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.
C1261T
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
G1645A
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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