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 H5N1 Cleavage Site in Duck Raises Pandemic Concerns
Recombinomics Commentary

August 31, 2006

The release of recent H5N1 bird sequences in Indonesia have identified a duck from that has the novel cleavage site, RESRRKKR.  This sequence has been detected in almost all human H5N1 isolates in West Java, including the Jakarta area (see list below).  The failure to find the sequence in domestic poultry has raised concerns regarding the origin of the human infections.  Since most H5N1 testing in humans require a link to dead or dying poultry, a non-poultry origin, would indicate many infections from an alternate source would be missed.

Although the duck listed below is the first reported bird isolate with the novel cleavage site, the sequence contains an additional change in the cleavage site that is present in a small subset of the human cases.  This change indicates the sequence in the duck is not the source of the majority of the human cases with the novel cleavage site, and suggests the duck H5N1 bird flu came FROM the human subset, which were isolated in 2005.  The source of the majority of the human sequences has not been identified.  The only non-human sequence to date is a cat sequence from Jakarta.

Since the new polymorphisms are acquired by recombination, the polymorphism provide a flight path that defines the origins of these polymorphisms.  The silent change in the cleavage site traces back to wild birds, including low path H5 in Primorie and Chany Lake in southern Russia, as well as isolates from Mongolia.  Last year the Qinghai strain of H5N1 was identified at Qinghai Lake in long range migratory birds.  Those bird flu isolates in May were followed by identification of the Qinghai strain at Chany Lake in southern Russia and Erhel Lake in northern Mongolia.  These reports compliment the earlier isolates of low path H5 in similar locations.

Wild birds were transmitting and transporting H5 sequences long before the Qinghai Lake reports, and continue to be a source of dual infections and recombination.  This evolution is clearly represented in the newly acquired polymorphisms, and Qinghai sequences have been found in earlier isolates as well as the duck described above.

The finding of the novel cleavage site in a duck indicates these sequences are being transported by birds locally in Indonesia.  The novel cleavage site has not been reported outside of Indonesia, and both bird and human isolates contain polymorphisms which are found in most or all Indonesian isolates.

The presence of these sequences in birds raises pandemic concern, but has yet to identify the reservoir for most of the human sequences from Java.

Sequences with change to create RESRRKKR cleavage site

   ISDN207241  A/Duck/Indramayu/BBPW109/2006    2006  H5N1  
   ISDN136817  A/Feline/Indonesia/CDC1/2006    2006  H5N1  
   ISDN133316  A/Indonesia/283H/2006    2006  H5N1  
   ISDN133323  A/Indonesia/286H/2006    2006  H5N1  
   ISDN138748  A/Indonesia/292H/2006    2006  H5N1  
   ISDN136841  A/Indonesia/298H/2006    2006  H5N1  
   ISDN136849  A/Indonesia/304H/2006    2006  H5N1  
   ISDN138764  A/Indonesia/321H/2006    2006  H5N1  
   ISDN138772  A/Indonesia/341H/2006    2006  H5N1  
   ISDN140926  A/Indonesia/542H/2006    2006  H5N1  
   ISDN187429  A/Indonesia/567H/2006    2006  H5N1  
   ISDN187437  A/Indonesia/569H/2006    2006  H5N1  
   ISDN187445  A/Indonesia/583H/2006    2006  H5N1  
   ISDN187453  A/Indonesia/604H/2006    2006  H5N1  
   ISDN136812  A/Indonesia/CDC326/2006  2006  H5N1  
   ISDN136810  A/Indonesia/CDC326N/2006  2006  H5N1  
   ISDN136811  A/Indonesia/CDC326N2/2006 2006  H5N1  
   ISDN136813  A/Indonesia/CDC326T/2006  2006  H5N1  
   ISDN136814  A/Indonesia/CDC326T/2006  2006  H5N1  
   ISDN136815  A/Indonesia/CDC329/2006   2006  H5N1  
   ISDN136816  A/Indonesia/CDC357/2006   2006  H5N1  
   ISDN136908  A/Indonesia/CDC370/2006   2006  H5N1  
   ISDN136909  A/Indonesia/CDC370E/2006  2006  H5N1  
   ISDN137412  A/Indonesia/CDC370P/2006  2006  H5N1  
   ISDN137413  A/Indonesia/CDC370T/2006  2006  H5N1  
   ISDN137414  A/Indonesia/CDC390/2006   2006  H5N1  
   ISDN181365  A/Indonesia/CDC523/2006   2006  H5N1  
   ISDN183297  A/Indonesia/CDC523E/2006 2006  H5N1  
   ISDN183305  A/Indonesia/CDC523T/2006   2006  H5N1  
   ISDN183313  A/Indonesia/CDC582/2006    2006  H5N1  
   ISDN183698  A/Indonesia/CDC610/2006    2006  H5N1  
   ISDN183706  A/Indonesia/CDC623/2006    2006  H5N1  
   ISDN183714  A/Indonesia/CDC623E/2006  2006  H5N1  
   ISDN183722  A/Indonesia/CDC624/2006   2006  H5N1  
   ISDN183730  A/Indonesia/CDC624E/2006   2006  H5N1  
   ISDN183746  A/Indonesia/CDC634/2006    2006  H5N1  
   ISDN183754  A/Indonesia/CDC634P/2006   2006  H5N1  
   ISDN183762  A/Indonesia/CDC634T/2006   2006  H5N1  
   ISDN207111  A/Indonesia/CDC644/2006    2006  H5N1  
   ISDN207103  A/Indonesia/CDC644T/2006   2006  H5N1  
   ISDN204133  A/Indonesia/CDC669/2006    2006  H5N1  
   ISDN204141  A/Indonesia/CDC669P/2006   2006  H5N1  
   ISDN204149  A/Indonesia/CDC699/2006    2006  H5N1  
   ISDN130373  A/Indonesia/160H/2005  2005  H5N1  
   ISDN130365  A/Indonesia/175H/2005    2005  H5N1  
   ISDN132826  A/Indonesia/177H/2005    2005  H5N1  
   ISDN130912  A/Indonesia/195H/2005    2005  H5N1  
   ISDN132406  A/Indonesia/239H/2005    2005  H5N1  
   ISDN132414  A/Indonesia/245H/2005    2005  H5N1  
   ISDN125873  A/Indonesia/5/05    2005  H5N1  
   ISDN125783  A/Indonesia/5/2005  2005  H5N1  
   ISDN129527  A/Indonesia/7/2005  2005  H5N1  
   ISDN129921  A/Indonesia/CDC184/2005    2005  H5N1  
   ISDN129922  A/Indonesia/CDC194P/2005   2005  H5N1  
   ISDN136806  A/Indonesia/CDC287E/2005   2005  H5N1  
   ISDN136807  A/Indonesia/CDC287T/2005   2005  H5N1  
   ISDN136808  A/Indonesia/CDC292N/2005   2005  H5N1  
   ISDN136809  A/Indonesia/CDC292T/2005   2005  H5N1  
   ISDN129582  A/Indonesia/CDC7/2005    2005  H5N1 

Media Sources

Phylogenetic Trees

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

© 2006 Recombinomics.  All rights reserved.