Novel Cleavage Site in Duck from Indonesian Reservoir
Recombinomics Commentary
August 31, 2006
New H5N1 from birds in Indonesia have been released at Los Alamos. Included in the sequences are a duck from Indramayu in northern West Java, A/Duck/Indramayu/BBPW109/2006. This H5N1 bird flu sequence has the novel HA cleavage site, RESRRKKR, which is found in most of the human H5N1 sequences in West Java. This is the first reported match of the novel cleavage site in birds.
However, the bird sequence has an additional change in the HA cleavage site that is silent, but traces origins. This change is found in a small subset of human cases, indicating the novel cleavage site in the duck is from the reservoir containing the novel cleavage site and is not the source (see discussion). The isolates containing the silent chnage in the cleavage site are listed below, pionting toward an origin in migrating birds.
The new sequences highlight the importance of a robust and public sequence database, which provide clear answers to important questions such as the origin of the novel cleavage site found in the human H5N1 sequences.
Silent change in following isolates. Human isolates in red bold.
ISDN207241 A/Duck/Indramayu/BBPW109/2006 2006 H5N1
ISDN133323 A/Indonesia/286H/2006 2006 H5N1
DQ320925 A/Chinese pond heron/Hong Kong/18/2005 2005 H5N1
ISDN130373 A/Indonesia/160H/2005 2005 H5N1
ISDN130365 A/Indonesia/175H/2005 2005 H5N1
ISDN129527 A/Indonesia/7/2005 2005 H5N1
ISDN129921 A/Indonesia/CDC184/2005 2005 H5N1
ISDN129922 A/Indonesia/CDC194P/2005 2005 H5N1
ISDN129582 A/Indonesia/CDC7/2005 2005 H5N1
DQ387854 A/mallard/Bavaria/1/2005 2005 H5N2
DQ838509 A/teal/Italy/3812/2005 2005 H5N3
DQ851561 A/teal/Italy/3931/2005 2005 H5N2
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
AB241624 A/duck/Hokkaido/101/04 2004 H5N3
AB241625 A/duck/Hokkaido/193/04 2004 H5N3
AB241626 A/duck/Hokkaido/299/04 2004 H5N3
AB259712 A/duck/Hokkaido/Vac-1/04 2004 H5N1
DQ320924 A/grey heron/Hong Kong/837/2004 2004 H5N1
DQ647648 A/ostrich/South Africa/1/2004 2004 H5N2
DQ007623 A/Anas platyrhynchos/Chany Lake/9/03 2003 H5N3
AY995883 A/mallard/Sweden/2/02 2002 H5N2
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
AY995895 A/mallard/Sweden/58/02 2002 H5N3
AY995896 A/mallard/Sweden/64/02 2002 H5N2
AY995884 A/mallard/Sweden/7/02 2002 H5N2
AY995897 A/mallard/Sweden/79/02 2002 H5N9
AY995898 A/mallard/Sweden/80/02 2002 H5N9
AB241621 A/duck/Mongolia/500/01 2001 H5N3
AB241614 A/duck/Mongolia/54/01 2001 H5N2
AB263192 A/duck/Mongolia/54/01-duck/Mongolia/47/01 2001 H5
AB241622 A/duck/Mongolia/596/01 2001 H5N3
AJ621811 A/duck/Primorie/2621/01 2001 H5N2
AJ621807 A/duck/Primorie/2633/01 2001 H5N3
ISDN38259 A/Duck/Viet Nam/342/2001 2001 H5N1
AY585371 A/duck/Zhejiang/15/2000 2000 H5N1
AY585377 A/duck/Zhejiang/52/2000 2000 H5N1
AY684894 A/mallard/Netherlands/3/99 1999 H5N2
DQ092869 A/Pekin duck/Singapore/F59/04/98 1998 H5N2
ISDN49024 A/duck/Singapore/3/97 1997 H5N3
AF303057 A/duck/Singapore/Q-F119-3/97 1997 H5N3
AB241616 A/swan/Hokkaido/4/96 1996 H5N3
AB241617 A/swan/Hokkaido/51/96 1996 H5N3
AB241618 A/swan/Hokkaido/67/96 1996 H5N3
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