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H7n9

gsgs

Registered User
H7-cleavage sites
------------------------

first I found that there is a 8aa deletion in H7 at 230-237.
I didn't know that. 388 H7s at genbank had the deletion and 884 had not
The deletion is only in American H7N2.
So I excluded these.

Code:
    331,KG
    302,KT
     22,KP
      7,KR
      6,KA
      5,RG
      4,RK
      3,KE
      4,KK
      1,XG
      1,KRR
     30,KRRK
     16,KRRR
      6,RKRK
      4,KKKK
      2,RRRK
      2,KRKK
      1,KRRN
      9,KKREK
      7,KKRRK
      5,KKRKK
      2,KRKRK
     33,KGSRVR
      2,KKKKKK
      1,KGTKPRPR
      1,KTTKPRPR
      4,KQAYRKRMT
      2,KQAYQKRMT
      2,KQAYQKQMT
      2,KQAHQKRMT
      1,KQAYKKRMT
      1,KQAYHKRMT
      1,KQACQKRMT
      1,RQAYRKRMT
      5,KDRKSRHRRT
     16,THKQLTHHMRKK
      5,AHKQLTHHMRKK
      5,KTCSPLSRCRET
      3,KTCSPLSRCRKT
      1,IHKQLTHHMRKK
 
Re: H7n9

5aa deletion in N9 at (nucleotide-?) position 205
not seen before

maybe we can compare it with deletions in other NAs
 
Re: H7n9

H7-receptor binding domains (rbd)

aa-positions 98,134-138,153-155,184-196,216-230 in H3-numbering
(as in H1 or H3, it could be different in H7)

Y GVTAA WIT HPPTTSEQQSLYQ EIAARPKVRGQAGRM

A/turkey/MN/1661/1981(H1N1)

aligning H1 to H7 ...


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

Code:
receptor binding domain of influenza-A viruses

positions 98,134-138,153-155,184-196,216-230 in hemagglutinin
(H3-numbering)


count,species-serotype,amino-acids at these positions,representative sequence
-----------------------------------------------------------------------------------------------------
                 Y GVTAA WIT HPPTTSEQQSLYQ EIAARPKVRGQAGRM
   9 A-H1N1:     Y GVTAA WIT HPPTTSEQQSLYQ EIAARPKVRGQAGRM     A/turkey/Minnesota/1661/81(H1N1)
   4 A-H1N1:     . ..... ... .....N....... ...............    A/pintail duck/Alberta/210/2002(H1N1)

                .....S.S..L.....NIGD.RA..H....K.....D.E..I
 325 H-H1N1:     Y GVSAS WLT HPPNIGDQRALYH EIAKRPKVRDQEGRI     A/Wyoming/4/2003(H1N1)
  64 H-H1N1:     . ..T.. ... ..S.......I.. ...............    A/Switzerland/5389/95 (H1N1)
  44 H-H1N1:     . ..... ... ......N...... ...............    A/Yokohama/62/200

                ....A.....LN..SESVS..TK....SPGA.--------..
  39 A-H7N2:     Y GATSA WLN HSESVSEQTKLYG SPGAR--------RI     A/turkey/VA/67/02(H7N2)
  22 A-H7N1:     . ..... ... ..G.TT....... .....PQVNGQSG..    A/turkey/Italy/977/99 (H7N1)
  22 A-H7N1:     . .T..T ... ..G.TT....... ...E.PQVNGQSG..    A/turkey/Italy/5074/99 (H7N1)
  20 A-H7N7:     . ..... ... ..G.TT....... .....PQVNGQSG..    A/turkey/Germany/R11/01(H7N7)
  15 A-H7N3:     . ..... ... ..G.TT....... .....PQVNGQSG..    A/turkey/Oregon/1971(H7N3)
  14 A-H7N3:     . ..... ... ..G.AT....... .....PQVNGQSG..    A/Turkey/Colorado/13356/91 (H7N3)
   8 A-H7N2:     . .T... ... ............. .T.............    A/Chicken/Pennsylvania/13552-1/98 (H7N2)
   8 A-H7N7:     . ...N. ... ..G.TT....... .....PQVNGQSG..    A/Mallard/Sweden/93/02(H7N7)
   7 A-H7N1:     . ..... ... ..G.TA....... .....PQVNGQSG..    A/parrot/England/1174/94(H7N1)
   7 A-H7N2:     . ..... ... ..G.......... .....PQVNGQSG..    A/Chicken/Rhode Island/4328/95 (H7N2)
   6 A-H7N3:     . .V... ... ..G.AN....... .....PQVNGQSG..    A/turkey/Chile/4418/02(H7N3)
   5 A-H7N1:     . .T... ... ..G.TT....... .....PQVNGQSG..    A/turkey/Italy/4857/99 (H7N1)
   4 A-H7N1:     . ..... ... ..V.TT....... .L...PQVNGQSG..    A/turkey/Italy/4042/99 (H7N1)
   4 A-H7N1:     . ..... ... ..V.TT....... .....PQVNGQSG..    A/turkey/Italy/2715/99 (H7N1)
   4 A-H7N2:     . ..... ... ............. N..............    A/guineafowl/NY/4649-18/2006(H7N2)
   4 A-H7N3:     . ..... ... ..G.AN....... .....PQVNGQSG..    A/Quail/Arkansas/16309-7/94 (H7N3)
   4 A-H7N3:     . ....S ... ..G.TT...R... .....PQVNGQSG..    A/peregrine falcon/U.A.E./188/2384/98(H7N3)
   4 A-H7N7:     - ----- --- ..G.TT....... .....PQVNGQSG..    A/Mongolia/736/02(H7N7)

                ....E..........G.TA...R....N..P.PQINGQSG..
   6 E-H7N7:     Y GETSA WLN HSGSTAEQTRLYG NPGPRPQINGQSGRI     A/equine/Sao Paulo/1/76(H7N7)

                ....A......S......T...K....S..A...V.......
   1 H-H7N1:     Y GATSA WLS HSGSTTEQTKLYG SPGARPQVNGQSGRI     A/Hong Kong/301/78(H7N1)

                ....T......N..........R...................
   1 S-H7N7:     Y GTTSA WLN HSGSTTEQTRLYG SPGARPQVNGQSGRI     A/seal/Mass/1/80(H7N7)

                .....SK....K..PPD.K...T..K.NI.P..L.R..Q..M
   7 A-H8N4:     Y GTSKA WLK HPPDTKEQTTLYK NIGPRPLVRGQQGRM     A/Turkey/Ontario/6118/68(H8N4)

                ...........T....TDTA..N..T.L.......N.L...I
  39 A-H9N2:     Y GTSKA WLT HPPTDTAQTNLYT LIGPRPLVNGLQGRI     A/Silky Chicken/Hong Kong/SF44/99(H9N2)
  17 A-H9N2:     . ..... ... ............I V......A.......    A/turkey/Tzur Moshe/1565/04(H9N2)



Code:
    187,GATSA WLL HSGSTTEQTKLYGSG SPGARPQVNGQSGRI 
    135,----- --- ----A---------- --------------- 
     68,----- --- ----AD--------- --------------- 
     44,----- --- -----A--------- --------------- 
     37,-T--T --- --------------- ---E----------- 
     34,----- --- ----VS--------- --------------- 
     22,----- --- --V------------ --------------- 
     21,-T--- --- --------------- --------------- 
     16,-V--- --- ----A---------- --------------- 
     16,----- --- ----AN--------- --------------- 
     12,-T--S --- ---------R----- --------------- 
     12,----S --- ---------R----- --------------- 
     11,----- --- --V----------G- -L------------- 
     10,-V--- --- --------------- --------------- 
     10,----- --- --------A------ --------------- 
      9,----- --- -------------G- --------------- 
      8,-E--- --- -----A---R----- N--P---I------- 
      8,---N- --- --------------- --------------- 
      7,-V--- --- ----AN--------- --------------- 
      7,----- --- --------------- --E------------ 
      6,-T--S --- ---------R----- ---V----------- 
      6,-E--- --- -----A---R----- ---P---I------- 
      6,----- --- --V-A---------- --------------- 
      6,----- --- ----A---------- ------P--------


Code:
RBD in flugenome.org-types
---------------------------
41A,EIAARPKVRGQAGRM, 235  8 
41B,EIAKRPKVRDQEGRI, 235  7 
41C,EIAARPKVRGQAGRM, 235  8 
41D,EIAARPKVRGQAGRM, 235  8 
41E,ELAARPKVRGQAGRI, 235  9 
42A,EIATRPKVNGLGSRM, 231  6 
42B,EIATRPNVNGQGGRM, 231  8 
42C,EIATRPKVNGQRGRM, 231  8 
42D,EIATRPKVNGQGGRM, 231  8 
42E,EIATRPKVNGQGGRM, 231  8 
42F,EIATRPKVNGQGGRM, 231  8 
42G,EIATRPKVNGQGGRM, 231  8 
42H,EIATRPKVNGQGGRM, 231  8 
42I,EIATRPAVNGQRGRM, 231  8 
43A,NIGSRPRVRDVSSRI, 237  7 
43B,NIGSRPWVRGQSGRI, 237  10 
43C,NIGSRPWVRGQSGRI, 237  10 
43D,NIGSRPWVRGQSGRI, 237  10 
43E,NIGSRPWVRGQSGRI, 237  10 
43F,NIGSRPWVRGQSGRI, 237  10 
44A,NIGSRPWVRGQSGRI, 234  10 
44B,NIGSRPWVRGQSGRI, 234  10 
44C,NIGSRPWVRGQSGRI, 234  10 
44D,NIGSRPWVRGQSGRI, 234  10 
45A,KIATRPKVNGQSGRM, 233  9 
45B,EIATRPKVNGQSGRM, 233  9 
45C,EIATRPKVNGQSGRM, 233  9 
45D,EIATRPRVNGQYGRI, 233  9 
45E,EIATRPKVNGQSGRM, 233  9 
45F,EIATRPKVNGQSGRM, 233  9 
45G,EIATRPKVNGQSGRM, 233  9 
45H,EIATRPKVNGQSGRM, 233  9 
45I,EIATRPKVNGQSGRM, 233  9 
45J,KIATRSKVNGQSGRM, 233  8 
45K,EIATRPKVNGQSGRM, 233  9 
46A,EIAARPAVNGQRGRI, 235  10 
46B,EIAARPAVNGQRGRI, 235  10 
46C,EIAARPAVNGQRGRI, 235  10 
46D,EIAARPAVNGQRGRI, 235  10 
46E,EIAARPAVNGQRGRI, 235  10 
46F,EIASRPPVNGQRGRI, 235  9 
46G,EIADRPPANGQRGRI, 235  8 
47A,SPGARPQVNGQSGRI, 230  15 
47B,SPGTRPQVNGQSGRI, 230  14 
47C,SPGARPQVNGQSGRI, 230  15 
47D,NPGPRPQINGQSGRI, 230  12 
47E,SPGARPQVNGQSGRI, 230  15 
47F,SPGAR--------RI, 230  7 
48A,NIGPRPLVRGQQGRM, 234  8 
49A,VIGPRPLVNGHKGRI, 229  9 
49B,VIGPRPLVNGLQGRI, 229  9 
49C,LIGPRPLVNGLQGRI, 229  9 
49D,VIGPRPLVNGQQGRI, 229  10 
49E,VIGPRPLVNGQQGRI, 229  10 
49F,VIGPRPLVNGQQGRI, 229  10 
49G,VIGPRPLVNGQQGRI, 229  10 
49H,MIGPRPLVNGQQGRI, 229  10 
49I,VIGPRPLVNGQQGRI, 229  10 
49J,VIGPRPLVNGQQGRI, 229  10 
4AA,VVGARPQVNGQSGRI, 231  13 
4AC,VVGARPQVNGQSGRI, 231  13 
4AD,VVGARPQVNGQSGRI, 231  13 
4AE,VVGARPQVNGQSGRI, 231  13 
4AF,VVGARPQVNGQSGRI, 231  13 
4BA,EISTRPKVNGQAGRM, 233  8 
4BB,EINTRPRVNGQAGRM, 233  8 
4BC,EISTRPKVNGQAGRM, 233  8 
4CA,NIGPRPLVRGQQGRM, 233  8 
4CB,NIGPRPLVREQQGRM, 233  7 
4DA,ETGVRPGYNGQRSWM, 234  6 
4DB,EIGIRPGYNGQKSWM, 234  6 
4DC,ETGVRPGYNGQRSWM, 234  6 
4EA,NIGSRPRVRNQSGRI, 238  9 
4EB,NIGSRPRVRNQSGRI, 238  9 
4FA,SPGARPKVNGQAGRI, 230  13 



42A,EIATRPKVNGLGSRM, 231  6 
43A,NIGSRPRVRDVSSRI, 237  7 

49A,VIGPRPLVNGHKGRI, 229  9 
49B,VIGPRPLVNGLQGRI, 229  9 
49C,LIGPRPLVNGLQGRI, 229  9 





4AB,IIGAPACDLHLTGRW, 82  4 
4GA,HTGTYCSLNGVSPIH, 61  4 
4GB,RPGERIMFESNGGLI, 256  5 
4GC,YPVVRGDYNNTTGRD, 180  5
 
Re: H7n9

snippets:

WHO update: http://www.who.int/csr/don/2013_04_07/en/index.html

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3165745/
A/Quail/Hong Kong/G1/1997 (H9N2) (H9N2/G1) with D253N and Q591K in the PB2

http://www.ncbi.nlm.nih.gov/pubmed/22416344
Q225L




2 other papers about h9n2 evolution

http://www.ncbi.nlm.nih.gov/pubmed/22416344
Samples of chicken, duck, quail, and pigeon were collected from Jiangsu, Anhui,
and Hebei in 2009-2011
amino acid motif of cleavage sites in the HA gene was P-S-R/K-S-S-R
Leucine (L) at the amino acid position 226 in the HA
AIVs originated from F98-like virus as backbone and formed two new genotypes through
reassortment with HA gene of Y280-like virus and PB2 and M genes of G1-like virus

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

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049224

there is variable homology among the various NA subtype sequences, especially
in the N1 and N2 subtypes with the deletion of 4~30 amino acids in the stalk domain [23,1993]
Meanwhile, the factors that influence NA include deletion of the stalk domain,
the mutations drug-resistance, as well as the changing of antigen sites or glycosites
and the variation of the topology of N-glycan structures [28,2011].
The pattern of stalk domain deletion in N2 NA is distinctive in different combinations of IVs.
The representative NA sequences in each available N2 subtypes are aligned in the stalk domain.
As can be observed, the number of deletions varies from 4 to 24 residues,
causing the loss of one or two potential glycosites.
9 NA subtypes are concentrated into two evolutionary groups: one group was represented by
N2 and contains N3, N6, N7, and N9; and another group contains N1, N4, N5, and N8.

deletion of 3 residues and one corresponding glycosite with the pattern “E-R-61N-3-64T-V-H”
(meaning 3 residues missing between 61N and 64T, e.g., A/chicken/Zhejiang/611/2011 (H9N2)),
appeared in most of the NA subtypes of the H9N2 virus.

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

the Shanghai/Ci {i=1..3} H9N2 chicken sequences from Jan.2012
look boguous.
Lots of clusters of mutations at neighboring nucleotides,
which is unusual
However, the other mutations look reasonable, so maybe
we should just delete all mutation-clusters in them ?!
C1 and C3 have N66S in PB1-F2

>A/chicken/Shanghai/C1/2012,2012/01/,H9N2
>A/chicken/Shanghai/C2/2012,2012/01/,H9N2
>A/chicken/Shanghai/C3/2012,2012/01/,H9N2

also some strange (pseudo)recombinations in the Zhejiang chickens
A/chicken/Zhejiang/329/2011(H9N2)
A/chicken/Zhejiang/607/2011(H9N2)



http://www.ncbi.nlm.nih.gov/nuccore/KC417064
REFERENCE 1 (bases 1 to 2274)
AUTHORS Ge,F.
TITLE Genetic variation of H9N2 subtype avian influenza virus isolates
from diseased chicken flocks of Shanghai in 2012
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 2274)
AUTHORS Ge,F.
TITLE Direct Submission
JOURNAL Submitted (22-DEC-2012) Veterinary Disease Diagnostic Center,
Shanghai Animal Disease Control Center, No. 30 Lane 855 Hongjing
Road Changning DC, Shanghai, Shanghai 201103, China
COMMENT GenBank Accession Numbers KC417046, KC417049, KC417052, KC417055,
KC417058, KC417061, KC417064, KC417067 represent sequences from the
8 segments of Influenza A virus (A/chicken/Shanghai/C1/2012(H9N2)).
Sequencing Technology :: Sanger dideoxy sequencing

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

AUTHORS Wu,H. and Wu,N.
TITLE Genetic characterization of subtype H9 avian influenza viruses in
Zhejiang, China
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1497)
AUTHORS Wu,H. and Wu,N.
TITLE Direct Submission
JOURNAL Submitted (05-JAN-2012) State Key Laboratory for Diagnosis and
Treatment of Infectious Diseases First Affiliated Hospital, School
of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou,
Zhejiang 310003, China
COMMENT GenBank Accession Numbers JQ356872, JQ356875, JQ356878, JQ356881,
JQ356884, JQ356887, JQ356890, JQ356893 represent sequences from the
8 segments of Influenza A virus
(A/chicken/Zhejiang/329/2011(H9N2)).

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

AUTHORS Wu,H. and Wu,N.
TITLE Genetic characterization of subtype H9 avian influenza viruses in
Zhejiang, China
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 2151)
AUTHORS Wu,H. and Wu,N.
TITLE Direct Submission
JOURNAL Submitted (05-JAN-2012) State Key Laboratory for Diagnosis and
Treatment of Infectious Diseases First Affiliated Hospital, School
of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou,
Zhejiang 310003, China
COMMENT GenBank Accession Numbers JQ356873, JQ356876, JQ356879, JQ356882,
JQ356885, JQ356888, JQ356891, JQ356894 represent sequences from the
8 segments of Influenza A virus
(A/chicken/Zhejiang/607/2011(H9N2)).

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





Code:
>A/chicken/Shanghai/C1/2012,2012/01/,H9N2,segment 5
>A/chicken/Jiangsu/Q3/2010,2010/02/,China,H9N2,segment 5
.....................................................o...... 1 
........o................................o.................. 2 
............................................................ 0 
............................................................ 0 
.........................................................o.. 1 
............................................................ 0 
.....o.............................o.....o.................. 3 
............................................................ 0 
............................................................ 0 
......o...o...o..o..........ooo......oo..............o...... 10 
.........o...............................o.....o............ 3 
......................................................o..... 1 
................................ooo............o............ 4 
...................................o.o...................... 2 
...........................oo....oo......................... 4 
.......................................oo......ooo......ooo. 8 
...........o.o..........................o.............oo.... 5 
..oo................o......................................o 4 
oo.....................ooo..................o...........ooo. 9 
........ooo................................................. 3 
...............o............................................ 1 
...................................o....o...oo........oo.... 6 
.....ooo.................................................... 3 
............................................................ 0 
.........................................................-- 70 


 70 ( 1497 )+ 70 ( 1497 )
 
Re: H7n9

H9N2 East-China Index (preliminary)

Code:
>A/poultry/index/East-China/2010,2009//,H9N2
ATGGAAAGAATAAAAGAACTAAGAGATTTGATGTCACAGTCTCGCACTCGCGAGATACTGACAAAAACAACTGTGGACCATATGGCCATAATCAAGAAATATACATCGGGAAGACAGGAGAAGAATCCTGCCCTTAGGATGAAGTGGATGATGGCGATGAAATATCCAATTACAGCAGACAAAAGGATAATGGAGATGATCCCGGAAAGAAATGAGCAAGGTCAGACCCTTTGGAGCAAGACAAATGATGCTGGATCAGACAGAGTGATGGTGTCACCTCTGGCTGTGACGTGGTGGAACAGAAATGGACCAACGACAAGTACAGTCCATTATCCAAAGGTCTATAAAACCTATTTTGAAAAGGTCGAAAGGCTAAAACATGGAACCTTCGGCCCCGTTCACTTCCGAAACCAGGTTAAAATACGCCGCAGGGTCGACATAAACCCAGGCCATGCAGATCTTAGTGCTAAAGAAGCACAAGATGTCATCATGGAGGTCGTATTCCCAAACGAAGTTGGAGCCAGAATATTGACATCAGAGTCACAGTTAACGATAACCAAGGAAAAGAAGGAGGAGCTTCAGGACTGCAAAATTGCCCCTTTAATGGTGGCCTACATGTTGGAGAGAGAACTGGTTCGCAAAACAAGATTTCTACCAGTAGCTGGAGGGACAAGCAGTGTGTATATCGAAGTGTTGCATTTGACCCAAGGGACCTGCTGGGAGCAAATGTACACACCGGGAGGGGAAGTGAGAAATGATGATGTTGATCAGAGTTTAATTATTGCTGCTAGAAATATTGTTAGAAGAGCAACAGTATCAGCAGACCCGTTGGCTTCGCTTTTGGAGATGTGCCATAGTACACAGATTGGCGGGGTTAGGATGGTTGACATCCTTAGACAAAACCCAACAGAAGAACAGGCTGTGGATATATGCAAGGCAGCAATGGGTCTAAGGATCAGTTCATCCTTCAGCTTTGGAGGTTTCACTTTCAAAAGGACAAGTGGGTCATCTGTCAAAAGGGAAGAAGAAGTGCTCACAGGCAACCTCCAAACATTGAAAATAAGAGTACATGAAGGATATGAGGAATTCACAATGGTCGGGCGAAGAGCAACAGCCATTCTAAGGAAAGCAACCAGAAGACTGATCCAACTGATAGTGAGTGGGAAAGACGAGCAATCAATCGCCGAGGCAATCATAGTGGCAATGGTGTTCTCACAAGAGGATTGTATGATAAAGGCAGTGAGAGGTGATTTGAACTTTGTCAACAGAGCGAACCAGCGGCTAAATCCCATGCATCAACTCCTGAGGCATTTCCAAAAGGATGCAAAGGTTCTGTTTCAAAACTGGGGAATTGAACCCATTGACAATGTAATGGGGATGATCGGAATATTGCCTGACATGACCCCCAGCACAGAGATGTCATTGAGAGGAGTGAGAGTTAGTAAAATGGGAGTAGATGAATATTCCAGTACTGAGAGAGTGGTCGTGAGTATTGATCGTTTCTTGAGGGTCCGAGACCAGAGGGGAAACGTACTCCTGTCTCCTGAAGAGGTTAGTGAAACACAGGGAACAGAAAAGCTGACTATAACATATTCATCGTCCATGATGTGGGAGATCAATGGTCCGGAATCAGTGCTAGTTAACACATATCAATGGATCATTAGAAATTGGGAAACTGTAAAGATTCAATGGTCCCAAGACCCTACAATGCTATACAATAAGATGGAGTTTGAACCCTTTCAATCCCTAGTGCCTAAAGCTGCCAGAGGCCAATATAGTGGGTTCGTAAGGGTGCTATTCCAGCAGATGCGTGACGTACTGGGGACATTTGATACTGTCCAAATAATAAAGCTATTACCATTTGCAGCAGCCCCGCCGGAGCAGAGTAGGATGCAGTTCTCTTCTCTAACTGTGAACGTGAGGGGTTCAGGAATGAGAATAGTTGTGAGAGGCAATTCTCCTGTGTTCAACTACAACAAGGCAACCAAGAGGCTTACAGTGCTTGGAAAGGATGCAGGTGCATTGATGGAAGACCCAGATGAGGGAACAGCAGGAGTGGAATCTGCGGTATTGAGAGGATTTCTGATTCTGGGCAAAGAAGACAAAAGATATGGGCCAGCATTGAGCATCAACGAATTGAGCAATCTTGCGAAAGGGGAGAAGGCTAATGTGTTGATAGGGCAAGGAGACGTGGTGTTGGTAATGAAACGGAAACGGGACTCTAGCATACTTACTGACAGTCAGACAGCGACCAAAAGGATTCGGATGGCCATCAATTAA
ATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTGCCAGTGCAAAATGCTATAAGTACCACGTTCCCTTATACTGGAGACCCTCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATAAATACTCAGAAAAAGGAAAGTGGACAACGAACACAGAGACTGGAGCACCCCAACTCAATCCGATTGATGGACCATTGCCTGAGGACAACGAGCCGAGTGGGTATGCACAAACGGATTGTGTATTGGAAGCAATGGCTTTCCTTGAAGAATCTCACCCAGGGATCTTTGAAAACTCGTGTCTCGAAACGATGGAAATTGTTCAGCAAACAAGAGTGGATAAACTGACCCAAGGCCGCCAGACCTATGACTGGACGTTGAATAGAAATCAGCCGGCTGCTACTGCATTGGCCAACACTATAGAGGTATTCAGATCGAATGGCCTGACAGCCAATGAATCAGGAAGGTTGATCGATTTCCTCAAGGACGTGATGGATTCAATGGATAAGGAAGAAATGGAGATTACAACACATTTCCAGAGGAAGAGGAGAGTGAGGGACAACATGACCAAGAAAATGGTCACACAGAGAACAATAGGAAAGAAAAAACAAAGACTGAACAAAAGGAGCTACCTAATAAGAGCACTGACATTGAACACAATGACAAAGGATGCTGAAAGAGGCAAGTTGAAAAGGAGGGCAATCGCAACACCCGGGATGCAAATCAGAGGATTCGTGTATTTTGTAGAAGCACTAGCGAGGAGCATCTGTGAGAAACTTGAGCAATCTGGCCTCCCTGTCGGAGGGAATGAGAAGAAAGCTAAATTGGCAAATGTTGTGAGGAAGATGATGACTAATTCACAAGATACAGAGCTCTCCTTCACAATTACTGGAGACAACACCAAATGGAATGAGAATCAAAACCCCCGGATGTTTCTAGCAATGATAACATACATCACAAGAAACCAGCCAGAATGGTTTAGAAATGTCTTAAGCATTGCTCCTATAATGTTCTCAAACAAGATGGCGAGATTAGGGAAAGGATACATGTTCGAAAGTAAGAGTATGAAGTTACGGACACAAGTACCAGCGGAAATGCTCGCAAATATTGACCTGAAATACTTCAACAAATCAACAAGAGAGAAAATCGAGAAAATAAGACCTCTACTGATAGATGGCACAGCCTCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGTTGAGTACAGTCTTAGGAGTTTCAATTCTGAATCTCGGGCAGAAGAAGTACACCAAAACCACATATTGGTGGGACGGACTCCAATCCTCAGATGACTTCGCCCTCATAGTGAATGCACCGAATCATGAGGGAATACAGGCAGGAGTGGATAGGTTCTATAGAACCTGCAAATTAGTTGGGATAAACATGAGCAAGAAGAAATCCTACATAAATCGGACAGGAACATTCGAATTCACAAGCTTTTTCTACCGCTATGGATTCGTAGCTAACTTCAGTATGGAGTTGCCCAGTTTTGGAGTGTCTGGGATTAATGAGTCAGCTGACATGAGCATTGGTGTTACAGTAATAAAGAACAATATGATAAACAACGATCTTGGACCAGCAACAGCTCAGATGGCCCTTCAGCTATTTATCAAAGACTACAGATACACATACCGATGTCACAGGGGTGATACGCAAATTCAAACGAGGAGAGCATTCGAGCTGAAGAAGCTGTGGGAGCAGACCCGTTCGAAGGCAGGACTGTTGGTTTCAGATGGAGGGCCAAACCTGTACAATATCCGGAACCTCCACATTCCAGAGGTCTGCTTGAAATGGGAATTGATGGATGAAGACTACCAAGGCAGGCTGTGTAATCCTATGAACCCGTTTGTCAGTCATAAGGAAATTGATTCCGTCAACAATGCTGTGGTGATGCCAGCTCATGGCCCAGCCAAAAGCATGGAGTATGATGCCGTTGCAACTACACATTCATGGATTCCTAAGAGGAATCGCTCCATTCTCAACACCAGCCAAAGGGGGATTCTTGAGGATGAACAGATGTACCAGAAGTGCTGCAACCTATTCGAAAAGTTCTTCCCCAGCAGTTCATACCGGAGGCCAGTTGGAATTTCCAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGAATTGATGCACGAATTGACTTCGAATCTGGAAGGATTAAGAAAGAAGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAGCTCAGACGGCAAAAATAG
ATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATCGTCGAGCTTGCGGAAAAGGCAATGAAAGAATATGGGGAAGATCCGAAAATCGAAACGAACAAATTCGCATCAATATGCACACACTTAGAAGTCTGCTTCATGTACTCTGATTTCCACTTCATTGACGAACGAGGCGAATCAACTATTATAGAATCTGGCGATCCAAATGCGTTGTTGAAACACCGATTTGAAATAATCGAAGGGAGAGACCGAACAATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACGGGAGTCGAGAAACCCAAATTTCTTCCGGATCTGTATGACTACAAGGAAAACCGATTCATTGAAATTGGAGTAACGAGGAGGGAAGTCCACATATACTACCTAGAGAAAGCCAATAAAATAAAATCCGAGAAGACACACATCCACATTTTCTCATTCACTGGAGAAGAGATGGCCACCAAAGCAGATTACACTCTTGACGAAGAAAGCAGGGCAAGAATCAAAACCAGGCTGTTCACCATAAGGCAGGAAATGGCCAGCAGGGGTCTATGGGATTCCTTTCGTCAGTCCGAAAGAGGCGAAGAAACAATTGAAGAAAGATTTGAAATCACAGGAACCATGCGCAGGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCAAAAGAAGTGAACGCCAGAATCGAGCCATTTCTAAGGACAACACCACGCCCTCTCAGATTGCCTAATGGGCCTCCCTGCTCTCAGCGGTCGAAATTCTTGCTGATGGATGCTCTGAAATTAAGCATTGAGGACCCGAGCCACGAAGGGGAGGGGATACCGCTATATGATGCGATCAAATGCATGAAAACGTTCTTCGGGTGGAAAGAGCCCAACATTATCAAACCACATGAGAAAGGCATAAACCCCAATTATCTCCTGACTTGGAAGCAGGTGCTAGCAGAACTTCAGGACATTGAAAATGAAGAGAAGATTCCAAAGACAAAGAACATGAAGAAAACAAGCCAATTAAAGTGGGCACTCGGTGAGAACATGGCACCGGAGAAGGTGGACTTTGAAGATTGCAAAGATGTCAACGACCTGAAACAGTACGACAGTGATGAGCCAGAGCCCAGATCACTAGCATGTTGGATCCAGAATGAATTCAACAAGGCATGTGAATTGACTGATTCAAGCTGGGTAGAACTTGATGAAATAGGGGAAGATGTTGCCCCAATCGAACACATTGCAAGCATGAGACGGAACTATTTTACAGCAGAGGTGTCCCACTGCAGGGCTACTGAATACATAATGAAGGGAGTGTACATAAATACAGCTTTGCTCAATGCATCTTGTGCGGCCATGGATGACTTTCAACTGATTCCAATGATAAGCAAATGCAGAACCAAAGAAGGAAGACGGAAAACAAACCTATATGGATTCATTATAAAAGGAAGATCTCATTTGAGGAATGATACCGACGTGGTAAACTTTGTAAGTATGGAATTTTCCCTTACCGACCCAAGGTTGGAACCACATAAATGGGAAAAGTATTGTGTTCTTGAAATAGGGGACATGCTCCTGCGAACTGCAGTAGGCCAAGTGTCAAGGCCCATGTTTCTGTATGTGAGAACCAATGGGACCTCCAAGATCAAGATGAAATGGGGTATGGAAATGAGACGCTGCCTTCTTCAATCTCTCCAACAGATTGAGAGCATGATTGAAGCTGAATCCTCCGTCAAAGAGAAAGACCTGACCAAAGAATTCTTTGAAAACAAATCAGAAACATGGCCAATTGGAGAATCACCTAAGGGAGTGGAGGAAGGTTCCATCGGAAAGGTGTGCAGAACCTTACTAGCAAAATCTGTATTCAACAGCCTATATGCATCTCCACAACTCGAGGGGTTCTCAGCTGAATCGAGAAAACTGCTACTCATTGTTCAGGCGCTTAGGGATAACCTGGAACCTGGAACCTTCGATCTTGAAGGGCTATATGAAGCAATCGAGGAGTGCCTGATTAATGATCCCTGGGTTTTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTAAGATAG
ATGGAAGTAGTATCACTAATAACTATACTACTAGTAGTAACAGTAAGCAATGCAGATAAGATCTGCATCGGCTATCAATCAACAAACTCCACAGAAACTGTAGACACACTAACAGAAAACAATGTCCCTGTGACACATGCCAAAGAACTGCTCCACACAGAGCATAATGGGATGCTGTGTGCAACAAGCTTGGGACACCCTCTTATTCTAGACACCTGTACCATTGAAGGACTAATCTATGGCAATCCTTCTTGTGATCTATTGTTGGGAGGAAGAGAATGGTCCTATATCGTCGAGAGACCATCAGCTGTTAACGGATTGTGTTATCCCGGGAATGTAGAAAATCTAGAAGAGCTAAGGTCACTTTTTAGTTCTGCTAGGTCTTATCAAAGGATCCAGATTTTCCCAGACACAATCTGGAATGTGTCTTACAGTGGGACAAGCAAAGCATGTTCAGATTCATTCTACAGAAGCATGAGATGGTTGACTCAAAAGAACAACGCTTACCCTATTCAAGACGCCCAATACACAAATAATCAAGAAAAGAACATTCTTTTCATGTGGGGCATAAATCACCCACCCACCGATACTGCGCAGACAAATCTGTACACAAGAACCGACACAACAACGAGTGTGGCAACAGAAGAAATAAATAGGACCTTCAAACCATTGATAGGACCAAGGCCTCTTGTCAACGGTTTGATGGGAAGAATTGATTATTATTGGTCGGTATTGAAACCGGGTCAAACACTGCGAATAAGATCTAATGGGAATCTAATAGCTCCATGGTATGGACACATTCTTTCAGGAGAGAGCCACGGAAGAATCCTGAAGACTGATTTAAAAAGGGGTAGCTGCACAGTGCAATGTCAGACAGAGAAAGGTGGCTTAAACACAACATTGCCATTCCAAAATGTAAGTAAGTATGCATTTGGAAACTGCTCGAAATACATTGGCATAAAGAGTCTCAAACTTGCAGTTGGTCTGAGGAATGTGCCTTCTAGATCTAGTAGAGGACTATTCGGGGCCATAGCAGGATTCATAGAGGGAGGTTGGTCAGGACTAGTTGCTGGTTGGTATGGATTCCAGCATTCAAATGACCAAGGGGTTGGTATGGCAGCAGATAGAGACTCAACCCAAAAGGCAATTGATAAAATAACATCCAAAGTGAATAACATAGTCGACAAAATGAACAAGCAGTATGAAATTATTGATCATGAATTCAGCGAGGTTGAAACTAGACTTAACATGATCAATAATAAGATTGATGATCAAATCCAAGATATATGGGCATATAATGCAGAATTGCTAGTTCTGCTTGAAAACCAGAAAACACTCGATGAGCATGATGCAAATGTAAACAATCTATATAATAAAGTGAAGAGGGCGTTGGGTTCCAATGCGGTGGAAGATGGGAAAGGATGTTTCGAGCTATACCACAAATGTGATGACCAGTGCATGGAGACAATTCGGAACGGGACCTACAACAGAAGGAAGTATCAAGAGGAGTCAAAATTAGAAAGACAGAAAATAGAGGGGGTCAAGCTGGAATCTGAAGGAACTTACAAAATCCTCACCATTTATTCGACTGTCGCCTCATCTCTTGTGATTGCAATGGGGTTTGCTGCCTTCTTGTTCTGGGCCATGTCCAATGGGTCTTGCAGATGCAACATTTGTATATAA
ATGGCGTCTCAAGGCACCAAACGATCCTATGAACAGATGGAAACTGGTGGGGAACGCCAGAATGCTACTGAGATCAGGGCATCTGTTGGAAGAATGGTTAGTGGCATTGGGAGATTCTACATACAGATGTGTACAGAACTCAAACTCAGTGACAATGAAGGGAGGCTGATTCAGAACAGTATAACAATAGAGAGAATGGTACTCTCTGCATTTGATGAAAGAAGGAACAGATACCTGGAAGAGCACCCCAGTGCAGGAAAGGACCCTAAGAAAACTGGAGGTCCAATTTACAGGAGAAGAGACGGGAAATGGGTGAGAGAGCTGATCCTGTATGACAAAGAGGAAATCAGGAGAATTTGGCGACAAGCGAACAATGGAGAGGATGCAACTGCTGGTCTTACCCATCTGATGATATGGCATTCCAACCTGAATGATGCCACCTATCAGAGAACGAGAGCTCTCGTGCGTACTGGAATGGATCCCCGGATGTGCTCTCTGATGCAAGGATCAACTCTTCCGAGGAGATCTGGAGCTGCAGGTGCAGCAGTAAAGGGGATAGGGACAATGGTGATGGAACTGATTCGGATGATAAAACGAGGGATCAACGACCGGAATTTCTGGAGAGGCGAAAATGGAAGAAGGACAAGGATTGCATACGAGAGGATGTGCAACATCCTCAAAGGGAAATTCCAAACAGCAGCACAAAGGGCAATGATGGATCAAGTGCGAGAGAGCAGAAATCCTGGGAATGCTGAAATAGAAGATCTCATTTTTCTGGCAAGGTCTGCACTCATCCTGAGAGGATCAGTGGCTCATAAGTCCTGCTTGCCTGCTTGTGTGTACGGACTTGCAGTGGCCAGTGGATATGACTTTGAGAGAGAAGGGTACTCCCTGGTTGGAATAGATCCTTTCCGTCTGCTTCAAAACAGCCAGGTCTTTAGTCTCATTAGACCAAATGAGAACCCAGCACATAAGAGCCAATTAGTGTGGATGGCATGCCACTCTGCAGCATTTGAGGACCTTAGGGTCTCAAGTTTCATTAGAGGGACAAGAATGGTCCCAAGAGGACAGCTATCCACTAGAGGGGTTCAAATTGCTTCAAATGAGAACATAGAAGCAATGGACTCCAATACTCTTGAACTGAGAAGTAGATATTGGGCTATAAGAACCAGAAGCGGAGGAAACACCAACCAACAGAGGGCATCTGCAGGACAGGTCAGCGTTCAACCCACTTTCTCAGTACAGAGAAATCTTCCCTTCGAAAGAGCAACCATTATGGCAGCATTTACAGGAAATACTGAGGGTAGAACGTCTGACATGAGGACTGAAATCATAAGAATGATGGAAAGTGCCAGACCAGAAGATGTGTCATTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAATAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAGGAGTATGACAATTAA
ATGAACCCAAATCAGAAGATAATAGCAATTGGCTCTGTTTCTCTAACCATTGCGATAATATGTTTTCTCATGCAGATTGCCATCTTAACAACGACCATGACACTACATTTCAGGCAGAATGAATGCAGCAATCCATCGAATAATCAAGTGGTGCCATGTGAACCTATCATAATAGAGAAGAACACAGTGCATTTGAATAGTACTACCATAGAGAAGGAAATTTGTCCTAAAGTGGCAGAATACAAGAATTGGTCAAAACCACAATGTCAAATTACAGGGTTCGCTCCTTTCTCAAAGGACAACTCAATTAGGCTTTCTGCAGGTGGAGATATCTGGGTGACAAGAGAACCTTATGTGTCGTGCAGTCTTGGCAAATGTTATCAATTTGCACTTGGGCAGGGAACCACTCTGAAAAACAAGCACTCAAATGGCACTACACATGATAGAATTCCTCACAGAACTCTCTTAATGAATGAGTTAGGTGTCCCATTTCATTTGGGAACCAAACAAGTGTGCATAGCATGGTCTAGTTCAAGCTGCCATGATGGGAAAGCATGGTTACATATTTGTGTGACTGGGGATGATAAAAATGCTACTGCTAGTATCATTTATGATGGGATGCTGGCTGACAGTATTGGTTCATGGTCCAAAAACATCCTAAGAACCCAGGAGTCAGAATGCGTTTGCATCAATGGAACTTGTGCAGTGGTAATGACTGATGGAAGTGCATCAGGAAAGGCTGACACTAGAATATTATTCATAAGAGAGGGGAAAATTATAAATATTAGCCCATTGTCAGGAAGTGCTCAGCATGTGGAGGAATGTTCCTGTTACCCCCGGTATCCTGAAGTTAGGTGTGTTTGCAGAGACAACTGGAAGGGCTCCAATAGGCCCGTTCTATATATAAATATGGCAGATTATAGTATTGAGTCCAGTTATGTATGCTCAGGACTTGTTGGCGACACACCAAGAGATGATGATAGCTCCAGCAGCAGTAACTGTAGAGACCCTAATAACGAAAGAGGGGCCCCAGGAGTGAAAGGGTGGGCCTTTGACGATGGGAATGACATTTGGATGGGACGAACAATCAAAAGTGATTCACGCTCAGGTTATGAGACTTTTAGGGTCGTTAATGGTTGGACCACGGCTAATTCCAAGTCACAGGTAAATAGGCAAGTCATAGTTGACAGTGACAGCTGGTCTGGGTATTCTGGTATCTTCTCTGTTGAAGGCAAGAACTGCATCAACAGGTGTTTTTATGTGGAGTTGATAAGAGGGAGACCACAGGAGACCAGAGTGTGGTGGACTTCAAACAGCATCATTGTATTCTGTGGAACCTCAGGTACATATGGAACAGGCTCATGGCCTGATGGAGCGAATATCGACTTCATGCCTATATAA
ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATTCCATCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAGGATGTTTTTGCAGGGAAGAACGCAGATCTCGAGGCTCTCATGGAGTGGATAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCCTAAATGGGAATGGAGACCCAAACAACATGGACAAGGCAGTTAAATTATACAAGAAACTGAAGAGGGAAATGACATTTCATGGAGCAAAGGAAGTTGCACTCAGTTACTCAACTGGTGCGCTTGCCAGCTGCATGGGTCTCATATACAACAGGATGGGGACAGTAACCGCAGAAGGGGCTCTTGGACTAGTATGTGCCACTTGTGAGCAGATTGCTGACGCACAACATCGGTCCCACAGGCAGATGGCGACTACTACCAACCCACTAATTAGGCATGAGAATAGAATGGTACTAGCCAGCACTACGGCTAAGGCTATGGAGCAGATGGCTGGATCAAGTGAACAGGCAGCGGAAGCCATGGAAGTCGCAAGTCAGGCTAGGCAAATGGTGCAGGCTATGAGAACAGTCGGGACTCACCCTAACTCCAGTACAGGTCTAAAAGATGATCTTATTGAAAATTTGCAGGCTTACCAGAACCGGATGGGAGTGCAACTGCAGCGGTTCAAGTGATCCTCTCGTTGTTGCAGCTAACATTATTGGGATATTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAATGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTG-AGTAA
ATGGATTCCAACACTGTGTCAAGCTTCCAGGTAGACTGCTTTCTTTGGCATGTCCGCAAACGATTTGCAGACCAAGAACTGGGTGATGCCCCATTTCTAGACCGGCTTCGCCGAGATCAGAAGTCCCTGAGAGGAAGAAGCAGCACTCTTGGTCTGGACATCAGAACTGCTACTCGTGAAGGAAAGCATATAGTGGAACGGATTTTAGAGGACGAGTCAGATGAAGCATTTAAAATGAGTATTGCTTCAGTGCCAGCTCCACGCTATCTAACTGACATGACTCTTGAAGAAATGTCAAGAGATTGGTTAATGCTCATTCCCAAACAGAAAGTGACAGGGTCCCTTTGCATTAGAATGGACCAAGCAATAGTGGACAAAAACATCACATTGAAAGCAAATTTCAGTGTGATTTTCAATCGACTTGAAGCCCTGATACTACTTAGAGCTTTTACGGAAGAAGGAGCAATTGTGGGCGAAATCTCACCATTACCTTCTCTTCCAGGACATACTGACAAGGATGTCAAAAATGCAATTGAGGTCCTCATCGGAGGATTTGAATGGAATGATAACACAGTTCGAGTCTCTGAAACTCTACAGAGATTCGCTTGGAGAAGCAGCGATGAGGATGGGAGACCTCCACTCTCTACAAAGTAGAAACGGGAAATGGAGAGAACAGCTAAGCCAGAAGTTCGAAGAAATAAGATGGTTGATTGAAGAAGTACGACATAGATTAAAGATTACGGAGAATAGCTTTGAGCAAATAACTTTTATGCAAGCCTTACAACTATTGCTTGAAGTGGAGCAAGAGATAAGAACTTTCTCGTTTCAGCTTATTTAA

d(i_bird)=(5,12,16,-,10,-,27,31)


-----------update 25.May.2013 , new segment 7 published from March,April from Nanjing,Taiwan,Shanghai------
Code:
>A/Index_poultry_East-China/2008//,H9N2
ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATTCCATCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAGGATGTTTTTGCAGGGAAGAACACAGATCTTGAGGCTCTCATGGAATGGATAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCCTAAATGGGAATGGAGACCCAAACAACATGGACAGGGCAGTTAAATTATACAAGAAGCTGAAGAGGGAAATGACATTTCATGGAGCAAAGGAAGTTGCACTCAGTTACTCAACTGGTGCGCTTGCCAGCTGCATGGGTCTCATATACAACAGGATGGGAACAGTGACCGCAGAAGGGGCTCTTGGCCTAGTATGTGCCACTTGTGAGCAGATTGCTGACGCCCAACATCGGTCCCACAGGCAGATGGCGACTACTACCAACCCACTAATTAGGCATGAGAATAGAATGGTACTAGCCAGCACTACGGCTAAGGCTATGGAGCAGATGGCTGGATCAAGTGAACAGGCAGCAGAAGCCATGGAAGTCGCAAGTCAGGCTAGGCAAATGGTGCAGGCTATGAGAACAGTCGGGACTCACCCTAGCTCCAGTACAGGTCTAAAAGATGATCTTATTGAAAATTTGCAGGCTTACCAGAAACGGATGGGAGTGCAACTGCAGCGATTCAAGTGATCCTCTCGTTGTTGCAGCAAGCATTATTGGGATATTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAGTGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTGGAGTAA

d=25,28
 
Re: Is H7N9 Spreading from Human to Human in China?

Re: Is H7N9 Spreading from Human to Human in China?

> The N9 gene was identical to a virus found in wild birds from South Korea.

I will believe it when I see the sequence at genbank

---------------------------------------------------
http://www.newfluwiki2.com/diary/1591/
08/19/2007,Nebraska,poultry farm near Seward,turkeys,H7N9 low path,
meaning it was not a threat to human health ... Steffen said
---------------
to low- pathogenicity H7N9 was detected in US flocks in 2007, 2009, and 2011. "I believe
chickens and turkeys in Nebraska, Minnesota, Illinois, Kentucky,
-----------------------------------------
 
risk statements

risk statements

Frieden:
> Because few people spend time around live chickens, it is unlikely to develop into a full-blown pandemic.
> we have a system in place that's more prepared than ever to respond to emergencies

Cox:
> In some ways, H7N9 is more worrisome than H1N1 was

One scientist:
> the sequence raised concern about a potential global epidemic but it was impossible
> to give a precise estimate of the likelihood

Webby:
> At this stage it's still unlikely to become a pandemic

Garcia Sastre:
> Most likely, the main sources of the virus are chickens and duck farms
> At this moment it’s very unclear how much of a danger the virus poses,
> The flu is very unpredictable.
> I don’t think it’s a threat unless it starts spreading from human to human,
> which I think is unlikely. We need to know a little more about the epidemiology
> of the virus, but I really don’t think it’s a big threat.

reporter:
> and public health officials are worried it could become a worldwide pandemic

WHO:
> a pandemic is unlikely, given that there is no evidence of person-to-person transmission of the virus.
Hartl:
> The source of contagion could be contact with birds or mere proximity to them

Garrett:
> We need to know how are these people getting infected.Who are they getting it from?
> We need to know what's the denominator. How many people out there in China are
> infected right now with this virus harmlessly or with very mild illness? Third, we need
> to know what species did this come from. Did it come from birds? Did it come from dead pigs?
> Did it come from other animals of some kind? Until we have those three big questions answered,
> we have no capacity to speculate about the probability that this will become the next great pandemic.

it seems that soon these questions will be answered, Will she speculate about the probability then
or will she find another excuse ? I'm at 80% for the latter currently.

http://biosurveillance.typepad.com/
Ascel Bio:
> NCoV Presently "Bigger Concern" Than H7N9
Ascel Bio's analysis is based on official disclosures and other open source reports.
Ascel Bio is monitoring over 200 seasonal diseases in over 17 countries on behalf of our customers
since 2010 www.ascelbio.com

CDC:
as CDC scientists stepped up efforts to determine its pandemic risk.
There is no evidence that the H7N9 bird flu

Cox:
> I'd have to say that it's very similar to the level of concern for H5N1 in many respects.
> H5N1 viruses have a very wide geographic spread, while that's not known to be the case with H7N9,
> But on the other hand, , the fact that we're hearing about an additional two to maybe five cases
> per day in China sort of raises the level of concern in the opposite direction in favor of H7N9.

Derek Smith:
> If what we know about these mutations in other flu subtypes is also the case for this virus,
> then it's already part way there,That's why everybody is concerned about this.

Fouchier:
> All pandemic viruses have acquired this [mammalian cell] binding and polymerase activity,
> The H7N9 has these characteristics. So the question is, what else does it need – if anything?

Garcia-Sastre
> while it is too early to be able to conclude anything … the probabilities are very low
> that a global pandemic is looming.
> I am comforted by the lack of a surge in the numbers of people with the disease.
> It’s not that it’s increasing by ten times per week, I think right now the number of cases
> is what you would have expected from the original numbers
> Right now there are no major indications to become highly alarmed.

Oxford
> the situation in China is getting a little more worrying.
> I don’t like the sound of it. Every day I open up the reports and find out someone else has died,
> I just don’t like to see the figures going up day after day.
> So far there’s no human-to-human transmission. What’s tomorrow going to bring, what’s the
> next day going to bring? You don’t know and I don’t know,
> there is no need for anyone to start flapping at the moment.
> I don’t think we should start thinking of 1918 scenarios, definitely not

McCauley
> We’re watching very carefully the events there [in China] because we are aware although
> there’s no human-to-human transmission, these are unusual infections people have been
> getting from an avian reservoir,“China will need to identify the source and hopefully be able
> to control the cross-species transmission,We’re watching very carefully to see how it does.
> In the meantime, the national influenza centers around the world are developing their ability
> to detect this newly emerging virus” and also working on vaccines,
> Experts need to find out how vaccines would perform in case this virus becomes pandemic

Webby
> My gut feeling, at this point in time, is that this guy [H7N9] is probably closer to
> doing it, [h2h as compared to H5N1]

Cox
> the coming weeks may tell whether H7N9 is only a bird disease that occasionally spills
> over into humans, the potential seed of a dangerous global flu pandemic, or something in between.

Haertl, 2013.04.16
> It is premature to dismiss the possibility of an #H7N9 pandemic or to say the outbreak is under control.

Lipsitch,2013.04.15
> It's too soon to say how big a threat H7N9 poses because we don't know how many animals
> of which species have it, how genetically diverse it is, or what the geographic extent is.
> It looks as though it will be at least as challenging as H5N1
> If that pace keeps up or accelerates, H7N9 "could be a significant public health problem
> even if it remains an infection that people catch from animals

Farrar,2013.04.15
> I think we need to be very, very concerned about the latest developments,
> Perhaps counterintuitively, such mild cases are very worrying. That is because reduced virulence
> can often point to further genetic adaptation of the virus to infection of human beings —
> and thus greater potential to spread.

Xinhua,2013.04.16
> H7N9 under control


-----------------------------------------
statflu
http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19256
-----------------------------------------------------------
May,08,2013
Dr. Daniel Jernigan, deputy director of CDC's influenza division,
> people who get it [H7N9] usually get very sick,
Fauci:
> The pandemic-preparedness engines are already humming,
After all, health officials can't just kill every chicken in China.
There are lots of chickens in China. (~14B)

---------------------------------------------------------
June,01,2013 , Liu W, Zhu Y, Qi X, Xu K, Ge A, Ji H, Ai J, Bao C, Tang F, Zhou M. write:
> Briefly, it is highly unlikely that a pandemic of human infection with avian influenza A (H7N9)
> Avirus will happen in Jiangsu Province in the near future.
http://www.ncbi.nlm.nih.gov/pubmed/23720670
----------------------------------------------------------------
 
Re: H7n9

onset2.txt : Sharon's list in computer-form

60 cases by 10-year-age-groups 0-4,5-14,15-24,etc.
60 cases by (estimated) onset-day
weekly cases by onset date
weekly hospitalisations

attachment.php



(to be updated)



here are better and bigger charts:
http://www.uq.edu.au/vdu/VDUInfluenza_H7N9.htm

http://www.cidrap.umn.edu/cidrap/files/78/mceirs_h7n9_graphs.pdf

-----------------------------------------
we observe that elderly individuals have strongest resistance to IVA partly by
presenting more terminal α2-3/6-linked sialic acid residues in their saliva,
which bind with the influenza viral hemagglutinations
------------------------------------------
 

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Re: H7n9

they have a full genome at genbank today:
A/Zheijiang/DTID-ZJU01/2013/04/03(H7N9) , male , Apr.3, severe case

627E(1),HA identical to Anhui/1,PA reassorted
(MRCAD ~2010/08 from public H9N2)

which of our cases is that

-----------------------
Apr.3:
The Zhejiang Provincial Health Department said laboratory tests have confirmed that a 38-year-old cook
who died last month was suffering from avian influenza, which is better known as bird flu.
The tests showed he had contracted H7N9, which is a relatively new strain that was only known to infect birds.
Authorities said the man, who worked in neighboring Jiangsu Province, became ill on March 7,
was hospitalized on March 18, and died on March 27. A second person, a 67-year-old retired man
from Zhejiang province, has also tested positive for H7N9 after becoming ill on March 25 with fever,
cough and other symptoms. He was later hospitalized but his condition was not immediately known.
 
Re: H7n9

A/chicken/Zhejiang/DTID-ZJU01/2013(H7N9) at genbank, call this Z2

fecal samples, Apr-2013

Z2 has 21 differences in HA and 11 in NA from S1
that makes me change my estimate of the first
H9N2+H7N9 reassortment to ~late 2011, 1-2 years ago
------edit----- but 10 of these mutations are concentrated at 108-321
and 6 are nonsynonymous, strange. So cancel my 1-2 year estimate again
we may be seeing strong selection in HA
that could mean frequent exchange between 2,3 and 2,6 hosts (speculation)
------------

KC899666-KC899673
http://www.ncbi.nlm.nih.gov/nuccore/KC899666
http://www.ncbi.nlm.nih.gov/nuccore/KC899667
http://www.ncbi.nlm.nih.gov/nuccore/KC899668
http://www.ncbi.nlm.nih.gov/nuccore/KC899669
http://www.ncbi.nlm.nih.gov/nuccore/KC899670
http://www.ncbi.nlm.nih.gov/nuccore/KC899671
http://www.ncbi.nlm.nih.gov/nuccore/KC899672
http://www.ncbi.nlm.nih.gov/nuccore/KC899673
 
Re: H7n9

when we remove the segments that are obviously reassorted
subsequently or look fishy, then the diversity is very low.
Much lower than what we saw with ****** after only
~3 months of evolution in end April 2009.
I remember we had a few sequences in Mexico that had
only 2-4 mutations in the whole genome as late as mid April
while the others had already 10-20 mutations.
We never found a good explanation for this.

In the list below I removed segments 2,4,5,6 from S1,3 from Z1, 4 from Z2.
1,2,3,5,8 from H1 were not available to me.
Maybe someone with access to gisaid can complete the list.
Also with the 3 missing nonhuman genomes.
I removed the position numbers and only used "X" for different nucleotides,
so the list should be gisaid-secrecy-compatible.

Code:
Index/2013_79,5                               ............ .... .X.X .... . ........ ..... .... 
A/Shanghai/1/2013,H7N9                        XXXX..XXX... ---- .XXX ---- - -------- .X... .XX. 
A/Anhui/1/2013,H7N9                           ............ .X.. X... .... . ...X.... ..... .... 
A/Shanghai/2/2013,H7N9                        .....X...X.. X... .... ..X. . X....... ..... .... 
A/Hangzhou/1/2013/03/24,H7N9                  ------------ ---- ---- X..X - .X...... ...XX ---- 
A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9        ......X...XX ...X ---- .... X ....X.XX X.... ...X 
A/Ck/Zhejiang/DTID-ZJU01/2013,2013/04/,H7N9   ....X.....X. ..X. .... .X.. . ..X..XX. ..X.. X...


differences from the index

|12345678|
--+--------+
S1|7-3---12|
A1|01100100|
S2|21010100|
H1|---2-12-|
Z1|31--1311|
Z2|21010311|
--+--------+

with an average of 2.8,1.0,1.0,1.0,0.3,1.8,.8,0.8
mutations away from the index in the 8 segments or
9.5 mutations in the whole genome. That gives a dating
of the index 3.6 months ago, well compatible with the
Chinese New Year movements.

The H7N9 reassortment may well have happened earlier,
but then there was a bottleneck ~3 months ago, and the
currently circulating H7N7 almost all descends from
that one bottleneck virus in all segments.


This is different from my first analysis, when only
S1,A1,S2 were available and I assumed reassortments.
In this new scenario/hypothesis the many mutations
in HA and NA would be due to selection pressure
or sequencing errors or prolonged disease in S1
and the initial H7N7 reassortment only happened
early this year.

We will soon get more reliable estimates when new
sequences come in. Hopefully also some H9N2 poultry
sequences, that show the subsequent reassortments.
 
Re: H7n9

here is my H7N9 index-virus, the one that I think made
the initial H9N2+H7N9-->H7N9 reassortment in early 2013

(or bottleneck/superspreader virus or subsequent reassortment virus,
while earlier viruses died or were not found yet)


Code:
>A/Index/H7N9-China/2013/03/,H7N9
ATGGAAAGAATAAAAGAACTAAGAGATTTGATGTCACAGTCTCGCACTCGCGAGATACTGACAAAAACAACTGTGGACCATATGGCCATAATCAAGAAATATACATCAGGAAGACAGGAGAAGAATCCTGCCCTTAGGATGAAGTGGATGATGGCAATGAAATATCCAATTACGGCAGACAAAAGGATAATGGAGATGATCCCGGAAAGAAATGAGCAAGGTCAGACCCTTTGGAGCAAGACAAATGATGCTGGATCAGACAGAGTGATGGTGTCACCTCTGGCTGTGACGTGGTGGAACAGAAATGGACCAACGACAAGCACAGTCCATTATCCAAAGGTCTATAAAACCTATTTTGAAAAGGTCGAAAGGCTAAAACATGGAACCTTCGGCCCCGTTCACTTCAGAAACCAGGTTAAAATACGCCGCAGGGTCGACATAAACCCGGGCCATGCAGATCTTAGTGCTAAAGAAGCACAGGATGTCATCATGGAGGTCGTATTCCCAAACGAAGTTGGAGCCAGAATATTGACATCAGAGTCACAGTTAACGATTACCAAGGAAAAGAAGAAGGAGCTTCAGGACTGCAAAATTGCCCCTTTAATGGTGGCTTACATGTTGGAGAGAGAACTGGTTCGCAAAACAAGATTCCTACCAGTAGCTGGAGGGACAAGCAGCGTGTATATCGAGGTGTTGCATTTGACCCAAGGGACCTGCTGGGAGCAAATGTACACACCGGGAGGGGAAGTGAGAAATGATGATGTTGATCAGAGTTTAATTATTGCTGCTAGAAATATTGTTAGAAGAGCAACAGTATCAGCAGACCCGTTGGCTTCGCTTTTGGAGATGTGCCATAGTACACAGATTGGCGGGGTTAGGATGGTTGACATCCTTAGACAAAACCCAACAGAAGAACAGGCTGTGGATATATGTAAGGCAGCAATGGGTCTAAGGATCAGTTCATCCTTCAGCTTTGGAGGTTTCACTTTCAAAAGGACAAGTGGGTCATCTGTCAAAAGGGAAGAAGAAGTGCTCACAGGCAACCTCCAAACATTGAAAATAAGAGTACATGAAGGATATGAGGAATTCACAATGGTCGGGCGAAGAGCAACAGCCATTCTAAGGAAAGCAACCAGAAGACTGATCCAACTGATAGTGAGTGGGAAAGACGAGCAATCAATCGCCGAGGCAATCATAGTGGCAATGGTATTCTCACAAGAGGATTGTATGATAAAGGCAGTGAGAGGTGATTTGAACTTTGTCAACAGAGCAAACCAGCGGCTAAATCCCATGCATCAACTCCTGAGGCATTTCCAAAAGGATGCAAAGGTCCTGTTTCAAAACTGGGGAATTGAACCCATTGACAATGTAATGGGGATGATCGGAATATTGCCTGACATGACCCCCAGCACAGAGATGTCATTGAGAGGAGTGAGAGTTAGTAAAATGGGAGTAGATGAATATTCCAGCACTGAGAGAGTGGTCGTGAGTATTGATCGTTTCTTGAGGGTCCGAGACCAGAGGGGAAACGTACTCCTGTCTCCTGAAGAGGTTAGTGAAACACAGGGAACAGAAAAGCTGACTATAACATATTCATCGTCCATGATGTGGGAGATCAATGGTCCGGAATCAGTGCTAGTTAACACATATCAATGGATCATTAGAAATTGGGAAAATGTAAAGATTCAATGGTCCCAAGATCCTACAATGCTATACAATAAGATGGAATTTGAACCCTTTCAATCCCTAGTGCCTAAAGCTGCCAGAGGCCAATATAGTGGGTTCGTGAGGGTTCTATTCCAACAGATGCGTGACGTACTGGGAACATTTGACACTGTCCAAATAATAAAGCTATTACCATTTGCAGCAGCCCCGCCGGAGCAGAGTAGGATGCAGTTCTCTTCTCTAACTGTGAATGTGAGGGGTTCCGGAATGAGAATAGTTGTGAGAGGCAATTCTCCTGTGTTCAACTACAACAAGGCAACCAAGAGGCTTACGGTGCTTGGAAAGGATGCAGGTGCATTGATGGAAGACCCCGATGAGGGAACAGCAGGAGTGGAATCTGCGGTATTGAGGGGATTTCTGATTCTGGGCAAAGAAGACAAAAGATATGGGCCAGCATTGAGCATCAACGAATTGAGCAATCTTGCGAAAGGAGAGAAGGCTAATGTGTTGATAGGGCAAGGAGACGTTGTGTTGGTGATGAAACGGAAACGGGACTCTAGCATACTTACTGACAGTCAGACAGCGACCAAAAGGATTCGGATGGCCATCAATTAA
ATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTGCCAGTGCAAAATGCTATAAGTACCACTTTCCCTTATACTGGAGACCCTCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATAAATACTCAGAAAAAGGAAAGTGGACAACGAACACAGAGACTGGAGCACCCCAACTCAATCCAATTGATGGACCATTACCTGAGGACAACGAGCCGAGTGGGTATGCACAAACGGATTGTGTATTGGAAGCAATGGCTTTCCTTGAAGAATCTCACCCAGGGATCTTTGAAAACTCGTGTCTCGAAACGATGGAAATTGTTCAGCAAACAAGAGTGGATAAACTGACCCAAGGCCGCCAGACCTATGACTGGACGTTGAATAGAAATCAGCCGGCTGCTACCGCATTGGCCAACACTATAGAGGTATTCAGATCGAATGGCCTGACAGCCAATGAATCAGGAAGGTTGATCGATTTCCTCAAGGACGTGATGGATTCAATGGATAAGGAAGAAATGGAGATTACAACACATTTCCAGAGGAAGAGGAGAGTGAGGGACAACATGACCAAGAAAATGGTCACACAGAGAACAATAGGAAAGAAAAAACAAAGACTGAACAAAAGGAGCTACCTAATAAGAGCACTGACATTGAACACAATGACAAAGGATGCTGAAAGAGGCAAGCTGAAAAGGAGGGCAATCGCAACACCCGGGATGCAAATCAGAGGATTCGTGTATTTTGTAGAAGCACTAGCGAGGAGCATCTGTGAGAAACTTGAGCAATCTGGCCTCCCTGTCGGAGGGAATGAGAAGAAAGCTAAATTGGCAAATGTTGTGAGGAAGATGATGACTAATTCACAAGATACAGAGCTCTCCTTCACAATTACTGGGGACAACACCAAATGGAATGAGAATCAAAACCCCCGGATGTTTCTAGCAATGATAACATACATCACAAGAAACCAGCCAGAATGGTTTAGAAATGTCTTAAGCATTGCTCCTATAATGTTCTCAAACAAGATGGCGAGATTAGGAAAAGGGTACATGTTCGAAAGTAAGAGTATGAAGTTACGGACACAAGTACCAGCGGAAATGCTCGCAAATATTGACCTGAAATACTTCAACAAATCAACAAGAGAGAAAATCGAGAAAATAAGACCTCTACTGATAGATGGCACAGCCTCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGTTGAGTACAGTCTTAGGAGTTTCAATTCTGAATCTCGGGCAGAAGAAGTACACCAAAACCACATATTGGTGGGACGGACTCCAATCCTCAGATGACTTCGCCCTCATAGTGAATGCACCGAATCATGAGGGAATACAGGCAGGAGTAGATAGGTTCTATAGAACCTGCAAATTAGTTGGGATAAACATGAGCAAGAAGAAATCCTACATAAATCGGACAGGAACATTCGAATTCACAAGCTTTTTCTACCGCTATGGATTCGTAGCTAACTTCAGTATGGAGTTGCCCAGTTTTGGAGTGTCCGGGATTAATGAGTCAGCTGACATGAGCGTTGGTGTTACAGTAATAAAGAACAATATGATAAACAACGATCTTGGACCAGCAACAGCCCAAATGGCCCTTCAGCTATTTATCAAAGACTACAGATACACATACCGATGTCACAGGGGTGATACGCAAATTCAAACGAGGAGAGCATTCGAGCTGAAGAAGCTGTGGGAGCAGACCCGTTCGAAGGCAGGACTGTTGGTTTCAGATGGAGGGCCAAACCTGTACAATATCCGGAACCTCCACATTCCAGAGGTCTGCTTGAAATGGGAATTGATGGATGAAGACTACCAAGGCAGGTTGTGTAATCCTATGAACCCGTTTGTCAGTCATAAGGAAATTGATTCAGTCAACAATGCTGTGGTGATGCCAGCTCATGGCCCAGCCAAAAGCATGGAGTATGATGCCGTTGCAACCACACATTCATGGATTCCTAAGAGGAATCGCTCCATTCTCAACACCAGCCAAAGGGGGATTCTTGAGGACGAACAGATGTACCAGAAGTGCTGCAACCTATTCGAAAAGTTCTTCCCCAGCAGTTCGTACAGGAGGCCAGTTGGAATTTCCAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGAATTGATGCACGAATTGACTTCGAATCTGGAAGGATTAAGAAAGAAGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAGCTCAGACGGCAAAAATAG
ATGGAAGACTTTGTGCGACAGTGCTTCAATCCAATGATCGTCGAGCTTGCGGAAAAGGCAATGAAAGAATATGGGGAAGATCCGAAAATCGAAACAAACAAATTCGCATCAATATGCACACACTTAGAAGTCTGCTTCATGTACTCTGATTTCCACTTCATCGACGAACGAGGCGAATCAACTATAATAGAATCTGGCGATCCAAATGCGCTGCTGAAACACCGATTTGAAATAATCGAAGGGAGAGACCGAACAATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACAGGAGCCGAAAAACCCAAATTTCTCCCGGATCTGTATGACTACAAGGAAAACCGTTTCATTGAAATTGGAGTGACGAGGAGGGAAGTCCACATATATTACCTAGAGAAAGCCAATAAAATAAAATCCGAGAAGACACACATCCATATTTTTTCATTCACTGGAGAAGAGATGGCCACCAAAGCAGATTACACTCTTGACGAAGAAAGCAGGGCAAGAATCAAAACCAGGCTGTTCACCATAAGGCAGGAAATGGCCAGCAGGGGTCTATGGGATTCCTTTCGTCAGTCTGAAAGAGGCGAAGAAACAATTGAAGAAAGATTTGAAATCACAGGAACCATGCGCAGGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAGATGTCAAAAGAAGTGAACGCCAGAATTGAGCCATTTCTAAGAACAACACCACGCCCTCTCAGATTGCCTAATGGGCCTCCCTGCTCTCAGCGGTCGAAATTCTTGCTGATGGATGCTCTGAAATTAAGCATTGAGGACCCGAGCCACGAAGGGGAGGGGATACCGCTATATGATGCGATCAAATGCATGAAAACGTTCTTCGGGTGGAAAGAGCCCAACATTATCAAACCACATGAGAAAGGCATAAACCCCAATTATCTCCTGACTTGGAAGCAGGTGCTAGCAGAACTTCAGGACATTGAAAATGAAGAGAAGATTCCAAGGACAAAGAACATGAAGAAAACAAGCCAATTAAAGTGGGCACTCGGTGAGAACATGGCACCGGAGAAGGTGGACTTTGAGGATTGCAAAGATGTCAACGACTTGAAACAGTACAACAGTGATGAGCCAGAGCCCAGATCACTAGCATGTTGGATCCAGAATGAATTCAACAAGGCGTGTGAACTGACTGACTCAAGCTGGGTAGAACTTGATGAAATAGGGGAAGATGTTGCCCCAATCGAACACATTGCAAGCATGAGACGGAACTATTTTACAGCAGAGGTGTCCCACTGCAGGGCTACTGAATATATAATGAAGGGAGTGTACATAAATACAGCTTTGCTCAATGCATCTTGTGCAGCCATGGATGACTTTCAACTGATTCCAATGATAAGTAAATGTAGAACCAAAGAAGGAAGACGGAAAACAAACCTGTATGGATTCATTATAAAAGGAAGATCTCATTTGAGGAATGATACCGACGTGGTAAACTTTGTAAGTATGGAATTTTCCCTTACCGACCCAAGGTTGGAACCACATAAATGGGAAAAGTATTGTGTTCTTGAAATAGGGGACATGCTCCTGCGAACTGCAGTAGGCCAAGTGTCAAGACCCATGTTTCTGTATGTGAGAACCAATGGGACCTCCAAGATCAAGATGAAATGGGGTATGGAAATGAGACGCTGCCTTCTTCAATCTCTCCAACAGATTGAGAGCATGATTGAAGCTGAATCCTCCGTCAAAGAGAAAGACCTGACCAAAGAATTCTTTGAAAACAAATCAGAAACATGGCCAATTGGAGAGTCACCTAAAGGAGTGGAGGAAGGTTCCATCGGGAAGGTGTGCAGAACCTTACTAGCAAAATCTGTATTCAACAGCCTATATGCATCTCCGCAACTCGAGGGGTTCTCAGCTGAATCGAGAAAACTGCTACTCATTGTTCAGGCGCTTAGGGATAACCTGGAACCTGGAACCTTTGATCTTGAAGGGCTATATGAAGCAATCGAGGAGTGCCTGATTAATGATCCCTGGGTTTTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTAAGATAG
ATGAACACTCAAATCCTGGTATTCGCTCTGATTGCGATCATTCCAACAAATGCAGACAAAATCTGCCTCGGACATCATGCCGTGTCAAACGGAACCAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTCAATGCAACTGAAACAGTGGAACGAACAAACATCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTCGGTCAATGTGGACTCCTGGGGACAATCACTGGACCACCTCAATGTGACCAATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGTGATGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGAGAATCAGGCGGAATTGACAAGGAAGCAATGGGATTCACATACAGTGGAATAAGAACTAATGGAGCAACCAGTGCATGTAGGAGATCAGGATCTTCATTCTATGCAGAAATGAAATGGCTCCTGTCAAACACAGATAATGCTGCATTCCCGCAGATGACTAAGTCATATAAAAATACAAGAAAAAGCCCAGCTCTAATAGTATGGGGGATCCATCATTCCGTATCAACTGCAGAGCAAACCAAGCTATATGGGAGTGGAAACAAACTGGTGACAGTTGGGAGTTCTAATTATCAACAATCTTTTGTACCGAGTCCAGGAGCGAGACCACAAGTTAATGGTCTATCTGGAAGAATTGACTTTCATTGGCTAATGCTAAATCCCAATGATACAGTCACTTTCAGTTTCAATGGGGCTTTCATAGCTCCAGACCGTGCAAGCTTCCTGAGAGGAAAATCTATGGGAATCCAGAGTGGAGTACAGGTTGATGCCAATTGTGAAGGGGACTGCTATCATAGTGGAGGGACAATAATAAGTAACTTGCCATTTCAGAACATAGATAGCAGGGCAGTTGGAAAATGTCCGAGATATGTTAAGCAAAGGAGTCTGCTGCTAGCAACAGGGATGAAGAATGTTCCTGAGATTCCAAAGGGAAGAGGCCTATTTGGTGCTATAGCGGGTTTCATTGAAAATGGATGGGAAGGCCTAATTGATGGTTGGTATGGTTTCAGACACCAGAATGCACAGGGAGAGGGAACTGCTGCAGATTACAAAAGCACTCAATCGGCAATTGATCAAATAACAGGAAAATTAAACCGGCTTATAGAAAAAACCAACCAACAATTTGAGTTGATAGACAATGAATTCAATGAGGTAGAGAAGCAAATCGGTAATGTGATAAATTGGACCAGAGATTCTATAACAGAAGTGTGGTCATACAATGCTGAACTCTTGGTAGCAATGGAGAACCAGCATACAATTGATCTGGCTGATTCAGAAATGGACAAACTGTACGAACGAGTGAAAAGACAGCTGAGAGAGAATGCTGAAGAAGATGGCACTGGTTGCTTTGAAATATTTCACAAGTGTGATGATGACTGTATGGCCAGTATTAGAAATAACACCTATGATCACAGCAAATACAGGGAAGAGGCAATGCAAAATAGAATACAGATTGACCCAGTCAAACTAAGCAGCGGCTACAAAGATGTGATACTTTGGTTTAGCTTCGGGGCATCATGTTTCATACTTCTAGCCATTGTAATGGGCCTTGTCTTCATATGTGTAAAGAATGGAAACATGCGGTGCACTATTTGTATATAA
ATGGCGTCTCAAGGCACCAAACGATCCTATGAACAGATGGAAACTGGTGGGGAACGCCAGAATGCTACTGAGATCAGGGCATCTGTTGGAAGAATGGTTAGCGGCATTGGGAGATTCTACATACAGATGTGTACAGAACTCAAACTCAGTGACAATGAAGGGAGGCTGATTCAGAACAGTATAACAATAGAGAGAATGGTACTCTCTGCATTTGATGAAAGAAGGAACAGATACCTGGAAGAGCACCCCAGTGCAGGAAAGGACCCTAAGAAAACTGGAGGTCCAATTTACAGGAGAAGAGACGGAAAATGGGTGAGAGAGCTGATCCTGTATGACAAAGAGGAAATCAGGAGAATTTGGCGACAAGCGAACAATGGAGAGGATGCAACTGCTGGTCTTACCCATCTGATGATATGGCATTCCAACCTGAATGATGCTACCTATCAGAGAACGAGAGCTCTCGTGCGTACTGGAATGGATCCCCGGATGTGCTCTCTGATGCAAGGATCAACTCTCCCGAGGAGATCTGGAGCTGCAGGTGCAGCAGTGAAGGGGATAGGGACAATGGTGATGGAACTGATTCGGATGATAAAACGAGGGATCAACGACCGGAATTTCTGGAGAGGCGAAAATGGAAGAAGGACAAGAATTGCATATGAGAGAATGTGCAACATCCTCAAAGGGAAATTCCAAACAGCAGCACAAAGGGCAATGATGGATCAAGTGCGAGAGAGCAGAAATCCTGGGAATGCTGAAATAGAAGATCTCATTTTTCTGGCAAGGTCTGCACTCATCCTGAGAGGATCAGTGGCTCATAAATCCTGCTTGCCTGCTTGTGTGTACGGACTTGCAGTGGCTAGTGGATATGACTTTGAGAGAGAAGGGTACTCCTTGGTTGGAATAGATCCTTTCCGTCTGCTTCAAAACAGCCAGGTCTTTAGTCTCATTAGACCAAATGAGAACCCAGCACATAAGAGCCAACTAGTGTGGATGGCATGCCACTCTGCAGCGTTTGAGGACCTTAGGGTCTCAAGTTTCATTAGAGGGACAAGAATGGTCCCAAGAGGACAGCTATCCACTAGAGGGGTTCAAATTGCTTCAAATGAGAACATGGAAGCAATGGACTCCAATACTCTTGAACTGAGAAGTAGATATTGGGCTATAAGAACCAGAAGCGGAGGGAACACCAACCAACAGAGGGCATCTGCAGGACAGGTCAGCGTTCAACCCACTTTCTCAGTACAGAGAAACCTTCCTTTCGAAAGAGCAACCATTATGGCAGCATTTACAGGAAATACTGAGGGTAGAACGTCTGACATGAGGACTGAAATCATAAGAATGATGGAAAGTGCCAGACCAGAAGATGTGTCATTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAATAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAGGAGTATGACAATTGA
ATGAATCCAAATCAGAAGATTCTATGCACTTCAGCCACTGCTATCATAATAGGCGCAATCGCAGTACTCATTGGAATAGCAAACCTAGGATTGAACATAGGACTGCATCTAAAACCGGGCTGCAATTGCTCACACTCACAACCTGAAACAACCAACACAAGCCAAACAATAATAAACAACTATTATAATGAAACAAACATCACCAACATCCAAATGGAAGAGAGAACAAGCAGGAATTTCAATAACTTAACTAAAGGGCTCTGTACTATAAATTCATGGCACATATATGGGAAAGACAATGCAGTAAGAATTGGAGAGAGCTCGGATGTTTTAGTCACAAGAGAACCCTATGTTTCATGCGACCCAGATGAATGCAGGTTCTATGCTCTCAGCCAAGGAACAACAATCAGAGGGAAACACTCAAACGGAACAATACACGATAGGTCCCAGTATCGCGCCCTGATAAGCTGGCCACTATCATCACCGCCCACAGTGTACAACAGCAGGGTGGAATGCATTGGGTGGTCAAGTACTAGTTGCCATGATGGCAAATCCAGGATGTCAATATGTATATCAGGACCAAACAACAATGCATCTGCAGTAGTATGGTACAACAGAAGGCCTGTTGCAGAAATTAACACATGGGCCCGAAACATACTAAGAACACAGGAATCTGAATGTGTATGCCACAACGGCGTATGCCCAGTAGTGTTCACCGATGGGTCTGCCACTGGACCTGCAGACACAAGAATATACTATTTTAAAGAGGGGAAAATATTGAAATGGGAGTCTCTGACTGGAACTGCTAAGCATATTGAAGAATGCTCATGTTACGGGGAACGAACAGGAATTACCTGCACATGCAGGGACAATTGGCAGGGCTCAAATAGACCAGTGATTCAGATAGACCCAGTAGCAATGACACACACTAGTCAATATATATGCAGTCCTGTTCTTACAGACAATCCCCGACCGAATGACCCAAATATAGGTAAGTGTAATGACCCTTATCCAGGTAATAATAACAATGGAGTCAAGGGATTCTCATACCTGGATGGGGCTAACACTTGGCTAGGGAGGACAATAAGCACAGCCTCGAGGTCTGGATACGAGATGTTAAAAGTGCCAAATGCATTGACAGATGATAGATCAAAGCCCATTCAAGGTCAGACAATTGTATTAAACGCTGACTGGAGTGGTTACAGTGGATCTTTCATGGACTATTGGGCTGAAGGGGACTGCTATCGAGCGTGTTTTTATGTGGAGTTGATACGTGGAAGACCCAAGGAGGATAAAGTGTGGTGGACCAGCAATAGTATAGTATCGATGTGTTCCAGTACAGAATTCCTGGGACAATGGAACTGGCCTGATGGGGCTAAAATAGAGTACTTCCTCTAA
ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATTCCATCAGGCCCCCTCAAAGCCGAGATCGCACAGAGACTTGAGGATGTTTTTGCAGGGAAGAACGCAGATCTCGAGGCTCTCATGGAGTGGATAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCCTAAATGGGAATGGAGACCCAAACAACATGGACAAGGCGGTTAAATTATACAAGAAACTGAAGAGGGAAATGACATTTCATGGAGCAAAGGAAGTTGCACTCAGTTACTCAACTGGTGCGCTTGCCAGCTGCATGGGTCTCATATACAACAGAATGGGGACTGTGACCGCAGAAGGGGCTCTTGGACTAGTATGTGCCACTTGTGAGCAGATTGCTGACGCACAACATCGGTCCCACAGGCAGATGGCGACTACTACTAACCCACTAATTAGGCATGAGAATAGAATGGTACTAGCCAGCACTACGGCTAAGGCTATGGAGCAGATGGCTGGATCAAGTGAACAGGCAGCGGAAGCCATGGAAGTTGCAAGTCAGGCTAGGCAAATGGTGCAGGCTATGAGAACAGTTGGGACTCACCCTAACTCCAGTACAGGTCTAAAAGATGATCTTATTGAAAATTTGCAGGCCTACCAGAACCGGATGGGAGTGCAACTGCAGCGGTTCAAGTGAGCCTCTAGTCGTTGCAGCTAACATTATTGGGATATTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGTTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAATGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTGAAGTAA
ATGGATTCCAATACTGTGTCAAGCTTCCAGGTAGACTGCTTTCTTTGGCATGTCCGCAAACGATTTGCAGACCAAGAAATGGGTGATGCCCCATTTCTAGACCGGCTTCGCCGAGATCAGAAGTCCCTGAGAGGAAGAAGCAGCACTCTTGGTCTGGACATCAGAACTGCCACGCGTGAAGGAAAGCATATAGTGGAGCGGATTTTAGAGGAAGAGTCAGATGAAGCATTTAAAATGAGTATTGCTTCAGTGCCAGCTCCACGCTATCTAACTGACATGACTCTTGAAGAAATGTCAAGAGATTGGTTAATGCTCATTCCCAAACAGAAAATAACAGGGTCCCTATGCATTAGAATGGACCAAGCAATAGTGGACAAAAACATCACATTGAAAGCAAATTTCAGTGTGATTTTCAATCGGCTTGAAGCCCTGATACTACTTAGAGCTTTTACGGAAGAAGGAGCAATTGTAGGCGAAATCTCACCATTACCTTCTCTTCCAGGACATACTGACAAGGATGTCAAAAATGCAATTGAGATCCTCATCGGAGGATTTGAATGGAATGATAACACAGTTCGAGTCTCTGAAACTCTACAGAGATTCGCTTGGAGAAGCAGCGATGAGGATGGGAGATCTCCACTCTCTACAAAGTAGAAACGGGAAATGGAGAGAACAGTTAAGCCAGAAGTTCGAAGAAATAAGATGGTTGATTGAAGAAGTACGACATAGATTAAAAATTACGGAGAATAGCTTTGAGCAAATAACTTTTATGCAAGCCTTACAACTATTGCTTGAAGTGGAGCAAGAGATAAGAACTTTCTCGTTTCAGCTTATTTAA

[ 2013/04/20,04:44ET changed: A1879G(1),A744G(3),C1178T(3) ]
[ 2013/04/29,07:01ET changed: T704A(4) {235Q,poultry-like} ]
[ 2013/05/02,02:53ET changed it back: A704T(4) ]
 
Re: H7n9

S1 is pretty different from all the other H7N9 viruses.
And it's not just only accumulation of mutations in the hosts
due to prolonged disease or H2H, nor just sequencing errors.
Because some of the mutations are also in the H9N2
poultry index (East China, ~2010)

so it could have been another introduction or the previous strain
which then died
segment 5 is clearly reassorted, but probably also 2 and maybe even 1,
which has 2 mutations in common with the poultry-index

Waiting for other sequences similar to S1 ... poultry H9N2 would be fine ...
they have 80000 samples, test them for H9N2 ?!?
 
Re: H7n9

we have a new MP(segment 7) now :

Code:
>A/Nanjing/1/2013/03/28,H7N9
ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATTCCATCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAGGATGTTTTTGCAGGGAAGAACGCAGATCTCGAGGCTCTCATGGAGTGGATAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCCTAAATGGGAATGGAGACCCAAACAACATGGACAAGGCAGTTAAATTATACAAGAAACTGAAGAGGGAAATGACATTTCATGGAGCAAAGGAAGTTGCACTCAGTTACTCAACTGGTGCGCTTGCCAGCTGCATGGGTCTCATATACAACAGGATGGGGACAGTAACTGCAGAAGGGGCTCTTGGATTGGTATGTGCCACTTGTGAGCAGATTGCTGACGCACAACATCGGTCCCACAGGCAGATGGCAACTACTACCAACCCACTAATTAGGCATGAGAATAGAATGGTACTAGCCAGTACTACGGCTAAGGCTATGGAGCAGATGGCTGGATCAAGTGAACAGGCAGCGGAAGCCATGGAAGTCGCAAGCCAGGCTAGGCAAATGGTGCAGGCTATGAGAACAGTCGGGACTCACCCTAACTCCAGTACAGGTCTAAAGGATGATCTTATTGAAAATTTGCAGGCTTACCAGAACCGGATGGGAGTGCAACTGCAGCGGTTCAAGTGACCCTCTCGTTGTTGCAGCTAACATTATTGGGATATTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAATGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTGAAGTAA

it's in the Nanjing,45f , in the Taiwan case in Hangzhou/3
and in several of the new Institut Pasteur samples from Shanghai.

It has 20 nucleotide-differences to the H7N9-index MP as in Anhui/1

The closest H9N2 neighbor is A/chicken/Zhejiang/329/2011/03/(H9N2)
with only 7 nucleotide differences, while the closest H9N2 neighbor
of the old index MP was A/chicken/Zhejiang/607/2011/06(H9N2)
with 14 differences.

So, is this the original MP that was in the initial
H9N2(123578)+H7N9(46)-->H7N9 reassortment ?
We can't know from MP alone, but since the other segments of N1,T1 have
more mutations than e.g. A1, probably the old MP is the original one and this
new one was only later reassorted into.

I see no signs of H7N9 reassortment with other H7N9 yet,
but quite a lot of reassortments with H9N2. So presumably
most poultry flu over there is still H9N2

It's also remarkable, that the new MP has only 18 amino-acid differences
to the bird-index, while the old one had 27.
That could hint to evolution in different species.
Remarkable also, that we have no close neighbors in H9N2 of the old MP
at genbank ------edit----ahh, nee, das stimmt nicht. 18 war der neue
poultry-H9N2 index (2005), die beiden H7N9 indices haben beide 27 in MP
 
Re: H7n9

best matches in the 8 segments for H7N9 , including best matches
for the new Nanjing segment 7
file 79.bes

differences in promille
differences in #nucleotides in the coding region
# nucleotides considered
number in file
sequence name

Code:
   0    0 2280    1 >A/Index/H7N9-China/2013/01/31,H7N9,China,throat-swab,65m,E1
-------segment 1-------------------
  70   16 2280 7436 >A/brambling/Beijing/16/2012,2012/11/07,H9N2
 118   27 2280 5985 >A/chicken/Zhejiang/329/2011,2011/03/,H9N2
 135   31 2280 7206 >A/chicken/Shanghai/C1/2012,2012/01/,H9N2
 149   34 2280    2 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)
 188   43 2280 5600 >A/chicken/Jiangsu/Q3/2010,2010/02/,H9N2
----------segment 2-----------------------------
  83   19 2274    2 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)
 114   26 2274 5770 >A/chicken/Jiangsu/Q3/2010,2010/02/,H9N2
 118   27 2274 6733 >A/chicken/Anhui/HF/2010,2010/04/,H9N2
 136   31 2274 7540 >A/brambling/Beijing/16/2012,2012/11/07,H9N2
 140   31 2213 5698 >A/chicken/Wuxi/7/2010,2010/07/10,H9N2
 153   35 2274 5149 >A/chicken/Shandong/KD/2009,2009/01/,H9N2
 158   36 2274 6132 >A/chicken/Zhejiang/329/2011,2011/03/,H9N2
 162   36 2213 5696 >A/duck/Wuxi/7/2010,2010/07/10,H9N2
 162   37 2274 7322 >A/chicken/Shanghai/C3/2012,2012/01/,H9N2
 171   39 2274 5771 >A/chicken/Zhejiang/Q1D4/2010,2010/02/,H9N2
 171   39 2274 6131 >A/chicken/Zhejiang/607/2011,2011/06/,H9N2
-----------segment 3-----------------
  79   17 2151 7532 >A/brambling/Beijing/16/2012,2012/11/07,H9N2
 120   26 2151 5923 >A/chicken/Zhejiang/607/2011,2011/06/,H9N2
 153   33 2151 7299 >A/chicken/Shanghai/C1/2012,2012/01/,H9N2
 172   37 2151    2 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)
-------------segment 4--------------------
 398   11  276   33 >A/quail/Thailand/CU-J1835/2009,2009/09/,H7N1
 409   69 1683   26 >A/duck/Zhejiang/12/2011,2011/06/,H7N3
 409   69 1683   27 >A/duck/Zhejiang/11/2011,2011/06/,H7N3
 433   73 1683   29 >A/duck/Zhejiang/2/2011,2011/06/,H7N3
 451   76 1683   28 >A/duck/Zhejiang/10/2011,2011/06/,H7N3
 482   81 1680   11 >A/wild bird feces/Korea/HDR22/2006,2006//,H7N7
 484   80 1650    7 >A/duck/Jiangxi/1786/03,2003//,H7N7
 485   80 1647    6 >A/duck/Jiangxi/1814/03,2003//,H7N7
-------------segment 5---------------------------
 113   17 1497 5931 >A/chicken/Zhejiang/611/2011,2011/06/,H9N2
 120   18 1497    2 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)
 133   20 1497 5553 >A/chicken/Jiangsu/Q3/2010,2010/02/,H9N2
 135   20 1478 5484 >A/chicken/Wuxi/7/2010,2010/07/10,H9N2
 140   21 1497 5554 >A/chicken/Zhejiang/Q1D4/2010,2010/02/,H9N2
 153   23 1497 5933 >A/chicken/Zhejiang/329/2011,2011/03/,H9N2
 160   24 1497 6420 >A/chicken/Anhui/HF/2010,2010/04/,H9N2
 162   24 1478 5487 >A/chicken/Qianzhou/12/2010,2010/12/18,H9N2
 173   26 1497 5872 >A/chicken/Hebei/1102/2010,2010/12/,H5N2
 180   27 1497 4919 >A/chicken/Shandong/KD/2009,2009/01/,H9N2
----------------segment 6----------------------------
 121   17 1398    3 >A/chicken/Jiangsu/RD5/2013(H10N9)
 257   36 1398  198 >A/mallard/Czech Republic/13438-29K/2010,2010/09/09,H11N9
 271   38 1398   90 >A/Baikal teal/Hongze/14/2005,2005/02/,H11N9
 275   38 1377  208 >A/wild bird/Korea/A14/2011,2011/02/,H7N9
 283   39 1378  210 >A/wild bird/Korea/A9/2011,2011/02/,H7N9
------------------segment 7-----------------
 132   13  982    2 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)
 142   14  982 6947 >A/chicken/Zhejiang/607/2011,2011/06/,H9N2
 143   14  975 6485 >A/chicken/Taixing/10/2010,2010/10/11,H9N2
 143   14  975 6488 >A/chicken/Yangzhou/11/2010,2010/11/16,H9N2
 152   15  982 6564 >A/chicken/Jiangsu/Q3/2010,2010/02/,H9N2
 153   15  975 6489 >A/chicken/Wuxi/7/2010,2010/07/10,H9N2
 162   16  982 6948 >A/chicken/Zhejiang/329/2011,2011/03/,H9N2
 164   16  975 6494 >A/chicken/Jiawang/2/2011,2011/02/15,H9N2
 164   16  975 6497 >A/chicken/Tongshan/1/2011,2011/01/31,H9N2
 169   16  944 7408 >A/chicken/Vietnam/OIE-1611/2012,2012/04/19,H9N2
 174   17  975 6496 >A/pigeon/Xuzhou/1/2011,2011/01/31,H9N2
 183   18  982 5937 >A/chicken/China/AH-10-01/2010,2010/12/02,H9N2
 184   18  975 6493 >A/chicken/Dawang/1/2011,2011/01/31,H9N2
 184   18  975 6495 >A/chicken/Xigou/1/2011,2011/01/31,H9N2
 184   18  975 6499 >A/chicken/Shuanggou/1/2011,2011/01/31,H9N2
 194   19  975 6498 >A/chicken/Yongcheng/1/2011,2011/01/31,H9N2
 203   20  982   21 >A/environment-poultry_cage/Nanjing/2913/2013/03/29,H7N9
 203   20  982   22 >A/Nanjing/1/throat_swab/2013/03/28,H7N9
 203   20  982 5924 >A/chicken/Shandong/BD/2010,2010/05/,H9N2
 203   20  982 5926 >A/chicken/Shandong/KD/2009,2009/01/,H9N2
 203   20  982 8376 >A/brambling/Beijing/16/2012,2012/11/07,H9N2
 213   21  982 6565 >A/chicken/Zhejiang/Q1D4/2010,2010/02/,H9N2
 213   21  982 6946 >A/chicken/Zhejiang/611/2011,2011/06/,H9N2
 213   21  982 8155 >A/chicken/Shanghai/C1/2012,2012/01/,H9N2
 213   21  982 8156 >A/chicken/Shanghai/C2/2012,2012/01/,H9N2
 224   22  982   18 >A/Taiwan/S02076/2013(H7N9)
 224   22  982 5921 >A/chicken/Shandong/02/2010,2010/02/,H9N2
 225   21  931   19 >A/Taiwan/T02081/2013(H7N9)
---------------segment 8--------------------------
  83    7  838 5198 >A/chicken/Dawang/1/2011,2011/01/31,H9N2
 107    9  838 5201 >A/pigeon/Xuzhou/1/2011,2011/01/31,H9N2
 107    9  838 5204 >A/chicken/Shuanggou/1/2011,2011/01/31,H9N2
 119   10  838 5200 >A/chicken/Xigou/1/2011,2011/01/31,H9N2
 178   15  838    2 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)
 202   17  838 4752 >A/chicken/Tibet/S1/2009,2009/09/10,H9N2
 202   17  838 4753 >A/chicken/Tibet/S4/2009,2009/09/10,H9N2
 202   17  838 4812 >A/chicken/China/AH-10-01/2010,2010/12/02,H9N2
 202   17  838 5190 >A/chicken/Taixing/10/2010,2010/10/11,H9N2
 202   17  838 5193 >A/chicken/Yangzhou/11/2010,2010/11/16,H9N2
 214   18  838 4754 >A/duck/Tibet/S2/2009,2009/09/10,H9N2
 226   19  838 4295 >A/chicken/Shandong/SG2/2009,2009/11/27,H9N2
 238   20  838 2869 >A/chicken/Zhejiang/HJ/2007,2007//,H9N2
 238   20  838 3300 >A/chicken/Shandong/1231/2008,2008/12/31,H9N2
 238   20  838 4797 >A/chicken/Shandong/KD/2009,2009/01/,H9N2
 238   20  838 6687 >A/brambling/Beijing/16/2012,2012/11/07,H9N2





   0    0  982   22 >A/Nanjing/1/throat_swab/2013/03/28,H7N9
-----------------------segment 7----------------------------
   0    0  982   21 >A/environment-poultry_cage/Nanjing/2913/2013/03/29,H7N9
  42    4  931   19 >A/Taiwan/T02081/2013(H7N9)
  50    5  982   18 >A/Taiwan/S02076/2013(H7N9)
  71    7  982 6948 >A/chicken/Zhejiang/329/2011,2011/03/,H9N2
  81    8  982    2 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)
  82    8  975 6489 >A/chicken/Wuxi/7/2010,2010/07/10,H9N2
  91    9  982 6947 >A/chicken/Zhejiang/607/2011,2011/06/,H9N2
  92    9  975 6485 >A/chicken/Taixing/10/2010,2010/10/11,H9N2
  92    9  975 6488 >A/chicken/Yangzhou/11/2010,2010/11/16,H9N2
 101   10  982 6564 >A/chicken/Jiangsu/Q3/2010,2010/02/,H9N2
 112   11  975 6494 >A/chicken/Jiawang/2/2011,2011/02/15,H9N2
 112   11  975 6497 >A/chicken/Tongshan/1/2011,2011/01/31,H9N2
 112   11  982 8376 >A/brambling/Beijing/16/2012,2012/11/07,H9N2
 116   11  944 7408 >A/chicken/Vietnam/OIE-1611/2012,2012/04/19,H9N2
 123   12  975 6496 >A/pigeon/Xuzhou/1/2011,2011/01/31,H9N2
 132   13  982 5937 >A/chicken/China/AH-10-01/2010,2010/12/02,H9N2
 133   13  975 6493 >A/chicken/Dawang/1/2011,2011/01/31,H9N2
 133   13  975 6495 >A/chicken/Xigou/1/2011,2011/01/31,H9N2
 133   13  975 6499 >A/chicken/Shuanggou/1/2011,2011/01/31,H9N2
 142   14  982 6946 >A/chicken/Zhejiang/611/2011,2011/06/,H9N2
 142   14  982 8155 >A/chicken/Shanghai/C1/2012,2012/01/,H9N2
 142   14  982 8157 >A/chicken/Shanghai/C3/2012,2012/01/,H9N2
 143   14  975 6498 >A/chicken/Yongcheng/1/2011,2011/01/31,H9N2
 162   16  982 6565 >A/chicken/Zhejiang/Q1D4/2010,2010/02/,H9N2
 162   16  982 8156 >A/chicken/Shanghai/C2/2012,2012/01/,H9N2
 164   16  975 6484 >A/chicken/Xiangshui/1/2011,2011/01/31,H9N2
 173   17  982 5921 >A/chicken/Shandong/02/2010,2010/02/,H9N2
 173   17  982 5924 >A/chicken/Shandong/BD/2010,2010/05/,H9N2
 173   17  982 5926 >A/chicken/Shandong/KD/2009,2009/01/,H9N2
 173   17  982 6888 >A/chicken/Hebei/1102/2010,2010/12/,H5N2
 176   17  962 5210 >A/chicken/Shandong/HY/2009,2009/02/12,H9N2
 203   20  982    1 >A/Index/H7N9-China/2013/01/31,H7N9,China,throat-swab,65m,E1
 
Re: H7n9

mutation table for MP:

Code:
                                                             0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
                                                             0000000111111111122233333334444444444445555555666666666667777777778888888899999999999999999999
                                                             0013577013366677837800234890011133357890234579122456667790124666680257999901112334444455555577
                                                             6806825976947849049809732702814726891087819591514273692502732016920309145760151030678901245667
-codon-position---------------------------------------------- 21 1  1 1122  2                 1                          112112211   1  12    112 12 1 1212
---Index-----------------------------------------------------TTCCCCGGCAATCTGTAGGACGTAATCGGAACTCAGAGGCGTCGTACTGGCTCTCCATTGCTCCTATTCCTCTAGAGAAAAGTGACGATGTCGA
   2 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)   ..............................................................................................
                                                                                                                                                           
   1 >A/Index/H7N9-China/2013/01/31,H7N9,China               ......A............G.......A.TG........T......T...T.......C..G.AC...T.........................
   3 >A/Shanghai/1/2013,H7N9                                 ......A............G.......A.TG........T......T...T.......C....AC...T.........................
   4 >A/Shanghai/2/2013,H7N9                                 ......A............G.......A.TG........T......T...T.......C..G.AC...T.........................
   5 >A/Anhui/1/2013,H7N9                                    ......A............G.......A.TG........T......T...T.......C..G.AC...T.........................
  30 >A/Hangzhao/1/2013,2013/03/24,H7N9,China,throat-swab,,  ......A............G.......A.TG........T......T...T.......C..G.AC...T.........................
  31 >A/Jiangsu/1/2013/03/30,H7N9,China,,45f,E1              ......A............G.......A.TG........T......T...T.......C..G.AC...T.......................AG
  32 >A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9                 ......A............G.......A.TG........T......T...T.......C.TG.AC...T.........................
  33 >A/chicken/Zhejiang/DTID-ZJU01/2013,2013/04/,H7N9       ......A............G.......A.TG........T......T...T.......C..G.AC.C.T.........................
  35 >A/Fujian/1/2013,2013/04/24,China,H7N9                  ......A............G.......A.TG........T......T...T.......C..G.AC...T.........................
  34 >A/Shanghai/4664T/2013,2013/03/05,China,H7N9            .....A.............G.......A.TG........T......T...T.......C..G.AC...T.........................
                                                                                                                                                           
   6 >A/chicken/Zhejiang/607/2011,2011/06/,H9N2              .....................................................C........................................
   7 >A/chicken/Dawang/1/2011,2011/01/31,H9N2                .........................C...........................................A.AA.....C.............--
   8 >A/chicken/Xigou/1/2011,2011/01/31,H9N2                 .......A.C........T......C.............................T....................................--
   9 >A/pigeon/Xuzhou/1/2011,2011/01/31,H9N2                 ........T.........T......C.............................T....................................--
  10 >A/chicken/Shuanggou/1/2011,2011/01/31,H9N2             ....G...T................C......................................................CC..........--
  11 >A/chicken/China/AH-10-01/2010,2010/12/02,H9N2          ........T.......................................TA.................C.........T................
  19 >A/chicken/Vietnam/OIE-1611/2012,2012/04/19,H9N2        ................................C...................T....C........................------------
  22 >A/chicken/Jiangsu/Q3/2010,2010/02/,H9N2                ..............A..............................................................................G
  23 >A/chicken/Shanghai/C2/2012,2012/01/,H9N2               CC............A.....T.....T................A....A............................................G
  24 >A/chicken/Tongshan/1/2011,2011/01/31,H9N2              ..............A.G..................A........................................................--
  25 >A/chicken/Jiawang/2/2011,2011/02/15,H9N2               ..............A....................A..........................A.............................--
  26 >A/chicken/Hebei/1102/2010,2010/12/,H5N2                ..............A....................A..A............................C.TC..GCTA...............A.
  20 >A/chicken/Yangzhou/11/2010,2010/11/16,H9N2             .................T..........................................................................--
  21 >A/chicken/Taixing/10/2010,2010/10/11,H9N2              .................T..........................................................................--
  12 >A/chicken/Zhejiang/611/2011,2011/06/,H9N2              ............GC.........GG..........A.....C.........C....G.....................................
  13 >A/brambling/Beijing/16/2012,2012/11/07,H9N2            .................T.....G....A.......TA.........C........G.....................................
  14 >A/chicken/Zhejiang/329/2011,2011/03/,H9N2              .................T.............................C........G.....................................
  15 >A/chicken/Wuxi/7/2010,2010/07/10,H9N2                  .................T......................................G...................................--
  16 >A/chicken/Shanghai/C3/2012,2012/01/,H9N2               ..........CC...C.T...A......A.....G...................T.G....................................G
  17 >A/chicken/Shanghai/C1/2012,2012/01/,H9N2               .................T....C.................A....G..........G..A.......C.........................G
  18 >A/chicken/Vietnam/OIE-2468/2012,2012/08/13,H9N2        ---..............T.......C..................AG..A.......G..A.....G.............G..GACGATGTCA--
                                                                                                                                                           
  36 >A/Taiwan/S02076/2013(H7N9)                             ..TA..................C........T.TG...A...T...TC........G.....................................
  37 >A/Taiwan/T02081/2013(H7N9)                             ---A..................C........T.TG...A...T...TC........G...................................--
  39 >A/environment/Nanjing/2913/2013/03/29,H7N9             ...............................T.TG...A...T....C........G....C................................
  40 >A/Nanjing/1/throat_swab/2013/03/28,H7N9                ...............................T.TG...A...T....C........G....C................................
                                                                                                                                                           
   1 >A/Index/H7N9-China/2013/01/31,H7N9,China               ......A............G.......A.TG........T......T...T.......C..G.AC...T.........................
                                                                                                                                                           
                                                                                                                                                           
---Index-----------------------------------------------------TTCCCCGGCAATCTGTAGGACGTAATCGGAACTCAGAGGCGTCGTACTGGCTCTCCATTGCTCCTATTCCTCTAGAGAAAAGTGACGATGTCGA
-codon-position---------------------------------------------- 21 1  1 1122  2                 1                          112112211   1  12    112 12 1 1212
                                                             0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
                                                             0000000111111111122233333334444444444445555555666666666667777777778888888899999999999999999999
                                                             0013577013366677837800234890011133357890234579122456667790124666680257999901112334444455555577
                                                             6806825976947849049809732702814726891087819591514273692502732016920309145760151030678901245667
 
Re: H7n9

how segment 7 evolved since ~1995
 

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