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 HOME   Wild Duck H5N2 Sequence from Canada
Wild Duck H5N2 Sequence from Canada
Published by: webmaster 2008-11-24

  • A/mallard/BC/373/2005(H5N2) sequence at GenBank

    http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=110287913


  • NA again

    DQ826532 (http://flu.lanl.gov/search/view_record.html?accession=DQ826532&database=fluA) A/mallard/BC/373/2005 HA (4) 1687 2005 H5N2
    CY005927 (http://flu.lanl.gov/search/view_record.html?accession=CY005927&database=fluA) A/shorebird/Delaware/101/2004 HA (4) 1766 2004 H5N7
    CY005969 (http://flu.lanl.gov/search/view_record.html?accession=CY005969&database=fluA) A/shorebird/Delaware/75/2004 HA (4) 1766 2004 H5N7
    AY296079 (http://flu.lanl.gov/search/view_record.html?accession=AY296079&database=fluA) A/duck/ME/151895-7A/02 HA (4) 1691 2002 H5N2
    AY296083 (http://flu.lanl.gov/search/view_record.html?accession=AY296083&database=fluA) A/turkey/CA/D0208651-C/02 HA (4) 1708 2002 H5N2
    AY296077 (http://flu.lanl.gov/search/view_record.html?accession=AY296077&database=fluA) A/duck/NJ/117228-7/01 HA (4) 1691 2001 H5N2
    AY296078 (http://flu.lanl.gov/search/view_record.html?accession=AY296078&database=fluA) A/unknown/NY/118547-11/01 HA (4) 1691 2001 H5N2
    AY296075 (http://flu.lanl.gov/search/view_record.html?accession=AY296075&database=fluA) A/unknown/NY/9899-6/01 HA (4) 1735 2001 H5N2
    AY296084 (http://flu.lanl.gov/search/view_record.html?accession=AY296084&database=fluA) A/ruddy turnstone/NJ/2242/00 HA (4) 1691 2000 H5N3
    AY497071 (http://flu.lanl.gov/search/view_record.html?accession=AY497071&database=fluA) A/chicken/Mexico/28159-541/95 HA (4) 996 1995 H5N2


  • Dr Niman, this commentary mentions a fatal human case in Maryland? Have we heard anything about that before? Seems like I would have remembered a fatal human case in Maryland. thx

    The sequences containing the tandem polymorphsims have been seen in three recent swine isolates. Two are from lab workers infected by experimental H1N1 and the other was a fatal case in Maryland in 1991. The other human isolates are WS/33 and WSN/33, which originated in a researcher in London in 1933.

    All other isolates are swine, except for the H5N1 in a mallard in British Columbia last August.

    Influenza isolates are name according to a convention which lists the influenza type, followed by species of origin.

    If no species is listed, the isolate was from a human.


  • I assume that's the swine with human H3N2 Neuraminidase?

    Are we brewing a unique American BF?

    .

    No, its H1N2

    DQ826532 A/mallard/BC/373/2005 2005 H5N2
    DQ280250 A/swine/Ontario/11112/04 2004 H1N1
    DQ447187 A/swine/Taiwan/CO935/2004 2004 H1N2
    DQ431990 A/swine/Taiwan/CO935/2004 2004 H1N2
    AY129156 A/Swine/Korea/CY02/02 2002 H1N2
    AY233393 A/Duck/NC/91347/01 2001 H1N2
    DQ058215 A/swine/Guangdong/2/01 2001 H1N1
    AF455682 A/Swine/Illinois/100084/01 2001 H1N2
    AF455681 A/Swine/Illinois/100085A/01 2001 H1N2
    AF455679 A/Swine/Iowa/930/01 2001 H1N2
    AY060050 A/Swine/MN/16419/01 2001 H1N2
    AY060048 A/Swine/MN/23124-S/01 2001 H1N2
    AY060047 A/Swine/MN/23124-T/01 2001 H1N2
    AY060051 A/Swine/MN/34893/01 2001 H1N2
    AF455677 A/Swine/North Carolina/93523/01 2001 H1N2
    AF455675 A/Swine/Ohio/891/01 HA (4) 2001 H1N2
    AF455680 A/Swine/Indiana/P12439/00 2000 H1N2
    AF455678 A/Swine/Minnesota/55551/00 2000 H1N2
    AF250124 A/Swine/Indiana/9K035/99 1999 H1N2
    AF222035 A/Swine/Wisconsin/458/98 1998 H1N1
    AF222036 A/Swine/Wisconsin/464/98 1998 H1N1
    AF222026 A/Swine/Wisconsin/125/97 1997 H1N1
    AF222027 A/Swine/Wisconsin/136/97 1997 H1N1
    AF222032 A/Swine/Wisconsin/235/97 1997 H1N1
    AF222033 A/Swine/Wisconsin/238/97 1997 H1N1
    U53162 A/Wisconsin/4754/94 1994 H1N1
    U53163 A/Wisconsin/4755/94 1994 H1N1
    S67220 A/Swine/Nebraska/1/92 1992 H1N1
    L09063 A/Swine/Nebraska/1/92 1992 H1
    L24362 A/Maryland/12/91 1991 H1N1
    U46783 A/Swine/Beijing/47/91 1991 H1N1
    U11857 A/Swine/St-Hyacinthe/106/91 1991 H1
    M81707 A/Swine/Indiana/1726/88 1988 H1N1
    Epidemiology of influenzavirus A (H5N1)::
    showed striking biological differences from its avian homologue in a duck model. The amino acid sequence of the M2 protein of clade 1 viruses as well as of HK
    http://focosi.immunesig.org/pathovirusesH5N1.html    HOME
    PRO/AH/EDR> Avian influenza - Canada (04): BC, MB::
    Officials speculated that the duck may have contracted the disease from migratory birds. (BC) 20051120.3370 Avian influenza - Canada (02): survey wild ducks
    http://www.promedmail.org/pls/otn/f?p=2400:1001:529814657537854481_PUB_MAIL_ID:10001,31137    HOME
    DQ508905 A/Wilson-Smith/1933 1933 H1N1
    J02176 A/WSN/33 1933 H1N1


  • I mean, BC flyway are linked with asia by Alaska.
    It will be interesting to see the H5N2 sequence from Quebec which could be linked to europe by Greenland.


    This H5N2 is 80.1% homologeous (from the nucleic acid seq) from the clasical Quigai sequence wich is the near the lowest we can expect from the same substrain.

    If we loom for the amino-acid sequence we found around 89% homology.

    So North American birds will have few or no immunity at all against an asiatic H5N1 if it come into america...

    There is more silent mutation than significative one for the protein sequence.

    However, silent mutation can show recombination event and I hope Dr.Niman will post more about that soon.

    While waiting, there is a clasical homology matrix of the experimental vaccine strain, the classical quigai strain and this North-American BC strain.
    476
    Orange is the North American Strain (with a wild low path cleavage site)
    Green are Reverse Genetic Modified strains (with a modified low path cleavage site)
    Yellow are Wild strain( with the high path cleavage site)

    I haven't had time to write up the sequence, but the H5 is picking up swine sequences.

    H5 in Canada will be a major problem.


  • You're right AD, I talk a bit too quick.


  • Nevermind. think I found the answer to my above post. Don't like it.:confused:

    Swine Sequences in H5 Wild Birds in British Columbia
    Recombinomics Commentary
    July 19, 2006
    SNIP>>>>>
    The acquisition of these polymorphisms in a health wild bird population is cause for concern. Recent data from Prince Edward Island suggests the Qinghai strain of H5N1 has already entered North America. Recombination between low path H5 and high path H5N1 is common and provides a mechanism for acquisition of these mammalian polymorphisms by the Qinghai strain of H5N1 bird flu.
    The initial H5N1 human isolates from Vietnam and Thailand had acquired a number of mammalian polymorphisms that were not found in other H5N1’s. The acquisition of swine polymorphisms in H5 in wild birds in Canada, and presumably the United States, is cause for concern.



    http://www.recombinomics.com/News/07...ard_Swine.html


  • ...........the H5 is picking up swine sequences.

    H5 in Canada will be a major problem.

    I assume that's the swine with human H3N2 Neuraminidase?

    Are we brewing a unique American BF?

    .


  • Since the Indonesian sequences are now at GenBank, the role of H5 positive birds in British Columibia is worth a revisit. Here is one buddy list showing an Indonesian connection

    ISDN136817 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136817&database=fluA) A/Feline/Indonesia/CDC1/2006 HA (4) 1659 2006 H5N1
    ISDN133316 (http://flu.lanl.gov/search/view_record.html?accession=ISDN133316&database=fluA) A/Indonesia/283H/2006 HA (4) 1752 2006 H5N1
    ISDN133323 (http://flu.lanl.gov/search/view_record.html?accession=ISDN133323&database=fluA) A/Indonesia/286H/2006 HA (4) 1729 2006 H5N1
    ISDN138748 (http://flu.lanl.gov/search/view_record.html?accession=ISDN138748&database=fluA) A/Indonesia/292H/2006 HA (4) 1696 2006 H5N1
    ISDN136841 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136841&database=fluA) A/Indonesia/298H/2006 HA (4) 1695 2006 H5N1
    ISDN136849 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136849&database=fluA) A/Indonesia/304H/2006 HA (4) 1707 2006 H5N1
    ISDN138764 (http://flu.lanl.gov/search/view_record.html?accession=ISDN138764&database=fluA) A/Indonesia/321H/2006 HA (4) 1072 2006 H5N1
    ISDN138772 (http://flu.lanl.gov/search/view_record.html?accession=ISDN138772&database=fluA) A/Indonesia/341H/2006 HA (4) 1696 2006 H5N1
    ISDN140810 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140810&database=fluA) A/Indonesia/534H/2006 HA (4) 1679 2006 H5N1
    ISDN140894 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140894&database=fluA) A/Indonesia/535H/2006 HA (4) 1703 2006 H5N1
    ISDN140895 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140895&database=fluA) A/Indonesia/536H/2006 HA (4) 1072 2006 H5N1
    ISDN140818 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140818&database=fluA) A/Indonesia/538H/2006 HA (4) 1716 2006 H5N1
    ISDN140926 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140926&database=fluA) A/Indonesia/542H/2006 HA (4) 1710 2006 H5N1
    ISDN187421 (http://flu.lanl.gov/search/view_record.html?accession=ISDN187421&database=fluA) A/Indonesia/546bH/2006 HA (4) 1706 2006 H5N1
    ISDN140896 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140896&database=fluA) A/Indonesia/546H/2006 HA (4) 1707 2006 H5N1
    ISDN185493 (http://flu.lanl.gov/search/view_record.html?accession=ISDN185493&database=fluA) A/Indonesia/560H/2006 HA (4) 1704 2006 H5N1
    ISDN187429 (http://flu.lanl.gov/search/view_record.html?accession=ISDN187429&database=fluA) A/Indonesia/567H/2006 HA (4) 1695 2006 H5N1
    ISDN187437 (http://flu.lanl.gov/search/view_record.html?accession=ISDN187437&database=fluA) A/Indonesia/569H/2006 HA (4) 1647 2006 H5N1
    ISDN187445 (http://flu.lanl.gov/search/view_record.html?accession=ISDN187445&database=fluA) A/Indonesia/583H/2006 HA (4) 1651 2006 H5N1
    ISDN187453 (http://flu.lanl.gov/search/view_record.html?accession=ISDN187453&database=fluA) A/Indonesia/604H/2006 HA (4) 1680 2006 H5N1
    ISDN136812 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136812&database=fluA) A/Indonesia/CDC326/2006 HA (4) 1659 2006 H5N1
    ISDN136810 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136810&database=fluA) A/Indonesia/CDC326N/2006 HA (4) 1659 2006 H5N1
    ISDN136811 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136811&database=fluA) A/Indonesia/CDC326N2/2006 HA (4) 1659 2006 H5N1
    ISDN136813 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136813&database=fluA) A/Indonesia/CDC326T/2006 HA (4) 1659 2006 H5N1
    ISDN136814 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136814&database=fluA) A/Indonesia/CDC326T/2006 HA (4) 1659 2006 H5N1
    ISDN136815 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136815&database=fluA) A/Indonesia/CDC329/2006 HA (4) 1659 2006 H5N1
    ISDN136816 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136816&database=fluA) A/Indonesia/CDC357/2006 HA (4) 1659
    Genetic Tracking of Disease - Commentaries & Analysis [Archive ::
    H5N1 Wild Bird Flu in Qinghai China (Retrospective H5N1 Human and Duck Sequence Identities in Indonesia Dr Niman Comment on H7N3 in Saskatchewan Canada
    http://www.flutrackers.com/forum/archive/index.php?f-459.html    HOME
    		• 2006 H5N1
    ISDN136908 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136908&database=fluA) A/Indonesia/CDC370/2006 HA (4) 1659 2006 H5N1
    ISDN136909 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136909&database=fluA) A/Indonesia/CDC370E/2006 HA (4) 1659 2006 H5N1
    ISDN137412 (http://flu.lanl.gov/search/view_record.html?accession=ISDN137412&database=fluA) A/Indonesia/CDC370P/2006 HA (4) 1659 2006 H5N1
    ISDN137413 (http://flu.lanl.gov/search/view_record.html?accession=ISDN137413&database=fluA) A/Indonesia/CDC370T/2006 HA (4) 1659 2006 H5N1
    ISDN137414 (http://flu.lanl.gov/search/view_record.html?accession=ISDN137414&database=fluA) A/Indonesia/CDC390/2006 HA (4) 1659 2006 H5N1
    ISDN181365 (http://flu.lanl.gov/search/view_record.html?accession=ISDN181365&database=fluA) A/Indonesia/CDC523/2006 HA (4) 1707 2006 H5N1
    ISDN183297 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183297&database=fluA) A/Indonesia/CDC523E/2006 HA (4) 1659 2006 H5N1
    ISDN183305 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183305&database=fluA)
    H5N1 Sequences from Switzerland - FluTrackers::
    DQ009917 A/Canada/720/05 HA (4) 1689 2005 H2N2 AJ972673 A/duck/France/05057b/2005 HA (4) 1706 2005 H5N2 which are in the human sequence from Nigeria
    http://www.flutrackers.com/forum/showthread.php?t=31306    HOME
    H5N1 Avian from 2007 - FluTrackers::
    H5N1 Avian from 2007 Egypt Sequences CY005575 A/duck/Hong Kong/342/1978 HA (4) 1767 1978 H5N2 In addition, four sequence had M230I.
    http://www.flutrackers.com/forum/showthread.php?t=51871    HOME
    		A/Indonesia/CDC523T/2006 HA (4) 1659 2006 H5N1
    ISDN183313 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183313&database=fluA) A/Indonesia/CDC582/2006 HA (4) 1659 2006 H5N1
    ISDN140835 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140835&database=fluA) A/Indonesia/CDC594/06 HA (4) 1707 2006 H5N1
    ISDN140843 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140843&database=fluA) A/Indonesia/CDC595/06 HA (4) 1707 2006 H5N1
    ISDN140851 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140851&database=fluA) A/Indonesia/CDC596/06 HA (4) 1707 2006 H5N1
    ISDN140859 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140859&database=fluA) A/Indonesia/CDC597/06 HA (4) 1707 2006 H5N1
    ISDN140866 (http://flu.lanl.gov/search/view_record.html?accession=ISDN140866&database=fluA) A/Indonesia/CDC599/06 HA (4) 1659 2006 H5N1
    ISDN183782 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183782&database=fluA) A/Indonesia/CDC599N/2006 HA (4) 1659 2006 H5N1
    ISDN183698 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183698&database=fluA) A/Indonesia/CDC610/2006 HA (4) 1659 2006 H5N1
    ISDN183706 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183706&database=fluA) A/Indonesia/CDC623/2006 HA (4) 1659 2006 H5N1
    ISDN183714 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183714&database=fluA) A/Indonesia/CDC623E/2006 HA (4) 1659 2006 H5N1
    ISDN183722 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183722&database=fluA) A/Indonesia/CDC624/2006 HA (4) 1659 2006 H5N1
    ISDN183730 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183730&database=fluA) A/Indonesia/CDC624E/2006 HA (4) 1659 2006 H5N1
    ISDN183738 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183738&database=fluA) A/Indonesia/CDC625/2006 HA (4) 1659 2006 H5N1
    ISDN183770 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183770&database=fluA) A/Indonesia/CDC625L/2006 HA (4) 1707 2006 H5N1
    ISDN183746 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183746&database=fluA) A/Indonesia/CDC634/2006 HA (4) 1659 2006 H5N1
    ISDN183754 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183754&database=fluA) A/Indonesia/CDC634P/2006 HA (4) 1659 2006 H5N1
    ISDN183762 (http://flu.lanl.gov/search/view_record.html?accession=ISDN183762&database=fluA) A/Indonesia/CDC634T/2006 HA (4) 1659 2006 H5N1
    ISDN207111 (http://flu.lanl.gov/search/view_record.html?accession=ISDN207111&database=fluA) A/Indonesia/CDC644/2006 HA (4) 1659 2006 H5N1
    ISDN207103 (http://flu.lanl.gov/search/view_record.html?accession=ISDN207103&database=fluA) A/Indonesia/CDC644T/2006 HA (4) 1659 2006 H5N1
    ISDN204133 (http://flu.lanl.gov/search/view_record.html?accession=ISDN204133&database=fluA) A/Indonesia/CDC669/2006 HA (4) 1707 2006 H5N1
    ISDN204141 (http://flu.lanl.gov/search/view_record.html?accession=ISDN204141&database=fluA) A/Indonesia/CDC669P/2006 HA (4) 1707 2006 H5N1
    ISDN204149 (http://flu.lanl.gov/search/view_record.html?accession=ISDN204149&database=fluA) A/Indonesia/CDC699/2006 HA (4) 1707 2006 H5N1
    DQ320932 (http://flu.lanl.gov/search/view_record.html?accession=DQ320932&database=fluA) A/chicken/Bantul/BBVet-I/2005 HA (4) 1698 2005 H5N1
    DQ497667 (http://flu.lanl.gov/search/view_record.html?accession=DQ497667&database=fluA) A/chicken/Dairi/BPPVI/2005 HA (4) 1698 2005 H5N1
    DQ497668 (http://flu.lanl.gov/search/view_record.html?accession=DQ497668&database=fluA) A/chicken/Deli Serdang/BPPVI/2005 HA (4) 1698 2005 H5N1
    DQ497651 (http://flu.lanl.gov/search/view_record.html?accession=DQ497651&database=fluA) A/chicken/Gunung Kidal/BBVW/2005 HA (4) 1698 2005 H5N1
    ISDN129601 (http://flu.lanl.gov/search/view_record.html?accession=ISDN129601&database=fluA) A/Chicken/Indonesia/CDC24/2005 HA (4) 1659 2005 H5N1
    ISDN129590 (http://flu.lanl.gov/search/view_record.html?accession=ISDN129590&database=fluA) A/Chicken/Indonesia/CDC25/2005 HA (4) 1659 2005 H5N1
    AM183670 (http://flu.lanl.gov/search/view_record.html?accession=AM183670&database=fluA) A/chicken/Indonesia/R60/05 HA (4) 1779 2005 H5N1
    ISDN187385 (http://flu.lanl.gov/search/view_record.html?accession=ISDN187385&database=fluA) A/Chicken/Indonesia/Wates1/2005 HA (4) 1714 2005 H5N1
    ISDN187389 (http://flu.lanl.gov/search/view_record.html?accession=ISDN187389&database=fluA) A/Chicken/Indonesia/Wates126/2005 HA (4) 1717 2005 H5N1
    ISDN187386 (http://flu.lanl.gov/search/view_record.html?accession=ISDN187386&database=fluA) A/Chicken/Indonesia/Wates130/2005 HA (4) 1704 2005 H5N1
    ISDN187388 (http://flu.lanl.gov/search/view_record.html?accession=ISDN187388&database=fluA) A/Chicken/Indonesia/Wates80/2005 HA (4) 1711 2005 H5N1
    ISDN187390 (http://flu.lanl.gov/search/view_record.html?accession=ISDN187390&database=fluA) A/Chicken/Indonesia/Wates83/2005 HA (4) 1714 2005 H5N1
    DQ497643 (http://flu.lanl.gov/search/view_record.html?accession=DQ497643&database=fluA) A/chicken/Magetan/BBVW/2005 HA (4) 1698 2005 H5N1
    DQ497648 (http://flu.lanl.gov/search/view_record.html?accession=DQ497648&database=fluA) A/chicken/Purworejo/BBVW/2005 HA (4) 1698 2005 H5N1
    DQ320928 (http://flu.lanl.gov/search/view_record.html?accession=DQ320928&database=fluA) A/chicken/Salatiga/BBVet-I/2005 HA (4) 1698 2005 H5N1
    DQ497665 (http://flu.lanl.gov/search/view_record.html?accession=DQ497665&database=fluA) A/chicken/Simalanggang/BPPVI/2005 HA (4) 1698 2005 H5N1
    DQ497669 (http://flu.lanl.gov/search/view_record.html?accession=DQ497669&database=fluA) A/chicken/Tarutung/BPPVI/2005 HA (4) 1698 2005 H5N1
    DQ497666 (http://flu.lanl.gov/search/view_record.html?accession=DQ497666&database=fluA) A/chicken/Tebing Tinggi/BPPVI/2005 HA (4) 1698 2005 H5N1
    DQ320933 (http://flu.lanl.gov/search/view_record.html?accession=DQ320933&database=fluA) A/chicken/Wajo/BBVM/2005 HA (4) 1698 2005 H5N1
    DQ497659 (http://flu.lanl.gov/search/view_record.html?accession=DQ497659&database=fluA) A/duck/Parepare/BBVM/2005 HA (4) 1689 2005 H5N1
    ISDN130373 (http://flu.lanl.gov/search/view_record.html?accession=ISDN130373&database=fluA) A/Indonesia/160H/2005 HA (4) 1708 2005 H5N1
    ISDN130365 (http://flu.lanl.gov/search/view_record.html?accession=ISDN130365&database=fluA) A/Indonesia/175H/2005 HA (4) 1709 2005 H5N1
    ISDN130912 (http://flu.lanl.gov/search/view_record.html?accession=ISDN130912&database=fluA) A/Indonesia/195H/2005 HA (4) 1700 2005 H5N1
    ISDN132406 (http://flu.lanl.gov/search/view_record.html?accession=ISDN132406&database=fluA) A/Indonesia/239H/2005 HA (4) 1647 2005 H5N1
    ISDN132414 (http://flu.lanl.gov/search/view_record.html?accession=ISDN132414&database=fluA) A/Indonesia/245H/2005 HA (4) 1653 2005 H5N1
    ISDN125873 (http://flu.lanl.gov/search/view_record.html?accession=ISDN125873&database=fluA) A/Indonesia/5/05 HA (4) 1729 2005 H5N1
    ISDN125783 (http://flu.lanl.gov/search/view_record.html?accession=ISDN125783&database=fluA) A/Indonesia/5/2005 HA (4) 1741 2005 H5N1
    ISDN128026 (http://flu.lanl.gov/search/view_record.html?accession=ISDN128026&database=fluA) A/Indonesia/6/2005 HA (4) 1712 2005 H5N1
    ISDN129527 (http://flu.lanl.gov/search/view_record.html?accession=ISDN129527&database=fluA) A/Indonesia/7/2005 HA (4) 1706 2005 H5N1
    ISDN129921 (http://flu.lanl.gov/search/view_record.html?accession=ISDN129921&database=fluA) A/Indonesia/CDC184/2005 HA (4) 1659 2005 H5N1
    ISDN129922 (http://flu.lanl.gov/search/view_record.html?accession=ISDN129922&database=fluA) A/Indonesia/CDC194P/2005 HA (4) 1659 2005 H5N1
    ISDN136806 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136806&database=fluA) A/Indonesia/CDC287E/2005 HA (4) 1659 2005 H5N1
    ISDN136807 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136807&database=fluA) A/Indonesia/CDC287T/2005 HA (4) 1659 2005 H5N1
    ISDN136808 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136808&database=fluA) A/Indonesia/CDC292N/2005 HA (4) 1659 2005 H5N1
    ISDN136809 (http://flu.lanl.gov/search/view_record.html?accession=ISDN136809&database=fluA) A/Indonesia/CDC292T/2005 HA (4) 1659 2005 H5N1
    ISDN129582 (http://flu.lanl.gov/search/view_record.html?accession=ISDN129582&database=fluA) A/Indonesia/CDC7/2005 HA (4) 1659 2005 H5N1
    DQ826532 (http://flu.lanl.gov/search/view_record.html?accession=DQ826532&database=fluA) A/mallard/BC/373/2005 HA (4) 1687 2005 H5N2
    DQ497655 (http://flu.lanl.gov/search/view_record.html?accession=DQ497655&database=fluA) A/chicken/Bangli Bali/BBPV6-1/2004 HA (4) 1698 2004 H5N1
    DQ497656 (http://flu.lanl.gov/search/view_record.html?accession=DQ497656&database=fluA) A/chicken/Bangli Bali/BPPV6-2/2004 HA (4) 1698 2004 H5N1
    DQ497657 (http://flu.lanl.gov/search/view_record.html?accession=DQ497657&database=fluA) A/chicken/Jembrana/BPPV6/2004 HA (4) 1659 2004 H5N1
    DQ320931 (http://flu.lanl.gov/search/view_record.html?accession=DQ320931&database=fluA) A/chicken/Kulon Progo/BBVet-XII-1/2004 HA (4) 1688 2004 H5N1
    DQ497650 (http://flu.lanl.gov/search/view_record.html?accession=DQ497650&database=fluA) A/chicken/Kulon Progo/BBVet-XII-2/2004 HA (4) 1695 2004 H5N1
    DQ497662 (http://flu.lanl.gov/search/view_record.html?accession=DQ497662&database=fluA) A/chicken/Kupang-1-NTT/BPPV6/2004 HA (4) 1695 2004 H5N1
    DQ497660 (http://flu.lanl.gov/search/view_record.html?accession=DQ497660&database=fluA) A/chicken/Kupang-2-NTT/BPPV6/2004 HA (4) 1698 2004 H5N1
    DQ497661 (http://flu.lanl.gov/search/view_record.html?accession=DQ497661&database=fluA) A/chicken/Kupang-3-NTT/BPPV6/2004 HA (4) 1698 2004 H5N1
    DQ497642 (http://flu.lanl.gov/search/view_record.html?accession=DQ497642&database=fluA) A/chicken/Malang/BBVet-IV/2004 HA (4) 1698 2004 H5N1
    DQ497658 (http://flu.lanl.gov/search/view_record.html?accession=DQ497658&database=fluA) A/chicken/Mangarai-NTT/BPPV6/2004 HA (4) 1698 2004 H5N1
    DQ497644 (http://flu.lanl.gov/search/view_record.html?accession=DQ497644&database=fluA) A/chicken/Ngawi/BPPV4/2004 HA (4) 1646 2004 H5N1
    DQ497663 (http://flu.lanl.gov/search/view_record.html?accession=DQ497663&database=fluA) A/chicken/Pangkalpinang/BPPV3/2004 HA (4) 1659 2004 H5N1
    DQ497653 (http://flu.lanl.gov/search/view_record.html?accession=DQ497653&database=fluA) A/chicken/Purwakarta/BBVet-IV/2004 HA (4) 1698 2004 H5N1
    DQ320930 (http://flu.lanl.gov/search/view_record.html?accession=DQ320930&database=fluA) A/chicken/Yogjakarta/BBVet-IX/2004 HA (4) 1687 2004 H5N1
    AY651325 (http://flu.lanl.gov/search/view_record.html?accession=AY651325&database=fluA) A/Ck/Indonesia/5/2004 HA (4) 1696 2004 H5N1
    AY651322 (http://flu.lanl.gov/search/view_record.html?accession=AY651322&database=fluA) A/Dk/Indonesia/MS/2004 HA (4) 1697 2004 H5N1
    DQ497647 (http://flu.lanl.gov/search/view_record.html?accession=DQ497647&database=fluA) A/quail/Boyolali/BPPV4/2004 HA (4) 1659 2004 H5N1
    DQ497654 (http://flu.lanl.gov/search/view_record.html?accession=DQ497654&database=fluA) A/quail/Tasikmalaya/BPPV4/2004 HA (4) 1659 2004 H5N1
    DQ497649 (http://flu.lanl.gov/search/view_record.html?accession=DQ497649&database=fluA) A/quail/Yogjakarta/BBVet-IX/2004 HA (4) 1686 2004 H5N1
    DQ497664 (http://flu.lanl.gov/search/view_record.html?accession=DQ497664&database=fluA) A/turkey/Kedaton/BPPV3/2004 HA (4) 1659 2004 H5N1
    ISDN111352 (http://flu.lanl.gov/search/view_record.html?accession=ISDN111352&database=fluA) A/Chicken/Indonesia/11/2003 HA (4) 1748 2003 H5N1
    ISDN111351 (http://flu.lanl.gov/search/view_record.html?accession=ISDN111351&database=fluA) A/Chicken/Indonesia/7/2003 HA (4) 1748 2003 H5N1
    AM183669 (http://flu.lanl.gov/search/view_record.html?accession=AM183669&database=fluA) A/chicken/Indonesia/R134/03 HA (4) 1482 2003 H5N1
    DQ497645 (http://flu.lanl.gov/search/view_record.html?accession=DQ497645&database=fluA) A/chicken/Pekalongan/BPPV4/2003 HA (4) 1659 2003 H5N1
    DQ497646 (http://flu.lanl.gov/search/view_record.html?accession=DQ497646&database=fluA) A/chicken/Sragen/BPPV4/2003 HA (4) 1659 2003 H5N1
    DQ320929 (http://flu.lanl.gov/search/view_record.html?accession=DQ320929&database=fluA) A/chicken/Wonosobo/BPPV4/2003 HA (4) 1659 2003 H5N1
    AY651323 (http://flu.lanl.gov/search/view_record.html?accession=AY651323&database=fluA) A/Ck/Indonesia/2A/2003 HA (4) 1689 2003 H5N1
    AY651321 (http://flu.lanl.gov/search/view_record.html?accession=AY651321&database=fluA) A/Ck/Indonesia/BL/2003 HA (4) 1659 2003 H5N1
    AY651320 (http://flu.lanl.gov/search/view_record.html?accession=AY651320&database=fluA) A/Ck/Indonesia/PA/2003 HA (4) 1696 2003 H5N1
    AB241623 (http://flu.lanl.gov/search/view_record.html?accession=AB241623&database=fluA) A/duck/Hokkaido/84/02 HA (4) 1637 2002 H5N3
    AY296083 (http://flu.lanl.gov/search/view_record.html?accession=AY296083&database=fluA) A/turkey/CA/D0208651-C/02 HA (4) 1708 2002 H5N2
    AY296077 (http://flu.lanl.gov/search/view_record.html?accession=AY296077&database=fluA) A/duck/NJ/117228-7/01 HA (4) 1691 2001 H5N2
    U79455 (http://flu.lanl.gov/search/view_record.html?accession=U79455&database=fluA) A/Turkey/Minnesota/10734/95 HA (4) 1647 1995 H5N2
    U05332 (http://flu.lanl.gov/search/view_record.html?accession=U05332&database=fluA) A/chicken/Florida/25717/93 HA (4) 996 1993 H5N2
    U05331 (http://flu.lanl.gov/search/view_record.html?accession=U05331&database=fluA) A/chicken/Pennsylvania/13609/93 HA (4) 996 1993 H5N2
    U28920 (http://flu.lanl.gov/search/view_record.html?accession=U28920&database=fluA) A/Emu/Texas/39442/93 (HP progeny) HA (4) 1650 1993 H5N2
    U05330 (http://flu.lanl.gov/search/view_record.html?accession=U05330&database=fluA) A/ruddy turnstone/Delaware/244/91 HA (4) 996 1991 H5N2
    U67783 (http://flu.lanl.gov/search/view_record.html?accession=U67783&database=fluA) A/Mallard/Ohio/556/1987 HA (4) 1740 1987 H5N9


  • Finally a sequence from Winnipeg.

    This one seem from British Columbia (West-coast)
    so on the same flyway than Alaska birds

    Never too late...:whistle:

    LOCUS DQ826532 1687 bp RNA linear VRL 16-JUL-2006
    DEFINITION Influenza A virus (A/mallard/BC/373/2005(H5N2)) hemagglutinin gene,
    partial cds.
    ACCESSION DQ826532
    VERSION DQ826532.1 GI:110287913
    KEYWORDS .
    SOURCE Influenza A virus (A/mallard/BC/373/2005(H5N2))
    ORGANISM Influenza A virus (A/mallard/BC/373/2005(H5N2))
    Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
    Influenzavirus A.
    REFERENCE 1 (bases 1 to 1687)
    AUTHORS Pasick,J., Handel,K., Robinson,J., Bowes,V., Li,Y., Leighton,T.,
    Kehler,H., Ridd,D. and Cottam-Birt,C.
    TITLE Relationship between H5N2 Avian Influenza Viruses Isolated from
    Wild and Domestic Ducks in British Columbia, Canada
    JOURNAL Avian Dis. (2006) In press
    REFERENCE 2 (bases 1 to 1687)
    AUTHORS Handel,K.A. and Pasick,J.
    TITLE Direct Submission
    JOURNAL Submitted (28-JUN-2006) CFIA-NCFAD, 1015 Arlington Street,
    Winnipeg, MB R3E 3M4, Canada


  • I mean, BC flyway are linked with asia by Alaska.
    It will be interesting to see the H5N2 sequence from Quebec which could be linked to europe by Greenland.


    This H5N2 is 80.1% homologeous (from the nucleic acid seq) from the clasical Quigai sequence wich is the near the lowest we can expect from the same substrain.

    If we look for the amino-acid sequence we found around 89% homology.

    So North American birds will have few or no immunity at all against an asiatic H5N1 if it come into america...

    There is more silent mutation than significative one for the protein sequence.

    However, silent mutation can show recombination event and I hope Dr.Niman will post more about that soon.

    While waiting, there is a clasical homology matrix of the experimental vaccine strain, the classical quigai strain and this North-American BC strain.
    476
    Orange is the North American Strain (with a wild low path cleavage site)
    Green are Reverse Genetic Modified strains (with a modified low path cleavage site)
    Yellow are Wild strain( with the high path cleavage site)


  • Best buddy list

    DQ826532 (http://flu.lanl.gov/search/view_record.html?accession=DQ826532&database=fluA) A/mallard/BC/373/2005 HA (4) 1687 2005 H5N2
    AY296079 (http://flu.lanl.gov/search/view_record.html?accession=AY296079&database=fluA) A/duck/ME/151895-7A/02 HA (4) 1691 2002 H5N2
    AY296083 (http://flu.lanl.gov/search/view_record.html?accession=AY296083&database=fluA) A/t

  • It look like NorthAmerican H5 is setting up the table for his asiatic cousin's visit.


  • Commentary at

    http://www.recombinomics.com/News/07190601/H5_BC_Mallard_Swine.html
    Dr Niman, this commentary mentions a fatal human case in Maryland? Have we heard anything about that before? Seems like I would have remembered a fatal human case in Maryland. thx


  • Thanks Mingus, appreciate it. I was particularly interested in this comment by Dr. Niman on flutrackers last April. I think it shows some of the complexities and subtleties to this recombination in that the donor did not actually have the exact polymorphism picked up by the recepient.... (I think it also shows how important it is to have sequence data from all of the genes of the viruses to do proper study)

    ""Homologous recombination just requires sequence homology (identity) so donor sequences do not have to be on the same gene or same location for the newly synthesized stand of RNA to hybridize with a template. In H9N2 the region of HA homology with H5N1 to produce S227N is at an upsteam location. Thus, H5N1 HA RNA is used initially. The polymerase themn jumps to the H9 template with the sequence identity and then jumps back to H5. This jump acquires S227N for H5N1, but does not involve an N at position 227 because the homologous RNA in H9N1 is upstream.

    Thus, H9N2 does not have an N at position 227, but does have the appropriate donor sequence to produce S227N in H5 in the Qinghai strain.""


  • Swine Sequences in H5 Wild Birds in British Columbia

    Recombinomics Commentary
    July 19, 2006

    The HA sequence of A/mallard/BC/317/2005(H5N2) has been released. This isolate was obtained via an expanded banding project by the Canadian Cooperative Wildlife Health Centre. Last year the agency reported that H5 had been found in live healthy wild birds throughout southern Canada. A remarkable 24% of the birds tested in British Columbia were H5 positive. The latest breakdown by species indicates bird flu was detected in 1165/2657 of the mallards tested and H5 was detected in 187/811. The update report by region indicates H5 was detected in 167/380 birds tested in British Columbia.

    Analysis of the above sequence indicates it has a HA cleavage site consistent with low path H5. However, analysis of individual polymorphisms indicates the H5 has acquired two tandem polymorphisms, C1367T and C1377T.

    Other isolates in the Los Alamos flu database having these two polymorphisms are listed below. The only H5 or avian isolate in the list is the H5N1 sequence from British Columbia. All other isolates are mammalian H1 isolates, including recent isolates from Canadian swine as well as a fatal human case in Maryland

    The most extensive homology is identified with a 25 bp probe which identifies the recent isolate A/swine/Ontario/11112/2004(H1N2), which was among a group of Canadian swine showing both extensive recombination as well as extreme conservation of sequences. As noted below, the 25 bp probe identifies A/Wilson-Smith/33 and A/WSN/33, the first human flu isolate as well as its neurotropic derivative.

    The acquisition of these polymorphisms in a health wild bird population is cause for concern. Recent data from Prince Edward Island suggests the Qinghai strain of H5N1 has already entered North America. Recombination between low path H5 and high path H5N1 is common and provides a mechanism for acquisition of these mammalian polymorphisms by the Qinghai strain of H5N1 bird flu.

    The initial H5N1 human isolates from Vietnam and Thailand had acquired a number of mammalian polymorphisms that were not found in other H5N1’s. The acquisition of swine polymorphisms in H5 in wild birds in Canada, and presumably the United States, is cause for concern.


  • So I gather that the H5N1 in BC is low Pathagen? Can it also change to High pathogen at any time?


  • Here is a North American series

    DQ826532 (http://flu.lanl.gov/search/view_record.html?accession=DQ826532&database=fluA) A/mallard/BC/373/2005 HA (4) 1687 2005 H5N2
    CY005927 (http://flu.lanl.gov/search/view_record.html?accession=CY005927&database=fluA) A/shorebird/Delaware/101/2004 HA (4) 1766 2004 H5N7
    CY005969 (http://flu.lanl.gov/search/view_record.html?accession=CY005969&database=fluA) A/shorebird/Delaware/75/2004 HA (4) 1766 2004 H5N7
    AY296079 (http://flu.lanl.gov/search/view_record.html?accession=AY296079&database=fluA) A/duck/ME/151895-7A/02 HA (4) 1691 2002 H5N2
    AY296083 (http://flu.lanl.gov/search/view_record.html?accession=AY296083&database=fluA) A/turkey/CA/D0208651-C/02 HA (4) 1708 2002 H5N2
    AY296077 (http://flu.lanl.gov/search/view_record.html?accession=AY296077&database=fluA) A/duck/NJ/117228-7/01 HA (4) 1691 2001 H5N2
    AY296078 (http://flu.lanl.gov/search/view_record.html?accession=AY296078&database=fluA) A/unknown/NY/118547-11/01 HA (4) 1691 2001 H5N2
    AY296075 (http://flu.lanl.gov/search/view_record.html?accession=AY296075&database=fluA) A/unknown/NY/9899-6/01 HA (4) 1735 2001 H5N2
    AY296084 (http://flu.lanl.gov/search/view_record.html?accession=AY296084&database=fluA) A/ruddy turnstone/NJ/2242/00 HA (4) 1691 2000 H5N3
    U79451 (http://flu.lanl.gov/search/view_record.html?accession=U79451&database=fluA) A/Mallard/Wisconsin/34/75 HA (4) 996 1975 H5N6
    U79456 (http://flu.lanl.gov/search/view_record.html?accession=U79456&database=fluA) A/Turkey/Wisconsin/68 HA (4) 1647 1968 H5N9


  • So I gather that the H5N1 in BC is low Pathagen? Can it also change to High pathogen at any time?


    I dont know exacly wich is the mechanism for the pathogenicity revertance and I wish Dr.Niman could put a light on this.

    But looking at the alignement we can see zone of homology each part of the cleavage site. So maybe a kind of homologeous recombination with lenght difference can happen :confused:

    478
    Dot represent homology to the North-american strain here


  • Virology. 1994 Oct;204(1):462-5. Related Articles, Links


    Nonhomologous recombination between the hemagglutinin gene and the nucleoprotein gene of an influenza virus.

    Orlich M, Gottwald H, Rott R.

    Institut fur Virologie, Justus-Liebig-Universitat Giessen, Germany.

    Mutants of the influenza virus A/seal/Mass/1/80 (H7N7) are described which contain an insertion of 60 nucleotides in the hemagglutinin (HA) gene, derived most probably by recombination between the HA gene and the nucleoprotein gene of the same virus. The nonhomologous RNA recombination resulted in an enhanced hemagglutinin cleavability associated with broadening of the host cell spectrum, increased hemolytic activity, and increased pathogenicity for chickens.

    PMID: 8091680 [PubMed - indexed for MEDLINE]

    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8091680&dopt=Abstract

    The above appears to be an example of a hemagglutinin gene picking up high pathogenecity by inserting some gene fragments from another one of its genes (NP, nucleoprotein) into its native HA gene to form a functional and more deadly recombinant. It seems amazing to me that this can happen and produce a functional offspring. It seems like it could be the result of an efficient 'storage mechanism' where this functional 'gene fragment' was stored in the NP for possible future use.

    Anyway, it brings up a few questions to me. Have there been examples of dual infections where a different virus has been able to pick up this HPAI function from a donating virus with the right NP sequence?

    Also have there been examples of homologous recombination between LPAI and HPAI where the LPAI picked up the HPAI sequence?


  • Mingus - ALaska has birds that fly through all Canadian flyways.

    The swans here are split between those that summer on the west coast and migrate down the Pacific flyway vs. those who summer on the Arctic Ocean coast and migrate across Canada - through central and Atlantic areas.

    The Tundra swan has a route across the top of Canada and down the West Atlantic flyway.

    The Trumpeter swan also travels from the top of Alaska and goes down through central Canada.

    Upland Sandpiper is one of several that also has a route through canada.

    .


  • Not to distract from your inteligent post but what may this mean or what could be the implications to the average person about BF?:)


  • Cleavage site : "RETR"

    For comparison...
    Quigai cleavage site is "GERRRKKR"
    VietNam cleavage site is "RERRRKKR"


  • Another Asian connection

    DQ826532 (http://flu.lanl.gov/search/view_record.html?accession=DQ826532&database=fluA) A/mallard/BC/373/2005 HA (4) 1687 2005 H5N2
    AY585370 (http://flu.lanl.gov/search/view_record.html?accession=AY585370&database=fluA) A/duck/Shanghai/08/2001 HA (4) 1708 2001 H5N1


  • Siam:

    low path to high path conversion timeframe is usually 6 to 12 months.

    Dr. Niman/Mingus:

    re: WS/33 and WSN/33, wasn't there some found (another "lab accident") in North & South Korean swine not long ago? considering the many birds passing north thru Korea, including the mallard which migrates to both hemispheres from here, is it possible the WS portion could come from there?

    .


  • ok, thanks for clearing that up for me. Sound as if lab workers are "cause for concern."


  • The cause for concern is the H1N2 in swine and H5 in wild birds.

    Are any specific polymorphisms particulary worrisome here?


  • Commentary at

    http://www.recombinomics.com/News/07190601/H5_BC_Mallard_Swine.html


  • I think this is in reference to an H1N1 case

    L24362 A/Maryland/12/91 1991 H1N1


  • It look like NorthAmerican H5 is setting up the table for his asiatic cousin's visit.

    I suspect H5N1 is already munching away. Although the H5N2 sequence was released this week, the sample is from an August 2005 collection (and the buried H5 data on PEI this year doesn't make H5N1 go away, it just keeps it out of the headlines).


  • Are any specific polymorphisms particulary worrisome here?

    Dr.Niman found two typical swine polymorphisms from H1N2 in the North american H5.
    That mean wild bird H5 haved and can pick up mammalian polymorphism from
    the H1N2 swine virus pool.
    The H1N2 swine virus pool is also closely connected with H1N1 and H3N2 swine virus and recombination and reassortment between theses substrains is pretty common as shonw by many recents articles. (sorry, I don't haved them on hand right now.)
    Also, this large pool of swine virus is well known to carry gene from human origin ( The NA gene for the canadian H3N2 and some others too, PB2 I think for some H1N2 strain.) and also from avian origin !

    Next to that, recombination from North american H5 and asian H5 is facilitated because they share many homologeous

    So this ecosystem is clearly in place to facilitate all kinds of genetic exchange from human origin to avian origin

    Human H1N1 & H3N2 <---> Swine H1N1 & H3N2 & H1N2 <---> Avian H1N1 & H3N2 & H1N2 & H5N2 & H5N1

    Maybe you already know that Dr.nickell , sorry, anyway it could be interesting for others readers.


  • ok, thanks for clearing that up for me. Sound as if lab workers are "cause for concern."

    The lab workers were infected in 1994. The cause for concern is the H1N2 in swine and H5 in wild birds.


  • You're right AD, I talk a bit too quick.

    It jumped out at me because it's part of my presentations.

    I'm getting the message out loud and clear that birds come to Alaska from every corner of the Americas, and as far away as Africa.

    It's great to see the lights turn on as people understand how migratory birds connect the entire globe.

    .


  • I think this is in reference to an H1N1 case

    L24362 A/Maryland/12/91 1991 H1N1

    You are correct

    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=438591&dopt=genbank





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