting Lake region of China
---------------------------------------------------------

Code: 
segment 4, HA:
   0    0 1683   49 >A/Index/H7N9-China/2013/03/,H7N9
--------------------------------------------------------
  53    9 1683   11 >KF609511,A/Shanghai/JS01/2013,2013/04/03,China,H7N9,Human

 219   37 1683  140 >KF259041,A/pigeon/Wenzhou/559/2013,2013//,China,H7N7,Avian
 231   39 1683    7 >KF258995,A/duck/Fujian/6390/2010,2010//,China,H7N3,Avian
 231   39 1683    8 >KF258963,A/duck/Fujian/6388/2010,2010//,China,H7N3,Avian
 231   39 1683   10 >KF258962,A/duck/Fujian/6380/2010,2010//,China,H7N3,Avian
 231   39 1683  141 >KF259040,A/duck/Wenzhou/47/2013,2013//,China,H7N7,Avian
 237   40 1683    9 >KF258994,A/duck/Fujian/6326/2010,2010//,China,H7N3,Avian
 237   40 1683  142 >KF259039,A/duck/Wenzhou/775/2013,2013//,China,H7N2,Avian
 237   40 1683  143 >KF259009,A/duck/Wenzhou/771/2013,2013//,China,H7N3,Avian
 243   41 1683  144 >KF258958,A/goose/Guangdong/7472/2012,2012//,China,H7N7,Avian
 272   42 1541  181 >KF297292,A/silkie chicken/Wenzhou/804b/2013,2013//,China,H7N7,Avian

 409   69 1683    3 >JQ906575,A/duck/Zhejiang/11/2011,2011/06/,China,H7N3,Avian

 463   78 1683  309 >KF259000,A/wild duck/Jiangxi/10179/2005,2005//,China,H7N3,Avian

 482   81 1680  294 >FJ750875,A/wild bird feces/Korea/HDR22/2006,2006//,South Korea,H7N7,Avian
 484   80 1650  324 >EU158102,A/duck/Jiangxi/1786/03,2003//,China,H7N7,Avian

 510   86 1683  314 >AB473543,A/duck/Mongolia/867/2002,2002//,Mongolia,H7N1,Avian

 558   94 1683  328 >AB269695,A/duck/Taiwan/4201/99,1999//,Taiwan,H7N7,Avian



Code: 
segment 4
   0    0 1413   24 >KF259728,A/northern shoveler/Hong Kong/MPL133/2010,2010//,Hong Kong,H2N9,Avian
----------------------------------------
  28    4 1413   21 >KF259698,A/duck/Jiangxi/21714/2011,2011//,China,H11N9,Avian
  28    4 1413   23 >KF259726,A/northern shoveler/Hong Kong/MPL961/2011,2011//,Hong Kong,H2N9,Avian
  35    5 1413   11 >KC609801,A/wild duck/Korea/SH19-47/2010,2010/12/,South Korea,H7N9,Avian
  35    5 1413   20 >KC609799,A/wild duck/Korea/SH19-27/2010,2010/12/,South Korea,H7N9,Avian
  36    5 1355   15 >KC609803,A/wild duck/Korea/MHC35-41/2011,2011/03/,South Korea,H7N9,Avian
  37    5 1345   13 >KC609800,A/wild duck/Korea/SH19-44/2010,2010/12/,South Korea,H7N9,Avian
  37    5 1348   12 >KC609798,A/wild duck/Korea/SH19-50/2010,2010/01/,South Korea,H7N9,Avian
  39    5 1253   14 >KC609804,A/wild duck/Korea/MHC35-25/2011,2011/03/,South Korea,H7N9,Avian
  55    3  541   42 >KF028388,A/Shanghai/5058T/2013,2013/04/19,China,H7N9,Human
  56    8 1413   22 >KF259703,A/wild waterfowl/Hong Kong/MPP1311/2013,2013//,Hong Kong,H2N9,Avian
  61    8 1309   19 >KC609808,A/wild duck/Korea/CSM42-1/2011,2011/03/,South Korea,H7N9,Avian
  63    9 1413   25 >KF006416,A/chicken/Jiangsu/RD5/2013,2013/03/,China,H10N9,Avian
  63    9 1413   26 >KF609513,A/Shanghai/JS01/2013,2013/04/03,China,H7N9,Human
  66    9 1354   16 >KC609806,A/wild duck/Korea/MHC39-26/2011,2011/03/,South Korea,H7N9,Avian
  72   10 1383   17 >KC609805,A/wild duck/Korea/MHC39-13/2011,2011/03/,South Korea,H7N9,Avian
  84   12 1413    2 >CY146614,A/duck/Hunan/S1607/2012,2012/03/24,China,H11N9,Avian
  84   12 1413    6 >CY146638,A/duck/Hunan/S4013/2011,2011/11/09,China,H11N9,Avian
  84   12 1413    7 >CY146686,A/duck/Hunan/S4137/2011,2011/11/11,China,H11N9,Avian
  84   12 1413   10 >KF259695,A/duck/Guizhou/1078/2011,2011//,China,H11N9,Avian
  92   13 1398   27 >CY147014,A/chicken/Shanghai/S1358/2013,2013/04/03,China,H7N9,Avian
  92   13 1398   43 >CY147038,A/chicken/Zhejiang/SD007/2013,2013/04/22,China,H7N9,Avian
  92   13 1398  108 >KC896765,A/environment/Nanjing/2913/2013,2013/03/29,China,H7N9,Environment
  92   13 1413    3 >CY146734,A/environment/Hunan/S11511/2012,2012/03/24,China,H4N9,Environment
  93   13 1392   18 >KC609809,A/wild duck/Korea/CSM42-34/2011,2011/03/,South Korea,H7N9,Avian

 100   14 1398  162 >A/Index/H7N9-China/2013/03/,H7N9




Code: 
segment 6, NA
   0    0 1398  162 >A/Index/H7N9-China/2013/03/,H7N9
---------------------------------------------------------
  50    7 1398   26 >KF609513,A/Shanghai/JS01/2013,2013/04/03,China,H7N9,Human

  78   11 1398   61 >KF226107,A/Jiangsu/2/2013,2013/04/20,China,H7N9,Human
 100   14 1398   24 >KF259728,A/northern shoveler/Hong Kong/MPL133/2010,2010//,Hong Kong,H2N9,Avian
 121   17 1398   25 >KF006416,A/chicken/Jiangsu/RD5/2013,2013/03/,China,H10N9,Avian
 128   18 1398   21 >KF259698,A/duck/Jiangxi/21714/2011,2011//,China,H11N9,Avian
 128   18 1398   23 >KF259726,A/northern shoveler/Hong Kong/MPL961/2011,2011//,Hong Kong,H2N9,Avian
 135   19 1398   11 >KC609801,A/wild duck/Korea/SH19-47/2010,2010/12/,South Korea,H7N9,Avian
 135   19 1398   20 >KC609799,A/wild duck/Korea/SH19-27/2010,2010/12/,South Korea,H7N9,Avian
 141   19 1340   15 >KC609803,A/wild duck/Korea/MHC35-41/2011,2011/03/,South Korea,H7N9,Avian
 142   19 1330   13 >KC609800,A/wild duck/Korea/SH19-44/2010,2010/12/,South Korea,H7N9,Avian
 142   19 1333   12 >KC609798,A/wild duck/Korea/SH19-50/2010,2010/01/,South Korea,H7N9,Avian
 

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http://www.pnas.org/content/early/2014/12/25/1422456112.abstract
Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus

http://news.xinhuanet.com/english/health/2014-12/30/c_127345176.htm
> the genetic diversity of H9N2 viruses fell sharply in 2009 and from 2010 to 2013,
> an H9N2 virus emerged as the predominant subtype thanks to its genetic makeup
> that allowed it to flourish despite widespread vaccination of chickens against H9N2 viruses.
> Liu: "The dominant H9N2 virus had changed antigenicity and improved adaptability in chickens,"
> That may be one reason for its widespread outbreak from 2010 to 2013.
> The emergence of this dominant H9N2 virus was the first step in the genesis of the H7N9
> viruses because it greatly increased the likelihood of reassortment between H9N2 and
> other flu subtypes. Reassortment refers to the tendency of flu viruses to swap genes.
 
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