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Human H5N1 Indonesian Sequences Available at Los Alamos

Recombinomics Commentary

August 4, 2006

Yesterday Indonesia pledged to release the H5N1 human sequence sequestered in the WHO private database.  Today the password protection on the sequences was removed and the sequences became publicly available.  Analysis of the sequences can help determine origins and predict targets for vaccines.  Orgins can be traced by monitoring informative polymorphisms. 

Below is one such series, showing the similarity between the various human isolates and relationship to other H5N1 bird flu sequences at Genbank or Los Alamos.

   ISDN136817  A/Feline/Indonesia/CDC1/2006        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   
   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   
   ISDN140835  A/Indonesia/CDC594/06                     2006  H5N1   
   ISDN140843  A/Indonesia/CDC595/06                      2006  H5N1   
   ISDN140851  A/Indonesia/CDC596/06                      2006  H5N1   
   ISDN140859  A/Indonesia/CDC597/06                      2006  H5N1   
   ISDN140866  A/Indonesia/CDC599/06                      2006  H5N1   
   ISDN183782  A/Indonesia/CDC599N/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   
   ISDN183738  A/Indonesia/CDC625/2006                   2006  H5N1   
   ISDN183770  A/Indonesia/CDC625L/2006                 2006  H5N1   
   ISDN183746  A/Indonesia/CDC634/2006                   2006  H5N1   
   ISDN183754  A/Indonesia/CDC634P/2006                 2006  H5N1   
   ISDN183762  A/Indonesia/CDC634T/2006                 2006  H5N1   
   DQ497667     A/chicken/Dairi/BPPVI/2005                  2005  H5N1   
   DQ497668     A/chicken/Deli Serdang/BPPVI/2005   2005  H5N1   
   DQ497651     A/chicken/Gunung Kidal/BBVW/2005   2005  H5N1   
   DQ497652     A/chicken/Kulon Progo/BBVW/2005    2005  H5N1   
   DQ497643     A/chicken/Magetan/BBVW/2005          2005  H5N1   
   DQ497648     A/chicken/Purworejo/BBVW/2005        2005  H5N1   
   DQ320928     A/chicken/Salatiga/BBVet-I/2005          2005  H5N1   
   DQ497665     A/chicken/Simalanggang/BPPVI/2005  2005  H5N1   
   DQ497669     A/chicken/Tarutung/BPPVI/2005            2005  H5N1   
   DQ497666     A/chicken/Tebing Tinggi/BPPVI/2005    2005  H5N1   
   DQ320933     A/chicken/Wajo/BBVM/2005                    2005  H5N1   
   DQ497659     A/duck/Parepare/BBVM/2005                  2005  H5N1   
   ISDN125873  A/Indonesia/5/05                                     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   
   DQ497662     A/chicken/Kupang-1-NTT/BPPV6/2004  2004  H5N1   
   DQ497663     A/chicken/Pangkalpinang/BPPV3/2004 2004  H5N1   
   DQ320930     A/chicken/Yogjakarta/BBVet-IX/2004      2004  H5N1   
   AY651372      A/Ck/YN/115/2004                                      2004  H5N1   
   DQ497707     A/goose/Vietnam/264/2004                       2004  H5N1   
   DQ497647     A/quail/Boyolali/BPPV4/2004                    2004  H5N1   
   DQ497649     A/quail/Yogjakarta/BBVet-IX/2004             2004  H5N1   
   AY651369      A/Dk/YN/6255/2003                                     2003  H5N1   
   AY651351      A/Ck/Hong Kong/3169.1/2002                   2002  H5N1 

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