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Qinghai H5N1 Bird Flu Sequences in Indonesian Karo Cluster

Recombinomics Commentary

August 8, 2006

The recent human-to-human-to human transmission of H5N1 bird flu in the Karo Regency in Indonesia has caused concern.  The cluster was the largest reported in Indonesia and represented yet another strain cable of causing human fatalities.  Data presented at the meeting in Jakarta indicated the H5N1 in the cluster was distinct from the earlier human cases in Indonesia and also was distinct from other avian isolates.

Initial analysis of changes between one of the cluster member and others in the clustered identified polymorphisms shared with Qinghai isolates.  Acquisition of Qinghai polymorphism are cause for concern because the Qinghai strain carries PB2 E627K, which is linked to increased virulence in mice and allows the polymerase to function more efficiently at lower temperatures.  Other polymorphisms associated with the Qinghai strain are also found in mammalian isolates, which was found in the M polymorphisms described previously.

On Friday, the CDC and Hong Kong labs released the human H5N1 sequences sequestered in the WHO private database.  Prior to the release, there were only two sequences from one isolate.  The release increased the number of public sequences to more than 500.

Analysis of the Karo cluster sequences indicated that there were a number of polymorphisms not found in other avian or human isolates from Indonesia.  Analysis of these polymorphisms indicates many are shared by Qinghai isolates.  Examples are listed below.

These polymorphism are on an Indonesian genetic background.  Thus, the isolates from the Karo cluster as well as the other human isolates are clearly from Indonesia.  They share a number of polymorphisms fund only or predominantly in Indonesia.  However, the punctuation of these sequences with Qinghai polymorphisms indicates these sequences are acquired via homologous recombination.  These acquisitions run across the Karo genes indicting a dual infection can generate new polymorphism across multiple genes facilitating rapid evolution.  The relationship of the polymorphisms to Qinghai isolates indicates these acquisitions are not random mutations, but are due to homologous recombination.

Earlier, the Qinghai cleavage site was found in an avian isolate in Bali.  In addition, the M gene of the father of the nephew in the cluster had another polymorphism found in both Qinghai isolates as well as human isolates.  Below are the such polymorphism in HA  The Qinghai isolates are in black bold. Karo cluster isolates are in red bold. Isolates from 2005 and 2006 with these shared polymorphisms are listed.

HA polymorphisms

First polymorphism

DQ661910    A/chicken/Afghanistan/1207/2006              2006 H5N1
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
DQ676834    A/chicken/Krasnodar/01/2006                     2006 H5N1
DQ676830    A/chicken/Mahachkala/05/2006                   2006 H5N1
AM262541    A/chicken/Lagos.NIE/10.06/BA209/2006   2006 H5N1
AM262542    A/chicken/Lagos.NIE/10.06/BA210/2006   2006 H5N1
AM262543    A/chicken/Lagos.NIE/10.06/BA211/2006   2006 H5N1
AM262546    A/chicken/Lagos.NIE/8.06/SO300 2006/    2006 H5N1
AM262547    A/chicken/Lagos.NIE/8.06/SO452/2006     2006 H5N1
AM262553    A/chicken/Lagos.NIE/8.06/SO493/2006     2006 H5N1
AM262572    A/chicken/Lagos.NIE/8.06/SO494/2006     2006 H5N1

DQ838517    A/chicken/Niger/2130-7/2006                       2006 H5N1
DQ838516    A/chicken/Niger/2130-8/2006                       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
DQ666146    A/Djibouti/5691NAMRU3/2006                    2006 H5N1
DQ862002    A/duck/Egypt/2253-3/2006                           2006 H5N1
DQ659113    A/duck/Niger/914/2006                                 2006 H5N1
DQ464377    A/Egypt/2782-NAMRU3/2006                      2006 H5N1
DQ852600    A/grebe/Tyva/Tyv06-2/06                             2006 H5N1
ISDN140810 A/Indonesia/534H/2006                                2006 H5N1
ISDN140894 A/Indonesia/535H/2006                                2006 H5N1
ISDN140895 A/Indonesia/536H/2006                                2006 H5N1
ISDN140818 A/Indonesia/538H/2006                                2006 H5N1
ISDN140896 A/Indonesia/546H/2006                                2006 H5N1
ISDN185493 A/Indonesia/560H/2006                                2006 H5N1
ISDN140835 A/Indonesia/CDC594/06                               2006 H5N1
ISDN140843 A/Indonesia/CDC595/06                               2006 H5N1
ISDN140851 A/Indonesia/CDC596/06                               2006 H5N1
ISDN140859 A/Indonesia/CDC597/06                               2006 H5N1
ISDN140866 A/Indonesia/CDC599/06                               2006 H5N1
ISDN183782 A/Indonesia/CDC599N/2006                        2006 H5N1
ISDN183738 A/Indonesia/CDC625/2006                           2006 H5N1
ISDN183770 A/Indonesia/CDC625L/2006                         2006 H5N1
DQ458992    A/mallard/Bavaria/1/2006                               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
DQ837590    A/turkey/Egypt/5613NAMRU3-T/2006        2006 H5N1
AB263752    A/whooper swan/Mongolia/2/06                  2006 H5N1
DQ643809    A/Zhejiang/16/2006                                           2006 H5N1
DQ659327    A/Bar headed goose/Qinghai/1A/2005       2005 H5N1
ISDN140934 A/Bar headed goose/Qinghai/1A/2005       2005 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
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
DQ650659    A/chicken/Crimea/04/2005                              2005 H5N1
DQ650663    A/chicken/Crimea/08/2005                              2005 H5N1
DQ676838    A/chicken/Dovolnoe/03/2005                         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
DQ449640    A/duck/Kurgan/08/2005                                    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
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
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
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

second polymorphism

AM262553    A/chicken/Lagos.NIE/8.06/SO493                 2006 H5N1
DQ676830    A/chicken/Mahachkala/05/2006                     2006 H5N1
ISDN138756 A/chicken/Malaysia/935/2006                            2006 H5N1
SDN140810  A/Indonesia/534H/2006                                    2006 H5N1
ISDN140894 A/Indonesia/535H/2006                                    2006 H5N1
ISDN140895 A/Indonesia/536H/2006                                    2006 H5N1
ISDN140818 A/Indonesia/538H/2006                                    2006 H5N1
ISDN140896 A/Indonesia/546H/2006                                    2006 H5N1
ISDN185493 A/Indonesia/560H/2006                                    2006 H5N1
ISDN140835 A/Indonesia/CDC594/06                                   2006 H5N1
ISDN140843 A/Indonesia/CDC595/06                                   2006 H5N1
ISDN140851 A/Indonesia/CDC596/06                                   2006 H5N1
ISDN140859 A/Indonesia/CDC597/06                                   2006 H5N1
ISDN140866 A/Indonesia/CDC599/06                                   2006 H5N1
ISDN183782 A/Indonesia/CDC599N/2006                           2006 H5N1
ISDN183738 A/Indonesia/CDC625/2006                              2006 H5N1
ISDN183770 A/Indonesia/CDC625L/2006                           2006 H5N1

ISDN133098 A/Turkey/12/2006                                              2006 H5N1
DQ643809    A/Zhejiang/16/2006                                             2006 H5N1
DQ371928    A/Anhui/1/2005                                                    2005 H5N1
DQ371929    A/Anhui/2/2005                                                    2005 H5N1
ISDN140934 A/Bar headed goose/Qinghai/1A/2005        2005 H5N1
DQ659327    A/Bar headed goose/Qinghai/1A/2005        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
DQ650659    A/chicken/Crimea/04/2005                               2005 H5N1
DQ650663    A/chicken/Crimea/08/2005                              2005 H5N1
DQ340848    A/chicken/Crimea/1/2005                                2005 H5N1
DQ676838    A/chicken/Dovolnoe/03/2005                         2005 H5N1
DQ320910    A/chicken/Hunan/999/2005                                2005 H5N1
ISDN129601 A/Chicken/Indonesia/CDC24/2005                  2005 H5N1
ISDN129590 A/Chicken/Indonesia/CDC25/2005                  2005 H5N1
DQ095626    A/Chicken/Shantou/810/05                                2005 H5N1
DQ279301    A/chicken/Tula/10/2005                                   2005 H5N1
DQ840519    A/chicken/Tula/Russia/Oct-5/2005               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
DQ320900    A/duck/Guangxi/951/2005                                 2005 H5N1
DQ320901    A/duck/Guangzhou/20/2005                              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
DQ230522    A/duck/Novosibirsk/56/2005                         2005 H5N1
DQ497699    A/duck/Vietnam/S649/2005                              2005 H5N1
DQ320922    A/Environment/Qinghai/31/2005                   2005 H5N1
DQ320896    A/goose/Guangxi/345/2005                               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
DQ371930    A/Guangxi/1/2005                                               2005 H5N1
DQ387854    A/mallard/Bavaria/1/2005                                2005 H5N2
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
DQ095627    A/Quail/Shantou/911/05                                     2005 H5N1
DQ838509    A/teal/Italy/3812/2005                                         2005 H5N3
DQ851561    A/teal/Italy/3931/2005                                         2005 H5N2
DQ231240    A/turkey/Suzdalka/Nov-01/05                        2005 H5N1

third polymorphism

SDN140810  A/Indonesia/534H/2006                                  2006 H5N1
ISDN140894 A/Indonesia/535H/2006                                  2006 H5N1
ISDN140895 A/Indonesia/536H/2006                                  2006 H5N1
ISDN140818 A/Indonesia/538H/2006                                  2006 H5N1
ISDN140896 A/Indonesia/546H/2006                                  2006 H5N1
ISDN185493 A/Indonesia/560H/2006                                  2006 H5N1
ISDN140835 A/Indonesia/CDC594/06                                 2006 H5N1
ISDN140843 A/Indonesia/CDC595/06                                 2006 H5N1
ISDN140851 A/Indonesia/CDC596/06                                 2006 H5N1
ISDN140859 A/Indonesia/CDC597/06                                 2006 H5N1
ISDN140866 A/Indonesia/CDC599/06                                 2006 H5N1
ISDN183782 A/Indonesia/CDC599N/2006                          2006 H5N1
ISDN183738 A/Indonesia/CDC625/2006                             2006 H5N1
ISDN183770 A/Indonesia/CDC625L/2006                          2006 H5N1

DQ497667    A/chicken/Dairi/BPPVI/2005                             2005 H5N1
DQ497668    A/chicken/Deli Serdang/BPPVI/2005               2005 H5N1
DQ497665    A/chicken/Simalanggang/BPPVI/2005             2005 H5N1
DQ497669    A/chicken/Tarutung/BPPVI/2005                       2005 H5N1
DQ497666    A/chicken/Tebing Tinggi/BPPVI/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
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
DQ497704    A/duck/Vietnam/376/2005                                  2005 H5N1
DQ676840    A/goose/Krasnoozerka/627/2005                  2005 H5N1
ISDN128026 A/Indonesia/6/2005                                             2005 H5N1
DQ320897    A/quail/Guangxi/575/2005                                  2005 H5N1
DQ320137    A/swan/Astrakhan/1/2005                               2005 H5N1
DQ840533    A/swan/Astrakhan/Russia/Nov-2/2005        2005 H5N1
ISDN117777 A/Viet Nam/JP4207/2005                                  2005 H5N1

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