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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.


   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


   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 


   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


   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


  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  


   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 


   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  


   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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