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Indonesian H5 Sequences in Wild Birds in North America
Recombinomics Commentary

August 30, 2006

In August 2005, a wildlife survey of wild birds in southern Canada included swabbing and testing for avian influenza.  The swabs yielded a remarkably high percentage of positives for H5 bird flu.  Serotypes H5N1, H5N2, H5N3, and H5N9 were identified.  24% of birds in British Columbia were H5 positive.  The first H5 sequence was released last month, and as expected, it was a low path H5N2 with polymorphisms commonly found in North America.  However, because the H5 was evolving via recombination, newly acquired polymorphisms could be traced. 

Earlier analysis identified polymorphisms acquired from swine in Canada.  These swine had obvious recombination in PB2 and PA and also had a human PB1 which served as a reservoir for seasonal flu polymorphisms.  The swine have also been infected in North America have also been infected with a number of reassortants with avian genes.

After the swine sequences weres made public, Indonesia released sequences from H5N1 infected patients, and these sequences had a number of polymorphisms that were widely found in both bird and human isolates from Indonesia.  One of those HA polymorphisms was also found in the H5 of the wild bird from Canada.

Recently, low path H5N1 was also found in Michigan, suggesting the H5 detected August of 2005 in southern Canada is also present in wild birds in the United States.  The interactions between birds and swine, which involve both reassortment and recombination, creates an increasingly unstable avian influenza gene pool, which is cause for concern.

   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  
   ISDN140810  A/Indonesia/534H/2006                 2006  H5N1  
   ISDN140894  A/Indonesia/535H/2006                 2006  H5N1  
   ISDN140895  A/Indonesia/536H/2006                 2006  H5N1  
   ISDN140818  A/Indonesia/538H/2006                 2006  H5N1  
   ISDN140926  A/Indonesia/542H/2006                 2006  H5N1  
   ISDN187421  A/Indonesia/546bH/2006               2006  H5N1  
   ISDN140896  A/Indonesia/546H/2006                 2006  H5N1  
   ISDN185493  A/Indonesia/560H/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  
   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  
   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  
   DQ320932     A/chicken/Bantul/BBVet-I/2005         2005  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  
   ISDN129601  A/Chicken/Indonesia/CDC24/2005   2005  H5N1  
   ISDN129590  A/Chicken/Indonesia/CDC25/2005   2005  H5N1  
   AM183670     A/chicken/Indonesia/R60/05                2005  H5N1  
   ISDN187385  A/Chicken/Indonesia/Wates1/2005     2005  H5N1  
   ISDN187389  A/Chicken/Indonesia/Wates126/2005  2005  H5N1  
   ISDN187386  A/Chicken/Indonesia/Wates130/2005  2005  H5N1  
   ISDN187388  A/Chicken/Indonesia/Wates80/2005    2005  H5N1  
   ISDN187390  A/Chicken/Indonesia/Wates83/2005    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  
   ISDN130373  A/Indonesia/160H/2005                          2005  H5N1  
   ISDN130365  A/Indonesia/175H/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  
   ISDN128026  A/Indonesia/6/2005                                 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  
   DQ826532     A/mallard/BC/373/2005                          2005  H5N2  
   DQ497655     A/chicken/Bangli Bali/BBPV6-1/2004    2004  H5N1  
   DQ497656     A/chicken/Bangli Bali/BPPV6-2/2004    2004  H5N1  
   DQ497657     A/chicken/Jembrana/BPPV6/2004         2004  H5N1  
   DQ320931     A/chicken/Kulon Progo/BBVet-XII-1/2004  2004  H5N1  
   DQ497650     A/chicken/Kulon Progo/BBVet-XII-2/2004   2004  H5N1  
   DQ497662     A/chicken/Kupang-1-NTT/BPPV6/2004      2004  H5N1  
   DQ497660     A/chicken/Kupang-2-NTT/BPPV6/2004      2004  H5N1  
   DQ497661     A/chicken/Kupang-3-NTT/BPPV6/2004      2004  H5N1  
   DQ497642     A/chicken/Malang/BBVet-IV/2004                2004  H5N1  
   DQ497658     A/chicken/Mangarai-NTT/BPPV6/2004       2004  H5N1  
   DQ497644     A/chicken/Ngawi/BPPV4/2004                     2004  H5N1  
   DQ497663     A/chicken/Pangkalpinang/BPPV3/2004      2004  H5N1  
   DQ497653     A/chicken/Purwakarta/BBVet-IV/2004         2004  H5N1  
   DQ320930     A/chicken/Yogjakarta/BBVet-IX/2004          2004  H5N1  
   AY651325      A/Ck/Indonesia/5/2004                                  2004  H5N1  
   AY651322      A/Dk/Indonesia/MS/2004                               2004  H5N1  
   DQ497647     A/quail/Boyolali/BPPV4/2004                       2004  H5N1  
   DQ497654     A/quail/Tasikmalaya/BPPV4/2004               2004  H5N1  
   DQ497649     A/quail/Yogjakarta/BBVet-IX/2004                2004  H5N1  
   DQ497664     A/turkey/Kedaton/BPPV3/2004                     2004  H5N1  
   ISDN111352  A/Chicken/Indonesia/11/2003                       2003  H5N1  
   ISDN111351  A/Chicken/Indonesia/7/2003                         2003  H5N1  
   AM183669     A/chicken/Indonesia/R134/03                        2003  H5N1  
   DQ497645     A/chicken/Pekalongan/BPPV4/2003            2003  H5N1  
   DQ497646     A/chicken/Sragen/BPPV4/2003                    2003  H5N1  
   DQ320929     A/chicken/Wonosobo/BPPV4/2003             2003  H5N1  
   AY651323      A/Ck/Indonesia/2A/2003                               2003  H5N1  
   AY651321      A/Ck/Indonesia/BL/2003                                2003  H5N1  
   AY651320      A/Ck/Indonesia/PA/2003                                2003  H5N1  
   AB241623     A/duck/Hokkaido/84/02                                  2002  H5N3  
   AY296083     A/turkey/CA/D0208651-C/02                        2002  H5N2  
   AY296077     A/duck/NJ/117228-7/01                                  2001  H5N2  
   U79455         A/Turkey/Minnesota/10734/95                        1995  H5N2  
   U05332         A/chicken/Florida/25717/93                            1993  H5N2  
   U05331         A/chicken/Pennsylvania/13609/93                  1993  H5N2  
   U28920         A/Emu/Texas/39442/93 (HP progeny)           1993  H5N2  
   U05330         A/ruddy turnstone/Delaware/244/91               1991  H5N2  
   U67783         A/Mallard/Ohio/556/1987                                 1987  H5N9 

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