Recombinomics | Elegant Evolution

Home Founder What's New In The News Contact Us

Paradigm Shift

Viral Evolution

Intervention Monitoring

Vaccine Screening

Vaccine Development

Expression Profiling

Drug Discovery

Custom Therapies


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 
Media Sources

Phylogenetic Trees

Home | Founder | What's New | In The News | Contact Us

© 2006 Recombinomics.  All rights reserved.