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Qinghai H5N1 Sequences Fly Into Indonesia
Recombinomics Commentary

August 24, 2006

The HA H5N1 sequence of a 2005 wild duck isolate from Omsk, A/wild duck/103-01/05, was released.  Like other newly released Qinghai sequences, the isolate had a small number of “new” polymorphisms which unique or detected in a subset of other Qinghai isolates.  One polymorphism, C1261T, is fairly common in a subset of recent Qinghai isolates.  However, it is also detected in isolates from two patients in Indonesia (see below).  Similarly, a second polymorphism is not found in other Qinghai isolates, but is detected in one of the two Indonesian patients which has C1261T, as well as a second Indonesian patient who was infected in 2005.

Thus, although these two polymorphisms had a restricted distribution in Qinghai isolates, the were detected in three patients from Indonesia.  These data extend the observations that the new isolates are shared by various sub-clades.  Recently the WHO announced new pandemic vaccine targets.  These isolates represent three sub-clades of Clade 2, representing human cases from Indonesia, China, and the Middle East and Africa.

The sharing of these “new” polymorphism by various sub-clades provides additional evidence for acquisition via recombination.  The shared polymorphisms are new acquisitions placed onto various genetic backgrounds.  The isolates sharing these polymorphisms are listed below.  Qinghai isolates are in black bold, while human Indonesian isolates are in red bold.


DQ862001    A/chicken/Egypt/2253-1/2006                       2006  H5N1   
DQ837587    A/chicken/Egypt/5610NAMRU3-F3/2006   2006  H5N1   
DQ837588    A/chicken/Egypt/5611NAMRU3-AN/2006  2006  H5N1   
DQ837589    A/chicken/Egypt/5612NAMRU3-S/2006     2006  H5N1   
DQ447199    A/chicken/Egypt/960N3-004/2006               2006  H5N1   
DQ673901    A/chicken/Ivory Coast/1787/2006                2006  H5N1   
AM262546    A/chicken/Lagos.NIE/SO300/2006               2006  H5N1   
AM262547    A/chicken/Lagos.NIE/SO452/2006               2006  H5N1   
AM262553    A/chicken/Lagos.NIE/SO493/2006               2006  H5N1   
AM262572    A/chicken/Lagos.NIE/SO494/2006               2006  H5N1   
DQ406728    A/chicken/Nigeria/641/2006                           2006  H5N1   
DQ862003    A/chicken/Sudan/1784/2006                         2006  H5N1   
DQ861999    A/chicken/Sudan/2115-12/2006                    2006  H5N1   
DQ862000    A/chicken/Sudan/2115-9/2006                      2006  H5N1   
DQ864719    A/chicken/Volgograd/236/06                         2006  H5N1   
DQ659679    A/common bussard/Bavaria/2/2006            2006  H5N1   
DQ515984    A/Cygnus olor/Czech Republic/5170/20062006 H5N1   
DQ666146     A/Djibouti/5691NAMRU3/2006                     2006  H5N1   
DQ435200     A/domestic cat/Iraq/820/2006                       2006  H5N1   
DQ435201     A/domestic goose/Iraq/812/2006                2006  H5N1   
DQ862002     A/duck/Egypt/2253-3/2006                           2006  H5N1   
DQ464377     A/Egypt/2782-NAMRU3/2006                       2006  H5N1   
ISDN140926  A/Indonesia/542H/2006                                 2006  H5N1   
ISDN187445  A/Indonesia/583H/2006                                 2006  H5N1   
ISDN183698  A/Indonesia/CDC610/2006                           2006  H5N1   
ISDN204133  A/Indonesia/CDC669/2006                           2006  H5N1   
ISDN204141  A/Indonesia/CDC669P/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   
DQ837590     A/turkey/Egypt/5613NAMRU3-T/2006       2006  H5N1   
AB233319     A/bar-headed goose/Mongolia/1/05           2005  H5N1   
DQ650659     A/chicken/Crimea/04/2005                            2005  H5N1   
DQ650663     A/chicken/Crimea/08/2005                            2005  H5N1   
DQ320910     A/chicken/Hunan/999/2005                              2005  H5N1   
DQ449632     A/chicken/Kurgan/05/2005                           2005  H5N1   
DQ323672     A/chicken/Kurgan/3/2005                             2005  H5N1   
DQ864716     A/chicken/Tambov/570-2/05                        2005  H5N1   
DQ279301     A/chicken/Tula/10/2005                                2005  H5N1   
DQ840519     A/chicken/Tula/Russia/Oct-5/2005             2005  H5N1   
DQ095630     A/Duck/Hunan/114/05                                      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   
DQ320908     A/duck/Hunan/166/2005                                  2005  H5N1   
DQ320909     A/duck/Hunan/182/2005                                  2005  H5N1   
DQ095631     A/Duck/Hunan/191/05                                      2005  H5N1   
DQ864711     A/duck/Novosibirsk/02/05                            2005  H5N1   
DQ230522     A/duck/Novosibirsk/56/2005                        2005  H5N1   
DQ864717     A/goose/Crimea/615/05                                 2005  H5N1   
DQ212792     A/goose/Novosibirsk/4/2005                        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   
DQ864721     A/wild duck/Omsk/103-01/05                        2005  H5N1   
AM183671     A/chicken/China/1204/04                                 2004  H5N1   
ISDN48980    A/Chicken/Guang xi/12/2004                           2004  H5N1   
DQ366330     A/chicken/Guangxi/12/2004                             2004  H5N1   
ISDN48989    A/Duck/Guang xi/13/2004                                2004  H5N1   
DQ366338     A/duck/Guangxi/13/2004                                 2004  H5N1   
ISDN40326    A/Chicken/Viet Nam/Ncvd8/2003                   2003  H5N1   
DQ497678     A/chicken/Vietnam/19/2003                            2003  H5N1  
CY003992      A/mallard/Alberta/79/2003                              2003  H2N3  
CY003984      A/mallard/Alberta/149/2002                            2002  H2N4  
AY633196      A/mallard/Alberta/205/1998                            1998  H2N3  
CY003968      A/mallard/Alberta/205/1998                            1998  H2N3  
AY633228      A/mallard/Alberta/226/1998                             1998  H2N3  
CY003976      A/mallard/Alberta/226/1998                             1998  H2N3  
CY003960      A/blue-winged teal/Alberta/16/1997                1997  H2N9  
AY633364      A/pintail/Alberta/22/97                                       1997  H2N9  
AY633388      A/teal/Alberta/16/97                                           1997  H2N9  
CY003944      A/mallard/Alberta/201/1996                              1996  H2N3  
CY003952      A/mallard/Alberta/202/1996                              1996  H2N5  
AY633180      A/mallard/Alberta/202/1996                              1996  H2N5  
AB241616     A/swan/Hokkaido/4/96                                       1996  H5N3  
AB241617     A/swan/Hokkaido/51/96                                     1996  H5N3  
AB241618     A/swan/Hokkaido/67/96                                     1996  H5N3  
L11131           A/guinea/NJ/3070/91                                         1991  H2N2  
CY005413     A/semi-palmated sandpiper/Brazil/43/1990    1990  H2N1


ISDN187445  A/Indonesia/583H/2006                                 2006  H5N1   
ISDN204133  A/Indonesia/CDC669/2006                           2006  H5N1   
ISDN204141  A/Indonesia/CDC669P/2006                        2006  H5N1   
ISDN128026  A/Indonesia/6/2005                                        2005  H5N1   
DQ864721     A/wild duck/Omsk/103-01/05                       2005  H5N1   
AY741219      A/tree sparrow/Henan/3/2004                         2004  H5N1   
AJ632268      A/duck/France/02166/2002                             2002  H5N3

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