Niger H5N1

Author: admin     03 14th, 2010 in enart.abczj.com     edit

  • HA sequence from Niger available at GenBank

    A/duck/Niger/914/2006(H5N1)

    Sequence is easily distinguished from Nigeria and has a number of polymorphisms not found in other Qinghai sequences, but readily detected in other H5N1's from Asia.

    Another advertisement for recombination.


  • Here is a tree of the European Qinghai sequences

    top of tree

    http://www.recombinomics.com/phylo/Brown_Italy_2_Top.html

    bottom of tree

    http://www.recombinomics.com/phylo/Brown_Italy_2_Bottom.html


  • Here is an earlier analyisis of the HA sequence from Nigeria

    http://www.recombinomics.com/News/02240604/H5N1_Chicken_Nigeria_Sequence.html

    It also had 6 "informative" polymorphisms, and all 6 matched other Qinghai sequences - 4 from Kurgan and 2 from Mongolia.


  • Stamped passport of A524G (also in Nigeria isolate)

    DQ447199 A/chicken/Egypt/960N3-004/2006 2006 H5N1
    DQ406728 A/chicken/Nigeria/641/2006 2006 H5N1
    DQ515984 A/Cygnus olor/Czech Republic/5170/2006 2006 H5N1
    DQ435200 A/domestic cat/Iraq/820/2006 2006 H5N1
    DQ435201 A/domestic goose/Iraq/812/2006 2006 H5N1
    DQ659113 A/duck/Niger/914/2006 2006 H5N1
    DQ464377 A/Egypt/2782-NAMRU3/2006 2006 H5N1
    DQ435202 A/Iraq/207-NAMRU3/2006 2006 H5N1
    DQ458992 A/mallard/Bavaria/1/2006 2006 H5N1
    DQ449031 A/mallard/Italy/332/2006 2006 H5N1
    AB233319 A/bar-headed goose/Mongolia/1/05 2005 H5N1
    DQ320898 A/chicken/Guangxi/604/2005 2005 H5N1
    DQ449632 A/chicken/Kurgan/05/2005 2005 H5N1
    DQ323672 A/chicken/Kurgan/3/2005 2005 H5N1
    DQ389158 A/Cygnus olor/Astrakhan/Ast05-2-1/2005 2005 H5N1
    DQ434889 A/Cygnus olor/Astrakhan/Ast05-2-10/2005 2005 H5N1
    DQ343502 A/Cygnus olor/Astrakhan/Ast05-2-2/2005 2005 H5N1
    DQ358746 A/Cygnus olor/Astrakhan/Ast05-2-3/2005 2005 H5N1
    DQ363918 A/Cygnus olor/Astrakhan/Ast05-2-4/2005 2005 H5N1
    DQ365004 A/Cygnus olor/Astrakhan/Ast05-2-5/2005 2005 H5N1
    DQ364996 A/Cygnus olor/Astrakhan/Ast05-2-6/2005 2005 H5N1
    DQ363923 A/Cygnus olor/Astrakhan/Ast05-2-7/2005 2005 H5N1
    DQ399540 A/Cygnus olor/Astrakhan/Ast05-2-8/2005 2005 H5N1
    DQ399547 A/Cygnus olor/Astrakhan/Ast05-2-9/2005 2005 H5N1
    DQ320899 A/duck/Guangxi/793/2005 2005 H5N1
    DQ449640 A/duck/Kurgan/08/2005 2005 H5N1
    DQ320897 A/quail/Guangxi/575/2005 2005 H5N1
    DQ320137 A/swan/Astrakhan/1/2005 2005 H5N1
    DQ407519 A/turkey/Turkey/1/2005 2005 H5N1
    AB233320 A/whooper swan/Mongolia/3/05 2005 H5N1
    AB233321 A/whooper swan/Mongolia/4/05 2005 H5N1
    AB233322 A/whooper swan/Mongolia/6/05 2005 H5N1
    ISDN140936 A/Whooping swan/Mongolia/244/2005 2005 H5N1
    AY651346 A/Ck/Hong Kong/31.2/2002 2002 H5N1
    AY651350 A/Ck/Hong Kong/3176.3/2002 2002 H5N1
    AY651347 A/Ck/Hong Kong/37.4/2002 2002 H5N1
    AY651345 A/Gf/Hong Kong/38/2002 2002 H5N1
    AY575880 A/pheasant/Hong Kong/675.14/02 2002 H5N1
    AY651348 A/SCk/Hong Kong/YU100/2002 2002 H5N1
    M18450 A/Duck/Ireland/113/83 1983 H5N8


  • G1240A matches only one Qinghai sequence, but matches low pat from Europe and North America

    DQ659113 A/duck/Niger/914/2006 2006 H5N1
    AB233319 A/bar-headed goose/Mongolia/1/05 2005 H5N1
    DQ309440 A/duck/BritishColumbia/CN26-6/05 2005 H5N2
    DQ095629 A/Duck/Fujian/1734/05 2005 H5N1
    DQ320897 A/quail/Guangxi/575/2005 2005 H5N1
    DQ320893 A/chicken/Guangxi/2439/2004 2004 H5N1
    DQ320883 A/duck/Guangxi/1311/2004 2004 H5N1
    DQ320885 A/duck/Guangxi/1586/2004 2004 H5N1
    DQ320886 A/duck/Guangxi/1681/2004 2004 H5N1
    DQ320887 A/duck/Guangxi/1793/2004 2004 H5N1
    DQ320890 A/duck/Guangxi/2291/2004 2004 H5N1
    DQ320892 A/duck/Guangxi/2396/2004 2004 H5N1
    DQ320881 A/goose/Guangxi/1097/2004 2004 H5N1
    DQ320882 A/goose/Guangxi/1198/2004 2004 H5N1
    DQ320888 A/goose/Guangxi/1832/2004 2004 H5N1
    DQ320889 A/goose/Guangxi/2112/2004 2004 H5N1
    DQ320891 A/goose/Guangxi/2383/2004 2004 H5N1
    AY590577 A/openbill/Thailand/CU-2/2004 2004 H5N1
    CY005927 A/shorebird/Delaware/101/2004 2004 H5N7
    CY005969 A/shorebird/Delaware/75/2004 2004 H5N7
    AY651336 A/Viet Nam/3062/2004 2004 H5N1
    AY573917 A/chicken/Taiwan/1209/03 2003 H5N2
    AY747609 A/swine/Fujian/1/2003 2003 H5N1
    AY296079 A/duck/ME/151895-7A/02 2002 H5N2
    AY296080 A/duck/NY/185502/02 2002 H5N2
    AY296081 A/duck/NY/186875/02 2002 H5N2
    AY296086 A/duck/NY/191255-59/02 2002 H5N8
    AY296082 A/duck/NY/191255-79/02 2002 H5N2
    AY995886 A/mallard/Sweden/22/02 2002 H5N9
    AY995887 A/mallard/Sweden/27/02 2002 H5N9
    AY995888 A/mallard/Sweden/28/02 2002 H5N9
    AY995889 A/mallard/Sweden/31/02 2002 H5N2
    AY995890 A/mallard/Sweden/37/02 2002 H5N9
    AY995892 A/mallard/Sweden/40/02 2002 H5N6
    AY995893 A/mallard/Sweden/49/02 2002 H5N9
    AY995894 A/mallard/Sweden/52/02 2002 H5N9
    AY995895 A/mallard/Sweden/58/02 2002 H5N3
    AY995896 A/mallard/Sweden/64/02 2002 H5N2
    AY995897 A/mallard/Sweden/79/02 2002 H5N9
    AY995898 A/mallard/Sweden/80/02 2002 H5N9
    AY296083 A/turkey/CA/D0208651-C/02 2002 H5N2
    AY075033 A/Duck/Hong Kong/380.5/2001 2001 H5N1
    AY296077 A/duck/NJ/117228-7/01 2001 H5N2
    AY747617 A/swine/Fujian/F1/2001 2001 H5N1
    AY296076 A/unknown/NY/101250-18/01 2001 H5N2
    AY296075 A/unknown/NY/9899-6/01 2001 H5N2
    AY296073 A/chukkar/NY/51375/00 2000 H5N2
    AY296072 A/duck/NY/44018-2/00 2000 H5N2
    AY585377 A/duck/Zhejiang/52/2000 2000 H5N1
    AJ305306 A/chicken/Italy/8/98 1998 H5N2
    AF194169 A/Chicken/Italy/312/97 1997 H5N2
    AF194990 A/Chicken/Italy/367/97 1997 H5N2
    AF194991 A/Guinea Fowl/Italy/330/97 1997 H5N2
    U79448 A/Chicken/Queretaro/7653-20/951659 1995 H5N2
    CY006040 A/chicken/Hidalgo/28159-232/1994 1994 H5N2
    U28920 A/Emu/Texas/39442/93 (HP progeny) 1993 H5N2
    U28919 A/Emu/Texas/39442/93 (non-HP parent) 1993 H5N2
    U67783 A/Mallard/Ohio/556/1987 1987 H5N9
    U69277 A/Mallard/Wisconsin/944/82 1982 H5
    AF082040 A/Duck/Minnesota/1525/81 1981 H5N1
    U79454 A/Turkey/Minnesota/3689-1551/81 1981 H5N2
    CY005918 A/mallard duck/Alberta/57/1976 1976 H5N2
    U79452 A/Mallard/Wisconsin/169/75 1975 H5N3
    U79456 A/Turkey/Wisconsin/68 1968 H5N9
    AB241613 A/turkey/Ontario/7732/66 1966 H5
    M30122 A/turkey/Ontario/7732/66 1966 H5N9
    U20460 A/tern/South Africa/61 1961 H5N3


  • C1198T shared by H5N1 but none are Qinghai sequences

    ISDN138756 A/chicken/Malaysia/935/2006 2006 H5N1
    DQ659113 A/duck/Niger/914/2006 2006 H5N1
    DQ095624 A/Chicken/Yunnan/447/05 2005 H5N1
    DQ095625 A/Chicken/Yunnan/493/05 2005 H5N1
    AY651322 A/Dk/Indonesia/MS/2004 2004 H5N1
    DQ017300 A/duck/Nakornsawan-2-02/2004 2004 H5N1
    AY651323 A/Ck/Indonesia/2A/2003 2003 H5N1
    AF509026 A/Chicken/Hong Kong/822.1/01 2001 H5N1
    AF509028 A/Chicken/Hong Kong/830.2/01 2001 H5N1
    AF509029 A/Chicken/Hong Kong/858.3/01 2001 H5N1
    AF509030 A/Chicken/Hong Kong/867.1/01 2001 H5N1
    AF509033 A/Chicken/Hong Kong/876.1/01 2001 H5N1
    AF509031 A/Chicken/Hong Kong/879.1/01 2001 H5N1
    AF509034 A/Chicken/Hong Kong/891.1/01 2001 H5N1
    AF509035 A/Chicken/Hong Kong/893.2/01 2001 H5N1
    AF509024 A/Chicken/Hong Kong/SF219/01 2001 H5N1
    AF509017 A/Chicken/Hong Kong/YU562/01 2001 H5N1
    AY221529 A/Chicken/Hong Kong/YU562/01 2001 H5N1
    AF509018 A/Chicken/Hong Kong/YU563/01 2001 H5N1
    AY221528 A/Chicken/Hong Kong/YU822.2/01 2001 H5N1
    AY221527 A/Chicken/Hong Kong/YU822.2/01-MB 2001 H5N1
    AF509023 A/Pigeon/Hong Kong/SF215/01 2001 H5N1
    AF509022 A/Quail/Hong Kong/SF203/01 2001 H5N1
    AF509021 A/Silky Chicken/Hong Kong/SF189/01 2001 H5N1


  • The Niger sequence has 6 polymorphisms that are present in a small subset of the Qinghai strain. The 6 polymorphisms are G253A, A524G, C1198T, G1240A, G1447A, T1603C.

    Notice that all changes are transitions (replacing a purine with a purine or a pyrimadine with a pyrimadine).

    These are all transitions and all have a clear H5N1 rap sheet.

    These changes are NOT random mutations.

    They were all acquired from kissin cousins.


  • Thanks Henry.


  • here the number of mutations between the nucleotides of the HAs of sequences from the Qinghai strain :

    {can someone help me to format this ?}









    01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
    -----------------------------------------------------------------------------------------------------------------------------------------------------------
    01 A/Cygnus olor/Italy/742/2006(H5N1) -- 08 07 08 08 09 10 13 10 11 14 14 18 18 16 15 14 18 16 17 19 21 16 16 13 08 13 06 14 14 11 10 405
    02 A/Cygnus cygnus/Iran/754/2006(H5N1) 08 -- 07 08 08 09 10 13 10 11 14 14 18 18 16 15 14 18 16 17 19 21 16 16 13 08 13 10 14 14 11 12 411
    03 A/Bar-headed Goose/Qinghai/59/05(H5N1) 07 07 -- 01 01 02 03 06 03 04 07 07 11 11 09 08 07 11 09 10 12 14 09 09 06 07 06 05 07 07 04 05 215
    04 A/Bar-headed Goose/Qinghai/65/05(H5N1) 08 08 01 -- 02 03 04 07 04 05 08 08 12 12 10 09 08 12 10 11 13 15 10 10 07 08 07 06 08 08 05 06 245
    05 A/Environment/Qinghai/31/2005(H5N1) 08 08 01 02 -- 01 02 05 02 05 08 08 12 12 10 09 08 12 10 11 13 13 10 10 07 08 07 06 08 08 05 06 235
    06 A/Brown-headed Gull/Qinghai/3/05(H5N1) 09 09 02 03 01 -- 01 06 03 06 09 09 13 13 11 10 09 13 11 12 14 14 11 11 08 09 08 07 09 09 06 07 263
    07 A/black-headed gull/Qinghai/1/2005(H5N1) 10 10 03 04 02 01 -- 05 02 05 10 10 14 14 12 11 10 14 12 13 15 15 12 12 09 10 09 08 10 10 07 08 287
    08 A/black-headed goose/Qinghai/1/2005(H5N1) 13 13 06 07 05 06 05 -- 05 08 13 13 17 17 15 14 12 16 14 15 18 18 15 15 12 13 12 11 11 13 10 11 373
    09 A/black-headed goose/Qinghai/2/2005(H5N1) 10 10 03 04 02 03 02 05 -- 05 10 10 14 14 12 11 10 14 12 13 15 15 12 12 09 10 09 08 10 10 07 08 289
    10 A/great black-headed gull/Qinghai/1/2005(H5N1) 11 11 04 05 05 06 05 08 05 -- 11 11 14 15 13 12 11 15 13 14 16 18 13 13 10 11 10 09 11 11 08 09 328
    11 A/bar-headed goose/Qinghai/0510/05(H5N1) 14 14 07 08 08 09 10 13 10 11 -- 14 18 18 16 15 14 18 16 17 19 21 16 16 13 14 13 12 14 14 11 12 425
    12 A/chicken/Nigeria/641/2006(H5N1) 14 14 07 08 08 09 10 13 10 11 14 -- 12 12 10 09 08 12 10 11 13 15 10 10 11 14 11 08 06 04 11 10 325
    13 A/mallard/Italy/835/2006(H5N1) 18 18 11 12 12 13 14 17 14 14 18 12 -- 04 14 13 12 16 14 15 11 13 12 14 15 18 15 14 12 12 15 14 426
    14 A/Cygnus olor/Czech Republic/5170/2006 (H5N1) 18 18 11 12 12 13 14 17 14 15 18 12 04 -- 14 13 12 16 14 15 09 11 14 14 15 18 15 14 12 12 15 14 425
    15 A/whooper swan/Mongolia/3/05(H5N1) 16 16 09 10 10 11 12 15 12 13 16 10 14 14 -- 03 04 14 12 13 15 17 12 12 13 16 13 12 10 10 13 12 379
    16 A/whooper swan/Mongolia/4/05(H5N1) 15 15 08 09 09 10 11 14 11 12 15 09 13 13 03 -- 03 13 11 12 14 16 11 11 12 15 12 11 09 09 12 11 349
    17 A/whooper swan/Mongolia/6/05(H5N1) 14 14 07 08 08 09 10 12 10 11 14 08 12 12 04 03 -- 12 10 11 13 15 10 10 11 14 11 10 08 08 11 10 320
    18 A/domestic cat/Iraq/820/2006(H5N1) 18 18 11 12 12 13 14 16 14 15 18 12 16 16 14 13 12 -- 04 07 17 19 14 14 15 18 15 14 11 10 15 14 431
    19 A/domestic goose/Iraq/812/2006(H5N1) 16 16 09 10 10 11 12 14 12 13 16 10 14 14 12 11 10 04 -- 05 15 17 12 12 13 16 13 12 09 08 13 12 371
    20 A/human/Iraq/207-NAMRU3/2006(H5N1) 17 17 10 11 11 12 13 15 13 14 17 11 15 15 13 12 11 07 05 -- 16 18 13 13 14 17 14 13 10 09 14 13 403
    21 A/chicken/Egypt/960N3-004/2006(H5N1) 19 19 12 13 13 14 15 18 15 16 19 13 11 09 15 14 13 17 15 16 -- 04 15 15 16 19 16 15 13 13 16 15 453
    22 A/Egypt/2782-NAMRU3/2006(H5N1) 21 21 14 15 13 14 15 18 15 18 21 15 13 11 17 16 15 19 17 18 04 -- 17 17 18 21 18 17 15 15 18 17 503
    23 A/mallard/Bavaria/1/2006(H5N1) 16 16 09 10 10 11 12 15 12 13 16 10 12 14 12 11 10 14 12 13 15 17 -- 12 13 16 13 12 10 10 13 12 391
    24 A/bar-headed goose/Mongolia/1/05(H5N1) 16 16 09 10 10 11 12 15 12 13 16 10 14 14 12 11 10 14 12 13 15 17 12 -- 11 16 11 12 08 10 13 12 387
    25 A/duck/Niger/914/2006(H5N1) 13 13 06 07 07 08 09 12 09 10 13 11 15 15 13 12 11 15 13 14 16 18 13 11 -- 13 08 09 11 11 10 11 357
    26 A/chicken/Afghanistan/1207/2006(H5N1) 08 08 07 08 08 09 10 13 10 11 14 14 18 18 16 15 14 18 16 17 19 21 16 16 13 -- 13 10 14 14 11 12 411
    27 A/duck/Kurgan/08/2005(H5N1) 13 13 06 07 07 08 09 12 09 10 13 11 15 15 13 12 11 15 13 14 16 18 13 11 08 13 -- 09 09 11 10 11 355
    28 A/chicken/Krasnodar/01/2006(H5N1) 06 10 05 06 06 07 08 11 08 09 12 08 14 14 12 11 10 14 12 13 15 17 12 12 09 10 09 -- 08 08 09 10 315
    29 A/chicken/Kurgan/05/2005(H5N1) 14 14 07 08 08 09 10 11 10 11 14 06 12 12 10 09 08 11 09 10 13 15 10 08 11 14 09 08 -- 06 11 10 318
    30 A/chicken/Kurgan/3/2005(H5N1) 14 14 07 08 08 09 10 13 10 11 14 04 12 12 10 09 08 10 08 09 13 15 10 10 11 14 11 08 06 -- 11 10 319
    31 A/grebe/Novosibirsk/29/2005(H5N1) 11 11 04 05 05 06 07 10 07 08 11 11 15 15 13 12 11 15 13 14 16 18 13 13 10 11 10 09 11 11 -- 09 335
    32 A/duck/Novosibirsk/56/2005(H5N1) 10 12 05 06 06 07 08 11 08 09 12 10 14 14 12 11 10 14 12 13 15 17 12 12 11 12 11 10 10 10 09 -- 333


  • T1603 matches the low path ducks from Japan and a series of Qinghai isolates from Astrakhan but no match with Nigeria.

    G253A has too many matches to list (several hundred H5N1's) but no sharing wth any other Qinghai strains.

    DQ659113 A/duck/Niger/914/2006 2006 H5N1
    DQ389158 A/Cygnus olor/Astrakhan/Ast05-2-1/2005 2005 H5N1
    DQ434889 A/Cygnus olor/Astrakhan/Ast05-2-10/2005 2005 H5N1
    DQ343502 A/Cygnus olor/Astrakhan/Ast05-2-2/2005 2005 H5N1
    DQ358746 A/Cygnus olor/Astrakhan/Ast05-2-3/2005 2005 H5N1
    DQ363918 A/Cygnus olor/Astrakhan/Ast05-2-4/2005 2005 H5N1
    DQ365004 A/Cygnus olor/Astrakhan/Ast05-2-5/2005 2005 H5N1
    DQ364996 A/Cygnus olor/Astrakhan/Ast05-2-6/2005 2005 H5N1
    DQ363923 A/Cygnus olor/Astrakhan/Ast05-2-7/2005 2005 H5N1
    DQ399540 A/Cygnus olor/Astrakhan/Ast05-2-8/2005 2005 H5N1
    DQ399547 A/Cygnus olor/Astrakhan/Ast05-2-9/2005 2005 H5N1
    DQ449640 A/duck/Kurgan/08/2005 2005 H5N1
    DQ320137 A/swan/Astrakhan/1/2005 2005 H5N1
    AB241624 A/duck/Hokkaido/101/04 2004 H5N3
    AB241625 A/duck/Hokkaido/193/04 2004 H5N3
    AB241626 A/duck/Hokkaido/299/04 2004 H5N3


  • G1447A Again no match with other Qinghai strains, but easily found in other H5N1s

    DQ659113 A/duck/Niger/914/2006 2006 H5N1
    DQ320876 A/chicken/Fujian/1042/2005 2005 H5N1
    DQ320875 A/duck/Fujian/897/2005 2005 H5N1
    DQ320900 A/duck/Guangxi/951/2005 2005 H5N1
    DQ320901 A/duck/Guangzhou/20/2005 2005 H5N1
    DQ320911 A/duck/Hunan/1265/2005 2005 H5N1
    DQ320912 A/duck/Hunan/1608/2005 2005 H5N1
    DQ320913 A/duck/Hunan/1652/2005 2005 H5N1
    DQ320939 A/duck/Vietnam/568/2005 2005 H5N1
    DQ320896 A/goose/Guangxi/345/2005 2005 H5N1
    DQ095628 A/Goose/Shantou/1621/05 2005 H5N1
    DQ320915 A/goose/Shantou/2216/2005 2005 H5N1
    DQ320916 A/migratory duck/Jiangxi/1653/2005 2005 H5N1
    DQ320917 A/migratory duck/Jiangxi/1657/2005 2005 H5N1
    DQ320918 A/migratory duck/Jiangxi/1701/2005 2005 H5N1
    ISDN117777 A/Viet Nam/JP4207/2005 2005 H5N1
    DQ320894 A/chicken/Guangxi/2448/2004 2004 H5N1
    DQ320895 A/chicken/Guangxi/2461/2004 2004 H5N1
    ISDN48972 A/Chicken/Hu bei/14/2004 2004 H5N1
    AY684706 A/chicken/Hubei/327/2004 2004 H5N1
    AY770079 A/chicken/Hubei/489/2004 2004 H5N1
    AY830774 A/chicken/Macheng/2004 2004 H5N1
    DQ083567 A/Ostrich/Samut Prakan/Thailand/CU-19/04 2004 H5N1
    DQ083574 A/ostrich/Samut Prakan/Thailand/CU-31/04 2004 H5N1
    AY651362 A/peregrine falcon/Hong Kong/D0028/2004 2004 H5N1
    AY950236 A/swan/Guangxi/307/2004 2004 H5N1
    AY651354 A/Ck/Hong Kong/NT93/2003 2003 H5N1
    AY651356 A/Ck/Hong Kong/SSP141/2003 2003 H5N1
    AY651355 A/Ck/Hong Kong/WF157/2003 2003 H5N1







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