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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