H5N1 in Niger and Nigeria Are Distinct
Recombinomics Commentary
July 5, 2006
A report in tomorrow's Nature describes H5N1 isolates from two farms in Lagos Nigeria which are distinct from each other and from a northern Nigerian isolate, as seen on the phylogenetic tree. These different lineages indicate that the H5N1 bird flu in Nigeria was not from trade, which would have generated a common H5N1, but rather was from wild birds which are transmitting and transporting various lineages of the Qinghai strain as seen in the phylogentic tree of Qinghai isolates in Europe. Recently the sequence of a isolate from southern Niger was published. Media reports suggested that the Niger outbreak was from the spread of the initial infection in neighboring Nigeria. However, the lineage in Niger is distinct from Nigeria and it too was introduced into the area via an independent route which was also wild birds.
All of the above isolates are clearly the Qinghai strain, with an HA cleavage site of GERRRKKR. These isolates have many polymorphisms in common, linking the lineages back to Qinghai Lake. However, each strain has a small number of polymorphisms that distinguish the isolate from other Qinghai strains and define separate branches of a phylogenetic tree. The Niger isolate, A/duck/Niger/914/2006, has six such polymorphisms, G253A, A524G, C1198T, G1240A, G1447A, T1603C. In contrast, the Nigerian isolate, A/chicken/Nigeria/641/2006, also has six such defining polymorphisms, but only A524G is share with the Niger isolate. The other five, G185A, A421G, G632A, G1951A, C1249T are largely shared with Qinghai isolates from Kurgan.
The Niger polymorphisms are unusual in that they are not widely shared with a subset of Qinghai isolates. Remarkably, G1240T was shared with a Mongolian Qinghai isolate as well as H7 isolates, including isolates from the H7N3 outbreak in England, A/chicken/England/4054/2006(H7N3) and A/chicken/England/4266/2006(H7N3).
These polymorphisms are acquired via recombination and therefore a travel history of the polymorphisms can be generated using the sequence database at Los Alamos. The shared polymorphisms are listed below, but the different profiles of the two isolates indicate that these H5N1's were independently introduced into the region and the Niger isolate did not come from the commercial farm that reported the first H5N1 outbreak in Nigeria. Instead the H5N1 in the area was introduced via migratory birds, and as some media reports suggested, this introduction was weeks or months prior to the initial report and confirmation of H5N1 in Nigeria.
G185A
DQ447199 A/chicken/Egypt/960N3-004/2006 2006 H5N1
DQ676830 A/chicken/Mahachkala/05/2006 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
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
ISDN133098 A/Turkey/12/2006 2006 H5N1
ISDN133105 A/Turkey/15/2006 2006 H5N1
ISDN133356 A/Turkey/651242/06 2006 H5N1
ISDN133364 A/Turkey/65596/06 2006 H5N1
AB233319 A/bar-headed goose/Mongolia/1/05 2005 H5N1
DQ449632 A/chicken/Kurgan/05/2005 2005 H5N1
DQ323672 A/chicken/Kurgan/3/2005 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
DQ659326 A/Whooping swan/Mongolia/244/2005 2005 H5N1
ISDN140936 A/Whooping swan/Mongolia/244/2005 2005 H5N1
DQ320893 A/chicken/Guangxi/2439/2004 2004 H5N1
DQ320883 A/duck/Guangxi/1311/2004 2004 H5N1
DQ320884 A/duck/Guangxi/1378/2004 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
DQ320879 A/duck/Guangxi/668/2004 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
DQ320880 A/goose/Guangxi/914/2004 2004 H5N1
ISDN40326 A/Chicken/Viet Nam/Ncvd8/2003 2003 H5N1
ISDN38689 A/Duck/Viet Nam/Ncvd1/2002 2002 H5N1
AY651352 A/teal/China/2978.1/2002 2002 H5N1
AF501235 A/duck/Shanghai/1/2000 2000 H5
AF501234 A/duck/Shanghai/1/2000 2000 H5
DQ201829 A/Goose/Huadong/1/2000 2000 H5N1
A421G
DQ676834 A/chicken/Krasnodar/01/2006 2006 H5N1
ISDN138756 A/chicken/Malaysia/935/2006 2006 H5N1
DQ406728 A/chicken/Nigeria/641/2006 2006 H5N1
DQ449632 A/chicken/Kurgan/05/2005 2005 H5N1
DQ323672 A/chicken/Kurgan/3/2005 2005 H5N1
A524G
DQ447199 A/chicken/Egypt/960N3-004/2006 2006 H5N1
DQ676834 A/chicken/Krasnodar/01/2006 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
ISDN133105 A/Turkey/15/2006 2006 H5N1
ISDN133356 A/Turkey/651242/06 2006 H5N1
ISDN133364 A/Turkey/65596/06 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
DQ676840 A/goose/Krasnoozerka/627/2005 2005 H5N1
DQ320897 A/quail/Guangxi/575/2005 2005 H5N1
DQ320137 A/swan/Astrakhan/1/2005 2005 H5N1
ISDN129523 A/turkey/Turkey/1/05 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
DQ659326 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
G632A
DQ406728 A/chicken/Nigeria/641/2006 2006 H5N1
DQ323672 A/chicken/Kurgan/3/2005 2005 H5N1
AB212649 A/blow fly/Kyoto/93/2004 2004 H5N1
AB188824 A/chicken/Kyoto/3/2004 2004 H5N1
AB188816 A/chicken/Oita/8/2004 2004 H5N1
AB166862 A/chicken/Yamaguchi/7/2004 2004 H5N1
ISDN49016 A/Chicken/Yamaguchi/7/2004 2004 H5N1
AB189053 A/crow/Kyoto/53/2004 2004 H5N1
AB189061 A/crow/Osaka/102/2004 2004 H5N1
AY676035 A/chicken/Korea/ES/03 2003 H5N1
ISDN40921 A/Chicken/Korea/es/2003 2003 H5N1
AY676036 A/duck/Korea/ESD1/03 2003 H5N1
G1051A
ISDN138756 A/chicken/Malaysia/935/2006 2006 H5N1
DQ406728 A/chicken/Nigeria/641/2006 2006 H5N1
ISDN138780 A/duck/Laos/3295/2006 2006 H5N1
DQ643809 A/Zhejiang/16/2006 2006 H5N1
DQ371928 A/Anhui/1/2005 2005 H5N1
DQ371929 A/Anhui/2/2005 2005 H5N1
DQ320898 A/chicken/Guangxi/604/2005 2005 H5N1
DQ320910 A/chicken/Hunan/999/2005 2005 H5N1
DQ095626 A/Chicken/Shantou/810/05 2005 H5N1
DQ497665 A/chicken/Simalanggang/BPPVI/2005 2005 H5N1
DQ095624 A/Chicken/Yunnan/447/05 2005 H5N1
DQ095625 A/Chicken/Yunnan/493/05 2005 H5N1
DQ320925 A/Chinese pond heron/Hong Kong/18/2005 2005 H5N1
DQ095629 A/Duck/Fujian/1734/05 2005 H5N1
DQ320899 A/duck/Guangxi/793/2005 2005 H5N1
DQ320900 A/duck/Guangxi/951/2005 2005 H5N1
DQ095630 A/Duck/Hunan/114/05 2005 H5N1
DQ320911 A/duck/Hunan/1265/2005 2005 H5N1
DQ320902 A/duck/Hunan/127/2005 2005 H5N1
DQ320903 A/duck/Hunan/139/2005 2005 H5N1
DQ320904 A/duck/Hunan/149/2005 2005 H5N1
DQ320905 A/duck/Hunan/152/2005 2005 H5N1
DQ320906 A/duck/Hunan/157/2005 2005 H5N1
DQ320907 A/duck/Hunan/160/2005 2005 H5N1
DQ320912 A/duck/Hunan/1608/2005 2005 H5N1
DQ320913 A/duck/Hunan/1652/2005 2005 H5N1
DQ320908 A/duck/Hunan/166/2005 2005 H5N1
DQ320909 A/duck/Hunan/182/2005 2005 H5N1
DQ095631 A/Duck/Hunan/191/05 2005 H5N1
DQ320939 A/duck/Vietnam/568/2005 2005 H5N1
DQ320896 A/goose/Guangxi/345/2005 2005 H5N1
DQ371930 A/Guangxi/1/2005 2005 H5N1
DQ320897 A/quail/Guangxi/575/2005 2005 H5N1
ISDN48980 A/Chicken/Guang xi/12/2004 2004 H5N1
AY737296 A/chicken/Guangdong/178/04 2004 H5N1
DQ320894 A/chicken/Guangxi/2448/2004 2004 H5N1
DQ320895 A/chicken/Guangxi/2461/2004 2004 H5N1
AY651372 A/Ck/YN/115/2004 2004 H5N1
AY651371 A/Ck/YN/374/2004 2004 H5N1
AY651365 A/Dk/HN/101/2004 2004 H5N1
AY651364 A/Dk/HN/303/2004 2004 H5N1
DQ320890 A/duck/Guangxi/2291/2004 2004 H5N1
DQ320877 A/duck/Guangxi/351/2004 2004 H5N1
DQ320878 A/duck/Guangxi/380/2004 2004 H5N1
ISDN48957 A/Duck/Hu nan/15/2004 2004 H5N1
DQ320923 A/grey heron/Hong Kong/728/2004 2004 H5N1
DQ320924 A/grey heron/Hong Kong/837/2004 2004 H5N1
AY651366 A/Ph/ST/44/2004 2004 H5N1
DQ211922 A/chicken/jiyuan/1/03 2003 H5N1
AY651363 A/Dk/HN/5806/2003 2003 H5N1
AY651369 A/Dk/YN/6255/2003 2003 H5N1
AY651370 A/Dk/YN/6445/2003 2003 H5N1
AY518362 A/duck/China/E319-2/03 2003 H5N1
DQ211923 A/chicken/zhengzhou/1/02 2002 H5N1
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
AY995897 A/mallard/Sweden/79/02 2002 H5N9
AY995898 A/mallard/Sweden/80/02 2002 H5N9
C1198T
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
DQ644959 A/duck/Badung-Bali/05/2005 2005 H5N1
DQ644955 A/chicken/Denpasar/01/2004 2004 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/YU562/0 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
G1447A
DQ659113 A/duck/Niger/914/2006 2006 H5N1
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
AY651336 A/Viet Nam/3062/2004 2004 H5N1
AY747609 A/swine/Fujian/1/2003 2003 H5N1
AY747617 A/swine/Fujian/F1/2001 2001 H5N1
AY585377 A/duck/Zhejiang/52/2000 2000 H5N1
T1603C
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
DQ676840 A/goose/Krasnoozerka/627/2005 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
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