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.
G59A
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
T211C
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
C268T
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
A539G
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
T796C
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
T868C
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
A1300G
AB263752 A/whooper swan/Mongolia/2/06 2006 H5N1
(plus many other H5N1 isolates)
C1330T
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
G1562T
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
C1618T
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
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