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Qinghai H5N1 Bird Flu Sequences in Bali Indonesia

Recombinomics Commentary

June 17, 2006

Five avian HA sequences from Bali Indonesia (see below) have become available at GenBank.  The partial sequences include the HA cleavage site and four of the five isolates have the common cleavage site for Asian H5N1, RERRRKKR.  However, A/duck/Badung-Bali/05/2005 has the Qinghai HA cleavage site, GERRRKKR.  This cleavage site is almost exclusively found in Qinghai isolates (see list below) and represents the third distinct cleavage site in H5N1 from Indonesia.  Human isolates in Western Java have the novel cleavage site RESRRKKR, which has not been identifiued in any reported H5N1 isolate.

In addition, the Bali isolate above has another polymorphism shared with Qinghai isolates as well A/chicken/Denpasar/01/04.  This isolate has a third polymorphism shared with other Qinghai isolates.

Although these Bali bird flu isolates have Qinhai polymorphisms, their genetic backbone is clearly Indonesian.  All five Bali isolates are most closely related to other Indonesian isolates.  Thus, these isolates have acquired Qinghai sequence via recombination, which punctuates an Indonesian sequence.

The acquisition of these sequences signal dual infection between Indonesian isolates and Qinghai isolates.  All Qinghai isolates reported to date have PB2 E627K, which has also been identified in the second human isolate, A/Indonesia/6/2005, and is suspected in the Medan cluster.  The sole surving member of thet 8 person cluster has developed neurological complications, which are also associated with E627K.

The Qinghai sequences, including the HA cleavage site highlight the complexity of H5N1 in Indonesia and again emphasizes the need for the release of the sequences sequestered at the WHO private database.

The acquisition of the Qinghai sequences, including the HA cleavage site, which has been acquired on an Indonesian genetic background, signal active evolution via recombination, which is cause for concern.

WHO affiliated researchers have ignored the role of recombination in H5N1 evolution, and the sequestered sequences should be made public for in depth analysis.

New isolates:


Matching sequences in HA cleavage site

   DQ661910    A/chicken/Afghanistan/1207/2006             2006  H5N1   
   DQ447199    A/chicken/Egypt/960N3-004/2006             2006  H5N1   
   DQ676834    A/chicken/Krasnodar/01/2006                    2006  H5N1   
   DQ676830    A/chicken/Mahachkala/05/2006                  2006  H5N1   
   DQ406728    A/chicken/Nigeria/641/2006                        2006  H5N1   
   AM231714    A/common pochard/France/06167/2006    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   
   DQ440535    A/swan/Iran/754/2006                                     2006  H5N1   
   DQ412997    A/swan/Italy/179/06                                         2006  H5N1   
   ISDN136919  A/swan/Italy/179/2006                                   2006  H5N1   
   AM236074    A/turkey/France/06222/2006                        2006  H5N1   
   AB233319    A/bar-headed goose/Mongolia/1/05            2005  H5N1   
   DQ137873    A/bar-headed goose/Qinghai/0510/05       2005  H5N1   
   DQ095621    A/Bar-headed Goose/Qinghai/12/05          2005  H5N1   
   DQ095617    A/Bar-headed Goose/Qinghai/5/05            2005  H5N1   
   DQ095612    A/Bar-headed Goose/Qinghai/59/05          2005  H5N1   
   DQ095615    A/Bar-headed Goose/Qinghai/60/05          2005  H5N1   
   DQ095618    A/Bar-headed Goose/Qinghai/61/05          2005  H5N1   
   DQ095620    A/Bar-headed Goose/Qinghai/62/05          2005  H5N1   
   DQ095622    A/Bar-headed Goose/Qinghai/65/05          2005  H5N1   
   DQ095623    A/Bar-headed Goose/Qinghai/67/05          2005  H5N1   
   DQ095613    A/Bar-headed Goose/Qinghai/68/05          2005  H5N1   
   DQ095619    A/Bar-headed Goose/Qinghai/75/05          2005  H5N1   
   DQ100554    A/black-headed goose/Qinghai/1/2005       2005  H5N1   
   DQ100555    A/black-headed goose/Qinghai/2/2005       2005  H5N1   
   DQ100556    A/black-headed gull/Qinghai/1/2005            2005  H5N1   
   DQ095616    A/Brown-headed Gull/Qinghai/3/05              2005  H5N1   
   DQ340848    A/chicken/Crimea/1/2005                             2005  H5N1   
   DQ676838    A/chicken/Dovolnoe/03/2005                        2005  H5N1   
   DQ449632    A/chicken/Kurgan/05/2005                            2005  H5N1   
   DQ323672    A/chicken/Kurgan/3/2005                              2005  H5N1   
   DQ190859    A/chicken/Novosibirsk/64/05                         2005  H5N1   
   DQ190860    A/chicken/Novosibirsk/65/05                         2005  H5N1   
   DQ190861    A/chicken/Novosibirsk/66/05                         2005  H5N1   
   DQ231242    A/chicken/Suzdalka/Nov-11/05                      2005  H5N1   
   DQ231241    A/chicken/Suzdalka/Nov-12/05                      2005  H5N1   
   DQ279301    A/chicken/Tula/10/2005                                  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   
   DQ644959    A/duck/Badung-Bali/05/2005                     2005  H5N1   
   DQ449640    A/duck/Kurgan/08/2005                                  2005  H5N1   
   DQ190858    A/duck/Novosibirsk/56/2005                         2005  H5N1   
   DQ230522    A/duck/Novosibirsk/56/2005                         2005  H5N1   
   DQ320922    A/Environment/Qinghai/31/2005                  2005  H5N1   
   DQ676840    A/goose/Krasnoozerka/627/2005                2005  H5N1   
   DQ212792    A/goose/Novosibirsk/4/2005                        2005  H5N1   
   DQ100557    A/great black-headed gull/Qinghai/1/2005  2005  H5N1   
   DQ095614    A/Great Black-headed Gull/Qinghai/2/05    2005  H5N1   
   DQ230521    A/grebe/Novosibirsk/29/2005                       2005  H5N1   
   DQ190857    A/grebe/Novosibirsk/29/2005                      2005  H5N1   
   DQ320919    A/migratory duck/Jiangxi/2136/2005            2005  H5N1   
   DQ320920    A/migratory duck/Jiangxi/2295/2005           2005  H5N1   
   DQ320921    A/migratory duck/Jiangxi/2300/2005           2005  H5N1   
   DQ453141    A/mute swan/Croatia/1/2005                        2005  H5N1   
   DQ320137    A/swan/Astrakhan/1/2005                             2005  H5N1   
   DQ231240    A/turkey/Suzdalka/Nov-01/05                       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   
   ISDN48972   A/Chicken/Hu bei/14/2004                           2004  H5N1   
   AY830774    A/chicken/Macheng/2004                              2004  H5N1  

One of the Qinghai polymorphims

   DQ231242   A/chicken/Suzdalka/Nov-11/05     2005  H5N1   
   DQ231241   A/chicken/Suzdalka/Nov-12/05     2005  H5N1   
   DQ644959   A/duck/Badung-Bali/05/2005     2005  H5N1   
   DQ231240   A/turkey/Suzdalka/Nov-01/05        2005  H5N1   
   DQ407519   A/turkey/Turkey/1/2005                   2005  H5N1   
   AB212649   A/blow fly/Kyoto/93/2004                2004  H5N1   
   DQ644955   A/chicken/Denpasar/01/2004     2004  H5N1   
   AY609312   A/chicken/Guangdong/174/04        2004  H5N1   
   DQ320893   A/chicken/Guangxi/2439/2004       2004  H5N1   
   AB188824   A/chicken/Kyoto/3/2004                  2004  H5N1   
   AB188816   A/chicken/Oita/8/2004                     2004  H5N1   
   ISDN49016  A/Chicken/Yamaguchi/7/2004       2004  H5N1   
   AB166862   A/chicken/Yamaguchi/7/2004         2004  H5N1   
   AB189053   A/crow/Kyoto/53/2004                     2004  H5N1   
   AB189061   A/crow/Osaka/102/2004                 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   
   DQ320890   A/duck/Guangxi/2291/2004           2004  H5N1   
   DQ320892   A/duck/Guangxi/2396/2004           2004  H5N1   
   DQ320879   A/duck/Guangxi/668/2004             2004  H5N1   
   AY639405   A/goose/China/F3/2004                 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   
   AY676035   A/chicken/Korea/ES/03                  2003  H5N1   
   ISDN40921  A/Chicken/Korea/es/2003             2003  H5N1   
   AY651368   A/Ck/ST/4231/2003                        2003  H5N1   
   AY676036   A/duck/Korea/ESD1/03                  2003  H5N1  

Third polymorphism

   DQ231242  A/chicken/Suzdalka/Nov-11/05       2005  H5N1   
   DQ231241  A/chicken/Suzdalka/Nov-12/05       2005  H5N1   
   DQ231240  A/turkey/Suzdalka/Nov-01/05          2005  H5N1   
   AB212649  A/blow fly/Kyoto/93/2004                  2004  H5N1   
   DQ644955  A/chicken/Denpasar/01/2004       2004  H5N1   
   AY609312  A/chicken/Guangdong/174/04          2004  H5N1   
   DQ320893  A/chicken/Guangxi/2439/2004         2004  H5N1   
   AB188824  A/chicken/Kyoto/3/2004                    2004  H5N1   
   AB188816  A/chicken/Oita/8/2004                       2004  H5N1   
   ISDN49016  A/Chicken/Yamaguchi/7/2004         2004  H5N1   
   AB166862  A/chicken/Yamaguchi/7/2004           2004  H5N1   
   AB189053  A/crow/Kyoto/53/2004                       2004  H5N1   
   AB189061  A/crow/Osaka/102/2004                   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   
   DQ320890  A/duck/Guangxi/2291/2004              2004  H5N1   
   DQ320892  A/duck/Guangxi/2396/2004              2004  H5N1   
   DQ320879  A/duck/Guangxi/668/2004                2004  H5N1   
   AY639405  A/goose/China/F3/2004                    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   
   AY676035  A/chicken/Korea/ES/03                     2003  H5N1   
   ISDN40921  A/Chicken/Korea/es/2003               2003  H5N1   
   AY651368  A/Ck/ST/4231/2003                           2003  H5N1   
   AY676036  A/duck/Korea/ESD1/03                     2003  H5N1  

Phylogenetic Tree

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