Recombinomics | Elegant Evolution

Home Founder What's New In The News Contact Us

Paradigm Shift

Viral Evolution

Intervention Monitoring

Vaccine Screening

Vaccine Development

Expression Profiling

Drug Discovery

Custom Therapies


H5N1 Qinghai Emergence in Mongolia

Recombinomics Commentary

July 6, 2006

In May, 2005 the Qinghai strain of H5N1 was identified at Qihgnai Lake in central China.  The presence of H5N1 in long range migratory birds provided an opportunity to track the evolution of H5N1 bird flu.  H5N1 migrated into southern Siberia, Kazakhstan, and Mongolia in the summer and then to Europe, the Middle East, and Africa in the fall and winter.  As the Qinghai strain returns to summer in the north, sequence analysis provides an unprecedented view of the strain's evolution.

This evolution can be monitored by the newly acquired polymorphisms.  These polymorphisms are added to the Qinghai background and can be identified by a limited distribution among other Qinghai isolates.  Recently the HA sequence of a new isolate from Mongolia, A/whooper swan/Mongolia/2/2006, was made public. Listing of shared isolates displays a travel history of these plymorphisms.  The HA sequences from the above isolate had 10 informative polymorphism, G59A, T211C, C268T, A539G, C796T, T868C, A1300G, C1330T, G1562T, C1618T.  All but one of the polymorphisms could be found in other Qingahi isolates (in bold below), but all such isolates were from 2006. These acquisitions may be related to the travel path of the H5N1 isolated. 

Qinghai isolates with shared polymorphisms are as far was west as Italy and did not include polymorphisms from Qinghai isolates in 2005.  Additional isolates will provide more useful travel histories of H5N1 migrating to new regions and returning to summer locations in the north.


   AB263752  A/whooper swan/Mongolia/2/06  2006  H5N1   
   DQ343150  A/chicken/Hebei/326/2005              2005  H5N1   
   DQ320915  A/goose/Shantou/2216/2005          2005  H5N1   
   AY609312  A/chicken/Guangdong/174/04         2004  H5N1   
   AY737289  A/chicken/Guangdong/191/04         2004  H5N1   
   DQ343151  A/chicken/Hebei/718/2001             2001  H5N1   
   AY585365  A/duck/Guangxi/35/2001                 2001  H5N1   


    DQ661910    A/chicken/Afghanistan/1207/2006    2006  H5N1   
   DQ676834    A/chicken/Krasnodar/01/2006           2006  H5N1   
   DQ440535    A/swan/Iran/754/2006                          2006  H5N1   
   DQ412997    A/swan/Italy/179/06                             2006  H5N1   
   ISDN136919  A/swan/Italy/179/2006                        2006  H5N1   
   AB263752    A/whooper swan/Mongolia/2/06       2006  H5N1  


   DQ661910    A/chicken/Afghanistan/1207/2006   2006  H5N1   
   AB263752    A/whooper swan/Mongolia/2/06       2006  H5N1   
   ISDN124038  A/Chicken/Viet Nam/NCVD09/2005   2005  H5N1   
   ISDN124037  A/Chicken/Viet Nam/NCVD10/2005   2005  H5N1   
   AM183674    A/chicken/Vietnam/P22/05                    2005  H5N1   
   AM183673    A/chicken/Vietnam/P78/05                    2005  H5   
   DQ497674    A/duck/Vietnam/272/2005                     2005  H5N1   
   AM183676    A/duck/Vietnam/AG40-O2/05                2005  H5   
   DQ497677    A/mallard/Vietnam/352/2005                 2005  H5N1   
   ISDN111351  A/Chicken/Indonesia/7/2003                2003  H5N1   
   DQ497646    A/chicken/Sragen/BPPV4/2003           2003  H5N1   
   DQ497681    A/chicken/Vietnam/28/2003                  2003  H5N1   
   DQ497693    A/chicken/Vietnam/8/2003                    2003  H5N1   
   AY585364    A/duck/Guangxi/22/2001                        2001  H5N1   
   ISDN38260   A/Goose/Viet Nam/113/2001               2001  H5N1   
   ISDN38261   A/Goose/Viet Nam/324/2001               2001  H5N1  


   DQ661910    A/chicken/Afghanistan/1207/2006   2006  H5N1   
   DQ440535    A/swan/Iran/754/2006                          2006  H5N1   
   DQ412997    A/swan/Italy/179/06                              2006  H5N1   
   ISDN136919  A/swan/Italy/179/2006                         2006  H5N1   
   AB263752    A/whooper swan/Mongolia/2/06        2006  H5N1   
   DQ320939    A/duck/Vietnam/568/2005                     2005  H5N1   
   AY737289    A/chicken/Guangdong/191/04               2004  H5N1   
   AY518362    A/duck/China/E319-2/03                        2003  H5N1   


  AB263752   A/whooper swan/Mongolia/2/06     2006  H5N1   
   DQ320939   A/duck/Vietnam/568/2005                 2005  H5N1   
   AY585373   A/duck/Guangdong/07/2000               2000  H5N1   
   AY059476   A/Duck/Hong Kong/ww381/2000       2000  H5N1   
   AY059477   A/Duck/Hong Kong/ww382/2000       2000  H5N1   
   AY059478   A/Duck/Hong Kong/ww461/2000       2000  H5N1   
   AY059479   A/Duck/Hong Kong/ww487/2000       2000  H5N1   
   AY059480   A/Goose/Hong Kong/ww491/2000      2000  H5N1   
   DQ092869   A/Pekin duck/Singapore/F59/04/98  1998  H5N2   
   AF194992   A/Chicken/Italy/9097/97                         1997  H5N9   
   ISDN49024  A/duck/Singapore/3/97                        1997  H5N3   
   AF303057   A/duck/Singapore/Q-F119-3/97          1997  H5N3   
   S68489     A/turkey/England/50-92/91                      1991  H5N1   
   AF082042   A/Duck/Potsdam/1402-6/86                1986  H5N2   
   CY006036   A/duck/Potsdam/2216-4/1984            1984  H5N6   
   AF082041   A/Duck/Potsdam/2216-4/84                1984  H5N6   
   M18450     A/Duck/Ireland/113/83                             1983  H5N8   
   M18451     A/Turkey/Ireland/1378/83                        1983  H5N8   
   AF082039   A/Duck/Hong Kong/698/79                   1979  H5N3   
   AF290443   A/Duck/Ho Chi Minh/14/78                    1978  H5N3   
   CY005575   A/duck/Hong Kong/342/1978               1978  H5N2   
   U20475     A/duck/Hong Kong/342/78                      1978  H5N2   
   CY006028   A/goose/Hong Kong/23/1978               1978  H5N3   
   AF082038   A/Duck/Hong Kong/205/77                   1977  H5N3   
   AB241615   A/duck/Miyagi/54/76                              1976  H5N3   

   DQ661910    A/chicken/Afghanistan/1207/2006    2006  H5N1   
   DQ440535    A/swan/Iran/754/2006                          2006  H5N1   
   DQ412997    A/swan/Italy/179/06                              2006  H5N1   
   ISDN136919  A/swan/Italy/179/2006                        2006  H5N1   
   AB263752    A/whooper swan/Mongolia/2/06       2006  H5N1   
   DQ104701    A/duck broiler/Malaysia/F118/08/04    2004  H5N2   
   DQ122147    A/duck broiler/Malaysia/F189/07/04    2004  H5N2   
   AB241624    A/duck/Hokkaido/101/04                       2004  H5N3   
   AB241625    A/duck/Hokkaido/193/04                       2004  H5N3   
   AB241626    A/duck/Hokkaido/299/04                       2004  H5N3   
   AJ715872    A/Hanoi/03/2004                                     2004  H5N1   
   AY651335    A/Viet Nam/3046/2004                         2004  H5N1   
   ISDN40278   A/Viet Nam/3212/2004                        2004  H5N1   
   AJ632269    A/chicken/France/03426a/03                2003  H5N2   
   DQ497679    A/chicken/Vietnam/20/2003                 2003  H5N1   
   DQ320938    A/chicken/Vietnam/27/2003                  2003  H5N1   
   DQ497681    A/chicken/Vietnam/28/2003                  2003  H5N1   
   DQ497693    A/chicken/Vietnam/8/2003                    2003  H5N1   
   AY995885    A/mallard/Sweden/21/02                        2002  H5N2   
   AY995895    A/mallard/Sweden/58/02                        2002  H5N3   
   AF194169    A/Chicken/Italy/312/97                           1997  H5N2   


AB263752  A/whooper swan/Mongolia/2/06    2006  H5N1
                      (plus many other H5N1 isolates)   


   DQ661910  A/chicken/Afghanistan/1207/2006    2006  H5N1   
   AB263752  A/whooper swan/Mongolia/2/06        2006  H5N1   
   DQ497651  A/chicken/Gunung Kidal/BBVW/2005   2005  H5N1   
   DQ497643  A/chicken/Magetan/BBVW/2005          2005  H5N1   
   DQ320933  A/chicken/Wajo/BBVM/2005                2005  H5N1   
   DQ497659  A/duck/Parepare/BBVM/2005             2005  H5N1   
   DQ387854  A/mallard/Bavaria/1/2005                     2005  H5N2   
   DQ647648  A/ostrich/South Africa/1/2004               2004  H5N2   
   DQ007623  A/Anas platyrhynchos/Chany Lake      2003  H5N3   
   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   
   AY995891  A/mallard/Sweden/39/02                        2002  H5N3   
   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   
   AJ621807  A/duck/Primorie/2633/01                       2001  H5N3   
   AY075030  A/Goose/Hong Kong/3014.5/2000      2000  H5N1   
   AY059482  A/Goose/Hong Kong/3014.8/2000      2000  H5N1   
   AY684894  A/mallard/Netherlands/3/99                  1999  H5N2   
   AJ305306  A/chicken/Italy/8/98                                1998  H5N2   
   AF194169  A/Chicken/Italy/312/97                          1997  H5N2   
   AF194990  A/Chicken/Italy/367/97                          1997  H5N2   
   AF194992  A/Chicken/Italy/9097/97                        1997  H5N9   
   AF194991  A/Guinea Fowl/Italy/330/97                    1997  H5N2 


  AB263752  A/whooper swan/Mongolia/2/06        2006  H5N1   
   DQ497642  A/chicken/Malang/BBVet-IV/2004        2004  H5N1   
   DQ497653  A/chicken/Purwakarta/BBVet-IV/2004  2004  H5N1  


   DQ661910    A/chicken/Afghanistan/1207/2006    2006  H5N1   
   ISDN133364  A/Turkey/65596/06                                2006  H5N1   
   AB263752    A/whooper swan/Mongolia/2/06        2006  H5N1   
   DQ320910    A/chicken/Hunan/999/2005                   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   
   DQ387854    A/mallard/Bavaria/1/2005                     2005  H5N2   
   AF509025    A/Chicken/Hong Kong/715.5/01            2001  H5N1   
   AY221524    A/Chicken/Hong Kong/FY150/01           2001  H5N1   
   AF509019    A/Chicken/Hong Kong/FY150/01          2001  H5N1   
   AY221523    A/Chicken/Hong Kong/FY150/01-MB    2001  H5N1   
   AF509016    A/Chicken/Hong Kong/FY77/01  HA      2001  H5N1   
   AY221522    A/Chicken/Hong Kong/NT873.3/01        2001  H5N1   
   AY221521    A/Chicken/Hong Kong/NT873.3/01-MB  2001  H5N1   
   AY221526    A/Pheasant/Hong Kong/FY155/01          2001  H5N1   
   AF509020    A/Pheasant/Hong Kong/FY155/01          2001  H5N1   
   AY221525    A/Pheasant/Hong Kong/FY155/01-MB    2001  H5N1   
   M18450      A/Duck/Ireland/113/83                                 1983  H5N8   
   M18451      A/Turkey/Ireland/1378/83                             1983  H5N8   
   X07869      A/chicken/Scotland/59                                  1959  H5N1   
   X07826      A/Chicken/Scotland/59                                 1959  H5N1  

Media Sources

Phylogenetic Trees

Home | Founder | What's New | In The News | Contact Us

© 2006 Recombinomics.  All rights reserved.