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Recombination possibility - My Question to Niman in sequences lingo...

Re: Recombination possibility - My Question to Niman in sequences lingo...

Take this
AACGGGCAA




Accession Strain Seg Length Year Serotype
DQ356886 A/chicken/Anhui/M HA (4) 1038 H5N1
AY834279 A/tiger/Thailand/SPB-1 HA (4) 1779 H5N1
ISDN140054 A/Azerbaijan/006-207/2006 HA (4) 1680 2006 H5N1
DQ864720 A/cat/Dagestan/87/06 HA (4) 1779 2006 H5N1
DQ643982 A/cat/Germany/606/2006 HA (4) 1779 2006 H5N1
DQ864715 A/chicken/Adygea/203/06 HA (4) 1751 2006 H5N1
DQ661910 A/chicken/Afghanistan/1207/2006 HA (4) 1602 2006 H5N1
CY016787 A/chicken/Afghanistan/1207/2006 HA (4) 1734 2006 H5N1
ISDN207242 A/Chicken/Bandar Lampung/BBPVIII/2006 HA (4) 1729 2006 H5N1
CY016811 A/chicken/Cote d'Ivoire/1787-34/2006 HA (4) 1722 2006 H5N1
DQ862001 A/chicken/Egypt/2253-1/2006 HA (4) 1707 2006 H5N1
DQ837587 A/chicken/Egypt/5610NAMRU3-F3/2006 HA (4) 1595 2006 H5N1
DQ837588 A/chicken/Egypt/5611NAMRU3-AN/2006 HA (4) 1613 2006 H5N1
DQ837589 A/chicken/Egypt/5612NAMRU3-S/2006 HA (4) 1604 2006 H5N1
DQ447199 A/chicken/Egypt/960N3-004/2006 HA (4) 1673 2006 H5N1
ISDN184026 A/chicken/Hong Kong/947/2006 HA (4) 1706 2006 H5N1
DQ673901 A/chicken/Ivory Coast/1787/2006 HA (4) 1690 2006 H5N1
DQ676834 A/chicken/Krasnodar/01/2006 HA (4) 1754 2006 H5N1
DQ864718 A/chicken/Krasnodar/199/06 HA (4) 1720 2006 H5N1
AM262541 A/chicken/Lagos.NIE/BA209/2006 HA (4) 1687 2006 H5N1
AM262542 A/chicken/Lagos.NIE/BA210/2006 HA (4) 1727 2006 H5N1
AM262543 A/chicken/Lagos.NIE/BA211/2006 HA (4) 1727 2006 H5N1
AM262546 A/chicken/Lagos.NIE/SO300/2006 HA (4) 1713 2006 H5N1
AM262547 A/chicken/Lagos.NIE/SO452/2006 HA (4) 1718 2006 H5N1
AM262553 A/chicken/Lagos.NIE/SO493/2006 HA (4) 1718 2006 H5N1
AM262572 A/chicken/Lagos.NIE/SO494/2006 HA (4) 1718 2006 H5N1
DQ676830 A/chicken/Mahachkala/05/2006 HA (4) 1683 2006 H5N1
ISDN138756 A/chicken/Malaysia/935/2006 HA (4) 1721 2006 H5N1
DQ838517 A/chicken/Niger/2130-7/2006 HA (4) 1707 2006 H5N1
DQ838516 A/chicken/Niger/2130-8/2006 HA (4) 1707 2006 H5N1
CY016939 A/chicken/Nigeria/1047-30/2006 HA (4) 1734 2006 H5N1
CY016947 A/chicken/Nigeria/1047-34/2006 HA (4) 1733 2006 H5N1
CY016923 A/chicken/Nigeria/1047-54/2006 HA (4) 1734 2006 H5N1
CY016931 A/chicken/Nigeria/1047-62/2006 HA (4) 1733 2006 H5N1
CY016907 A/chicken/Nigeria/1047-8/2006 HA (4) 1734 2006 H5N1
DQ406728 A/chicken/Nigeria/641/2006 HA (4) 1669 2006 H5N1
CY016276 A/chicken/Nigeria/641/2006 HA (4) 1732 2006 H5N1
CY016284 A/chicken/Nigeria/957-20/2006 HA (4) 1731 2006 H5N1
CY016300 A/chicken/Sudan/1784-10/2006 HA (4) 1734 2006 H5N1
CY016292 A/chicken/Sudan/1784-7/2006 HA (4) 1734 2006 H5N1
DQ862003 A/chicken/Sudan/1784/2006 HA (4) 1690 2006 H5N1
DQ861999 A/chicken/Sudan/2115-12/2006 HA (4) 1707 2006 H5N1
DQ862000 A/chicken/Sudan/2115-9/2006 HA (4) 1707 2006 H5N1
DQ864719 A/chicken/Volgograd/236/06 HA (4) 1779 2006 H5N1
ISDN207243 A/Chicken/Way Kanan/BBPVIII/2006 HA (4) 1725 2006 H5N1
DQ659679 A/common bussard/Bavaria/2/2006 HA (4) 1707 2006 H5N1
ISDN184030 A/Common Magpie/Hong Kong/645/2006 HA (4) 1662 2006 H5N1
CY016779 A/Cygnus cygnus/Iran/754/2006 HA (4) 1739 2006 H5N1
DQ515984 A/Cygnus olor/Czech Republic/5170/2006 HA (4) 1745 2006 H5N1
CY017035 A/Cygnus olor/Italy/742/2006 HA (4) 1722 2006 H5N1
DQ666146 A/Djibouti/5691NAMRU3/2006 HA (4) 1311 2006 H5N1
DQ435200 A/domestic cat/Iraq/820/2006 HA (4) 1647 2006 H5N1
DQ435201 A/domestic goose/Iraq/812/2006 HA (4) 1647 2006 H5N1
CY016803 A/duck/Cote d'Ivoire/1787-18/2006 HA (4) 1734 2006 H5N1
CY016899 A/duck/Egypt/2253-3/2006 HA (4) 1743 2006 H5N1
DQ862002 A/duck/Egypt/2253-3/2006 HA (4) 1707 2006 H5N1
ISDN207241 A/Duck/Indramayu/BBPW109/2006 HA (4) 1729 2006 H5N1
ISDN138780 A/duck/Laos/3295/2006 HA (4) 1719 2006 H5N1
DQ845348 A/duck/Laos/3295/2006 HA (4) 1719 2006 H5N1
DQ659113 A/duck/Niger/914/2006 HA (4) 1602 2006 H5N1
CY017027 A/duck/Niger/914/2006 HA (4) 1732 2006 H5N1
DQ464377 A/Egypt/2782-NAMRU3/2006 HA (4) 1640 2006 H5N1
CY014208 A/feline/Indonesia/CDC1/2006 HA (4) 1659 2006 H5N1
ISDN136817 A/Feline/Indonesia/CDC1/2006 HA (4) 1659 2006 H5N1
DQ914808 A/grebe/Tyva/Tyv06-1/06 HA (4) 1754 2006 H5N1
DQ852600 A/grebe/Tyva/Tyv06-2/06 HA (4) 1754 2006 H5N1
DQ863503 A/grebe/Tyva/Tyv06-8/2006 HA (4) 1754 2006 H5N1
ISDN133317 A/Indonesia/283H/2006 NA (6) 1393 2006 H5N1
ISDN133316 A/Indonesia/283H/2006 HA (4) 1752 2006 H5N1
ISDN133323 A/Indonesia/286H/2006 HA (4) 1729 2006 H5N1
ISDN133324 A/Indonesia/286H/2006 NA (6) 1396 2006 H5N1
ISDN138748 A/Indonesia/292H/2006 HA (4) 1696 2006 H5N1
ISDN136841 A/Indonesia/298H/2006 HA (4) 1695 2006 H5N1
ISDN136849 A/Indonesia/304H/2006 HA (4) 1707 2006 H5N1
ISDN138764 A/Indonesia/321H/2006 HA (4) 1072 2006 H5N1
ISDN138772 A/Indonesia/341H/2006 HA (4) 1696 2006 H5N1
ISDN140926 A/Indonesia/542H/2006 HA (4) 1710 2006 H5N1
ISDN187429 A/Indonesia/567H/2006 HA (4) 1695 2006 H5N1
ISDN187437 A/Indonesia/569H/2006 HA (4) 1647 2006 H5N1
ISDN187445 A/Indonesia/583H/2006 HA (4) 1651 2006 H5N1
ISDN187453 A/Indonesia/604H/2006 HA (4) 1680 2006 H5N1
CY014204 A/Indonesia/CDC326/2006 HA (4) 1659 2006 H5N1
ISDN136812 A/Indonesia/CDC326/2006 HA (4) 1659 2006 H5N1
CY014202 A/Indonesia/CDC326N/2006 HA (4) 1659 2006 H5N1
ISDN136810 A/Indonesia/CDC326N/2006 HA (4) 1659 2006 H5N1
CY014203 A/Indonesia/CDC326N2/2006 HA (4) 1659 2006 H5N1
ISDN136811 A/Indonesia/CDC326N2/2006 HA (4) 1659 2006 H5N1
ISDN136813 A/Indonesia/CDC326T/2006 HA (4) 1659 2006 H5N1
ISDN136814 A/Indonesia/CDC326T/2006 HA (4) 1659 2006 H5N1
CY014205 A/Indonesia/CDC326T/2006 HA (4) 1659 2006 H5N1
ISDN136816 A/Indonesia/CDC357/2006 HA (4) 1659 2006 H5N1
CY014207 A/Indonesia/CDC357/2006 HA (4) 1659 2006 H5N1
CY014209 A/Indonesia/CDC370/2006 HA (4) 1659 2006 H5N1
ISDN136908 A/Indonesia/CDC370/2006 HA (4) 1659 2006 H5N1
CY014210 A/Indonesia/CDC370E/2006 HA (4) 1659 2006 H5N1
ISDN136909 A/Indonesia/CDC370E/2006 HA (4) 1659 2006 H5N1
ISDN137412 A/Indonesia/CDC370P/2006 HA (4) 1659 2006 H5N1
CY014211 A/Indonesia/CDC370P/2006 HA (4) 1659 2006 H5N1
ISDN137413 A/Indonesia/CDC370T/2006 HA (4) 1659 2006 H5N1
CY014212 A/Indonesia/CDC370T/2006 HA (4) 1659 2006 H5N1
ISDN137414 A/Indonesia/CDC390/2006 HA (4) 1659 2006 H5N1
CY014213 A/Indonesia/CDC390/2006 HA (4) 1659 2006 H5N1
CY014311 A/Indonesia/CDC523/2006 HA (4) 1707 2006 H5N1
ISDN181365 A/Indonesia/CDC523/2006 HA (4) 1707 2006 H5N1
CY014368 A/Indonesia/CDC523E/2006 HA (4) 1659 2006 H5N1
ISDN183297 A/Indonesia/CDC523E/2006 HA (4) 1659 2006 H5N1
ISDN183305 A/Indonesia/CDC523T/2006 HA (4) 1659 2006 H5N1
CY014376 A/Indonesia/CDC523T/2006 HA (4) 1659 2006 H5N1
ISDN183313 A/Indonesia/CDC582/2006 HA (4) 1659 2006 H5N1
CY014384 A/Indonesia/CDC582/2006 HA (4) 1659 2006 H5N1
CY014393 A/Indonesia/CDC610/2006 HA (4) 1659 2006 H5N1
ISDN183698 A/Indonesia/CDC610/2006 HA (4) 1659 2006 H5N1
CY014401 A/Indonesia/CDC623/2006 HA (4) 1659 2006 H5N1
ISDN183706 A/Indonesia/CDC623/2006 HA (4) 1659 2006 H5N1
ISDN183714 A/Indonesia/CDC623E/2006 HA (4) 1659 2006 H5N1
CY014409 A/Indonesia/CDC623E/2006 HA (4) 1659 2006 H5N1
ISDN183722 A/Indonesia/CDC624/2006 HA (4) 1659 2006 H5N1
CY014417 A/Indonesia/CDC624/2006 HA (4) 1659 2006 H5N1
CY014425 A/Indonesia/CDC624E/2006 HA (4) 1659 2006 H5N1
ISDN183730 A/Indonesia/CDC624E/2006 HA (4) 1659 2006 H5N1
ISDN183746 A/Indonesia/CDC634/2006 HA (4) 1659 2006 H5N1
CY014441 A/Indonesia/CDC634/2006 HA (4) 1659 2006 H5N1
CY014449 A/Indonesia/CDC634P/2006 HA (4) 1659 2006 H5N1
ISDN183754 A/Indonesia/CDC634P/2006 HA (4) 1659 2006 H5N1
ISDN183762 A/Indonesia/CDC634T/2006 HA (4) 1659 2006 H5N1
CY014457 A/Indonesia/CDC634T/2006 HA (4) 1659 2006 H5N1
ISDN207111 A/Indonesia/CDC644/2006 HA (4) 1659 2006 H5N1
CY014518 A/Indonesia/CDC644/2006 HA (4) 1659 2006 H5N1
CY014510 A/Indonesia/CDC644T/2006 HA (4) 1659 2006 H5N1
ISDN207103 A/Indonesia/CDC644T/2006 HA (4) 1659 2006 H5N1
ISDN204133 A/Indonesia/CDC669/2006 HA (4) 1707 2006 H5N1
CY014481 A/Indonesia/CDC669/2006 HA (4) 1707 2006 H5N1
ISDN204141 A/Indonesia/CDC669P/2006 HA (4) 1707 2006 H5N1
CY014489 A/Indonesia/CDC669P/2006 HA (4) 1707 2006 H5N1
CY014497 A/Indonesia/CDC699/2006 HA (4) 1707 2006 H5N1
ISDN204149 A/Indonesia/CDC699/2006 HA (4) 1707 2006 H5N1
CY014529 A/Indonesia/CDC739/2006 HA (4) 1659 2006 H5N1
CY014543 A/Indonesia/CDC759/2006 HA (4) 1659 2006 H5N1
DQ435202 A/Iraq/207-NAMRU3/2006 HA (4) 1647 2006 H5N1
ISDN184028 A/Japanese White Eye/Hong Kong/1038/2006 HA (4) 1693 2006 H5N1
DQ458992 A/mallard/Bavaria/1/2006 HA (4) 1707 2006 H5N1
DQ449031 A/mallard/Italy/332/2006 HA (4) 1670 2006 H5N1
CY016795 A/mallard/Italy/835/2006 HA (4) 1731 2006 H5N1
ISDN184024 A/Munia/Hong Kong/2454/2006 HA (4) 1693 2006 H5N1
CY016915 A/ostrich/Nigeria/1047-25/2006 HA (4) 1740 2006 H5N1
DQ464354 A/swan/Germany/R65/2006 HA (4) 1779 2006 H5N1
DQ440535 A/swan/Iran/754/2006 HA (4) 1653 2006 H5N1
DQ412997 A/swan/Italy/179/06 HA (4) 1247 2006 H5N1
ISDN136919 A/swan/Italy/179/2006 HA (4) 1247 2006 H5N1
CY017043 A/swan/Slovenia/760/2006 HA (4) 1731 2006 H5N1
ISDN133098 A/Turkey/12/2006 HA (4) 1659 2006 H5N1
ISDN133105 A/Turkey/15/2006 HA (4) 1659 2006 H5N1
ISDN133356 A/Turkey/651242/06 HA (4) 1659 2006 H5N1
ISDN133364 A/Turkey/65596/06 HA (4) 1659 2006 H5N1
DQ837590 A/turkey/Egypt/5613NAMRU3-T/2006 HA (4) 1603 2006 H5N1
AB263752 A/whooper swan/Mongolia/2/06 HA (4) 1745 2006 H5N1
DQ643809 A/Zhejiang/16/2006 HA (4) 1281 2006 H5N1
DQ371928 A/Anhui/1/2005 HA (4) 1704 2005 H5N1
DQ659327 A/Bar headed goose/Qinghai/1A/2005 HA (4) 1767 2005 H5N1
ISDN140934 A/Bar headed goose/Qinghai/1A/2005 HA (4) 1767 2005 H5N1
AB233319 A/bar-headed goose/Mongolia/1/05 HA (4) 1737 2005 H5N1
DQ137873 A/bar-headed goose/Qinghai/0510/05 HA (4) 1679 2005 H5N1
DQ095621 A/Bar-headed Goose/Qinghai/12/05 HA (4) 1704 2005 H5N1
DQ095617 A/Bar-headed Goose/Qinghai/5/05 HA (4) 1710 2005 H5N1
DQ095612 A/Bar-headed Goose/Qinghai/59/05 HA (4) 1707 2005 H5N1
DQ095615 A/Bar-headed Goose/Qinghai/60/05 HA (4) 1701 2005 H5N1
DQ095618 A/Bar-headed Goose/Qinghai/61/05 HA (4) 1708 2005 H5N1
DQ095620 A/Bar-headed Goose/Qinghai/62/05 HA (4) 1698 2005 H5N1
DQ095622 A/Bar-headed Goose/Qinghai/65/05 HA (4) 1697 2005 H5N1
DQ095623 A/Bar-headed Goose/Qinghai/67/05 HA (4) 1697 2005 H5N1
DQ095613 A/Bar-headed Goose/Qinghai/68/05 HA (4) 1704 2005 H5N1
DQ095619 A/Bar-headed Goose/Qinghai/75/05 HA (4) 1697 2005 H5N1
DQ100554 A/black-headed goose/Qinghai/1/2005 HA (4) 1555 2005 H5N1
DQ100555 A/black-headed goose/Qinghai/2/2005 HA (4) 1555 2005 H5N1
DQ100556 A/black-headed gull/Qinghai/1/2005 HA (4) 1555 2005 H5N1
DQ095616 A/Brown-headed Gull/Qinghai/3/05 HA (4) 1707 2005 H5N1
ISDN121986 A/Cambodia/JP52a/2005 HA (4) 1707 2005 H5N1
DQ320932 A/chicken/Bantul/BBVet-I/2005 HA (4) 1698 2005 H5N1
ISDN122143 A/chicken/Cambodia/013LC1b/2005 HA (4) 1659 2005 H5N1
ISDN122146 A/chicken/Cambodia/022LC3b/2005 HA (4) 1657 2005 H5N1
DQ650659 A/chicken/Crimea/04/2005 HA (4) 1754 2005 H5N1
DQ650663 A/chicken/Crimea/08/2005 HA (4) 1754 2005 H5N1
DQ340848 A/chicken/Crimea/1/2005 HA (4) 1319 2005 H5N1
DQ676838 A/chicken/Dovolnoe/03/2005 HA (4) 1015 2005 H5N1
DQ320876 A/chicken/Fujian/1042/2005 HA (4) 1698 2005 H5N1
DQ320898 A/chicken/Guangxi/604/2005 HA (4) 1695 2005 H5N1
DQ497651 A/chicken/Gunung Kidal/BBVW/2005 HA (4) 1698 2005 H5N1
DQ343150 A/chicken/Hebei/326/2005 HA (4) 1707 2005 H5N1
DQ320910 A/chicken/Hunan/999/2005 HA (4) 1695 2005 H5N1
ISDN129601 A/Chicken/Indonesia/CDC24/2005 HA (4) 1659 2005 H5N1
CY014193 A/chicken/Indonesia/CDC24/2005 HA (4) 1659 2005 H5N1
ISDN129590 A/Chicken/Indonesia/CDC25/2005 HA (4) 1659 2005 H5N1
CY014185 A/chicken/Indonesia/CDC25/2005 HA (4) 1659 2005 H5N1
AM183670 A/chicken/Indonesia/R60/05 HA (4) 1779 2005 H5N1
ISDN187385 A/Chicken/Indonesia/Wates1/2005 HA (4) 1714 2005 H5N1
ISDN187389 A/Chicken/Indonesia/Wates126/2005 HA (4) 1717 2005 H5N1
ISDN187386 A/Chicken/Indonesia/Wates130/2005 HA (4) 1704 2005 H5N1
ISDN187388 A/Chicken/Indonesia/Wates80/2005 HA (4) 1711 2005 H5N1
DQ497652 A/chicken/Kulon Progo/BBVW/2005 HA (4) 1446 2005 H5N1
DQ449632 A/chicken/Kurgan/05/2005 HA (4) 1754 2005 H5N1
DQ323672 A/chicken/Kurgan/3/2005 HA (4) 1754 2005 H5N1
DQ497643 A/chicken/Magetan/BBVW/2005 HA (4) 1698 2005 H5N1
ISDN208031 A/Chicken/Murao Jambi/BBPV-II/2005 HA (4) 1711 2005 H5N1
ISDN208035 A/Chicken/Pakun Baru/BPPV-II/2005 HA (4) 1710 2005 H5N1
ISDN208036 A/Chicken/Palembang/BPPV-III/2005 HA (4) 1704 2005 H5N1
DQ497648 A/chicken/Purworejo/BBVW/2005 HA (4) 1698 2005 H5N1
ISDN208037 A/Chicken/Sembawa/BPPV-III/2005 HA (4) 1703 2005 H5N1
DQ095626 A/Chicken/Shantou/810/05 HA (4) 1693 2005 H5N1
DQ864716 A/chicken/Tambov/570-2/05 HA (4) 1765 2005 H5N1
DQ153251 A/chicken/Thailand/Kamphaengphet-3-01/2005 HA (4) 1075 2005 H5N1
DQ153252 A/chicken/Thailand/Kamphaengphet-3-02/2005 HA (4) 1104 2005 H5N1
DQ251796 A/chicken/Thailand/Kamphaengphet-3-03/2005 HA (4) 1104 2005 H5N1
DQ251797 A/chicken/Thailand/Kamphaengphet-3-04/2005 HA (4) 1107 2005 H5N1
DQ251798 A/chicken/Thailand/Kamphaengphet-3-05/2005 HA (4) 1074 2005 H5N1
DQ251799 A/chicken/Thailand/Kamphaengphet-3-06/2005 HA (4) 1107 2005 H5N1
DQ251800 A/chicken/Thailand/Kamphaengphet-3-07/2005 HA (4) 1068 2005 H5N1
DQ334760 A/chicken/Thailand/Kanchanaburi/CK-160/2005 HA (4) 1761 2005 H5N1
DQ334776 A/chicken/Thailand/Nontaburi/CK-162/2005 HA (4) 1726 2005 H5N1
DQ279301 A/chicken/Tula/10/2005 HA (4) 1308 2005 H5N1
DQ840519 A/chicken/Tula/Russia/Oct-5/2005 HA (4) 1308 2005 H5N1
CY016867 A/chicken/Viet Nam/10/2005 HA (4) 1731 2005 H5N1
CY016875 A/chicken/Viet Nam/11/2005 HA (4) 1731 2005 H5N1
CY017059 A/chicken/Viet Nam/17/2005 HA (4) 1731 2005 H5N1
CY016835 A/chicken/Viet Nam/2/2005 HA (4) 1731 2005 H5N1
CY016843 A/chicken/Viet Nam/6/2005 HA (4) 1729 2005 H5N1
CY016851 A/chicken/Viet Nam/8/2005 HA (4) 1741 2005 H5N1
CY016859 A/chicken/Viet Nam/9/2005 HA (4) 1731 2005 H5N1
ISDN124038 A/Chicken/Viet Nam/NCVD09/2005 HA (4) 1707 2005 H5N1
ISDN124037 A/Chicken/Viet Nam/NCVD10/2005 HA (4) 1709 2005 H5N1
DQ497676 A/chicken/Vietnam/348/2005 HA (4) 1692 2005 H5N1
DQ497712 A/chicken/Vietnam/393/2005 HA (4) 1695 2005 H5N1
DQ497703 A/chicken/Vietnam/398/2005 HA (4) 1695 2005 H5N1
AM183674 A/chicken/Vietnam/P22/05 HA (4) 1776 2005 H5N1
AM183672 A/chicken/Vietnam/P41/05 HA (4) 1776 2005 H5
AM183673 A/chicken/Vietnam/P78/05 HA (4) 1776 2005 H5
DQ320933 A/chicken/Wajo/BBVM/2005 HA (4) 1698 2005 H5N1
DQ095624 A/Chicken/Yunnan/447/05 HA (4) 1700 2005 H5N1
DQ095625 A/Chicken/Yunnan/493/05 HA (4) 1678 2005 H5N1
DQ320925 A/Chinese pond heron/Hong Kong/18/2005 HA (4) 1695 2005 H5N1
DQ389158 A/Cygnus olor/Astrakhan/Ast05-2-1/2005 HA (4) 1754 2005 H5N1
DQ434889 A/Cygnus olor/Astrakhan/Ast05-2-10/2005 HA (4) 1754 2005 H5N1
DQ343502 A/Cygnus olor/Astrakhan/Ast05-2-2/2005 HA (4) 1754 2005 H5N1
DQ358746 A/Cygnus olor/Astrakhan/Ast05-2-3/2005 HA (4) 1754 2005 H5N1
DQ363918 A/Cygnus olor/Astrakhan/Ast05-2-4/2005 HA (4) 1754 2005 H5N1
DQ365004 A/Cygnus olor/Astrakhan/Ast05-2-5/2005 HA (4) 1754 2005 H5N1
DQ364996 A/Cygnus olor/Astrakhan/Ast05-2-6/2005 HA (4) 1754 2005 H5N1
DQ363923 A/Cygnus olor/Astrakhan/Ast05-2-7/2005 HA (4) 1754 2005 H5N1
DQ399540 A/Cygnus olor/Astrakhan/Ast05-2-8/2005 HA (4) 1754 2005 H5N1
DQ399547 A/Cygnus olor/Astrakhan/Ast05-2-9/2005 HA (4) 1754 2005 H5N1
CY016819 A/cygnus olor/Croatia/1/2005 HA (4) 1734 2005 H5N1

(...)
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

Now take this instead

AACGGGCTA

<TABLE class=resultstable cellSpacing=0 cellPadding=4 width="100%" border=0><TBODY><TR class=navbox bgColor=#5879db><TD class=navboxrow>Accession </TD><TD class=navboxrow>Strain</TD><TD class=navboxrow>Seg</TD><TD class=navboxrow>Length</TD><TD class=navboxrow>Year</TD><TD class=navboxrow>Serotype</TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=127772 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>DQ124150 </TD><TD>A/canine/Florida/43/2004 </TD><TD>NP (5) </TD><TD>1497 </TD><TD>2004 </TD><TD>H3N8 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=134429 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY004446 </TD><TD>A/shorebird/Delaware/68/2004 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>2004 </TD><TD>H13N9 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=127766 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>DQ124158 </TD><TD>A/canine/Florida/242/2003 </TD><TD>NP (5) </TD><TD>1497 </TD><TD>2003 </TD><TD>H3N8 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=127758 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>DQ124169 </TD><TD>A/equine/Massachussetts/213/2003 </TD><TD>NP (5) </TD><TD>810 </TD><TD>2003 </TD><TD>H3N8 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=127744 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>DQ124184 </TD><TD>A/equine/Ohio/1/2003 </TD><TD>NP (5) </TD><TD>1522 </TD><TD>2003 </TD><TD>H3N8 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=129668 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>DQ222915 </TD><TD>A/equine/Wisconsin/1/03 </TD><TD>NP (5) </TD><TD>1497 </TD><TD>2003 </TD><TD>H3N8 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=119698 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>AY855342 </TD><TD>A/equine/Kentucky/5/02 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>2002 </TD><TD>H3N8 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=127745 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>DQ124183 </TD><TD>A/equine/Kentucky/5/2002 </TD><TD>NP (5) </TD><TD>1381 </TD><TD>2002 </TD><TD>H3N8 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=130680 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>DQ021842 </TD><TD>A/ruddy turnstone/NJ/1407/01 </TD><TD>NP (5) </TD><TD>1476 </TD><TD>2001 </TD><TD>H4N6 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=1732 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>AF156419 </TD><TD>A/Duck/Hong Kong/Y280/97 </TD><TD>PB1 (2) </TD><TD>2218 </TD><TD>1997 </TD><TD>H9N2 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=208788 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY014801 </TD><TD>A/turkey/Minnesota/1012/1990 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1990 </TD><TD>H13N2 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=135439 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY005388 </TD><TD>A/herring gull/Delaware/660/1988 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1988 </TD><TD>H13N6 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=134887 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY004877 </TD><TD>A/herring gull/Delaware/665/1988 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1988 </TD><TD>H4N6 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=134547 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY004563 </TD><TD>A/herring gull/Delaware/712/1988 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1988 </TD><TD>H16N3 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=135434 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY005383 </TD><TD>A/laughing gull/Delaware/554/1988 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1988 </TD><TD>H13N3 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=135093 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY005067 </TD><TD>A/laughing gull/Delaware/2838/1987 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1987 </TD><TD>H13N2 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=133872 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY003897 </TD><TD>A/herring gull/Delaware/475/1986 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1986 </TD><TD>H13N2 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=134367 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY004388 </TD><TD>A/herring gull/New Jersey/780/1986 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1986 </TD><TD>H1N3 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=134437 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY004453 </TD><TD>A/herring gull/New Jersey/782/1986 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1986 </TD><TD>H13N2 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=135423 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY005372 </TD><TD>A/shorebird/New Jersey/840/1986 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1986 </TD><TD>H13N3 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=3503 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>M27520 </TD><TD>A/whale/Maine/328/84 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1984 </TD><TD>H13N2 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=3535 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>M30757 </TD><TD>A/Gull/Minnesota/945/80 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1980 </TD><TD>H13N6 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=135934 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>CY005861 </TD><TD>A/gull/MN/945/1980 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1980 </TD><TD>H13N6 </TD><TD></TD></TR><TR bgColor=white><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=3533 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>M30756 </TD><TD>A/gull/Maryland/1815/79 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1979 </TD><TD>H13N6 </TD><TD></TD></TR><TR bgColor=#a7c4ef><TD align=left><INPUT onclick=setAll(this.checked) type=checkbox value=3531 name=checkbox> </TD><TD class=displaytablerow align=left></TD><TD>M30755 </TD><TD>A/gull/Maryland/1824/78 </TD><TD>NP (5) </TD><TD>1565 </TD><TD>1978 </TD><TD>H13N9 </TD></TR></TBODY></TABLE>
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

The change is silent in the NP gene.
So it can spread in every NP gene of every strain without consequences.

But it can give to a H5N1 strain a built-in ability to recombine from his own inside gene without the need of a dual infection for a a-2,3 to a-2,6 affinity switch if this segment recombine from the NP to the HA gene.

I'm sure you'll have no problem to see what change it could cause in the HA.

So now...

Is it possible ?
 
Last edited:
Re: Recombination possibility - My Question to Niman in sequences lingo...

You can get lots of gene crosses if the sequence is short enough.

I would not consider silent changes to be without consequences. The thrid base transitions are NOT random.
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

But it can give to a H5N1 strain a built-in ability to recombine from his own inside gene without the need of a dual infection
Click to expand...

Mingus, I'd like to read some more about not needing a dual infection. If you have them.
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

Ming, I think I found it.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=abstractplus&db=pubmed&cmd=Retrieve&dopt=abstractplus&list_uids=8091680
<dl class="PubmedArticle" id="dlPubmedArticle8091680"><dt class="head" id="head8091680">1: Virology. 1994 Oct;204(1):462-5. <script language="JavaScript1.2"> <!-- var PopUpMenu2_LocalConfig_jsmenu3Config = [ ["ShowCloseIcon","yes"], ["Help","window.open('/entrez/query/static/popup.html','Links_Help','resizable=no,scrollbars=yes,toolbar=no,location=no,directories=no,status=no,menubar=no,copyhistory=no,alwaysRaised=no,depend=no,width=400,height=500');"], ["TitleText"," Links "] ] var jsmenu3Config = [ ["UseLocalConfig","jsmenu3Config","",""] ] //--> </script> <script language="JavaScript1.2"> <!-- var Menu8091680 = [ ["UseLocalConfig","jsmenu3Config","",""], ["Substance via MeSH","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_AbstractPlus&db=pubmed&cmd=Display&dopt=pubmed_pcsubstance_mesh&from_uid=8091680'","",""], ["Nucleotide","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_AbstractPlus&db=pubmed&cmd=Display&dopt=pubmed_nucleotide&from_uid=8091680'","",""], ["Protein","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_AbstractPlus&db=pubmed&cmd=Display&dopt=pubmed_protein&from_uid=8091680'","",""], ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=8091680'","",""], ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_AbstractPlus&cmd=Retrieve&db=pubmed&list_uids=8091680&dopt=Books'","",""], ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_AbstractPlus&cmd=Retrieve&db=pubmed&list_uids=8091680&dopt=ExternalLink'","",""] ] //--> </script> Links
</dt><dd class="abstract" id="abstract8091680">Nonhomologous recombination between the hemagglutinin gene and the nucleoprotein gene of an influenza virus.

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]
</dd><dd class="links" id="links8091680">Related Links

</dd></dl>
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

niman said:
You can get lots of gene crosses if the sequence is short enough.
I would not consider silent changes to be without consequences. The thrid base transitions are NOT random.
Click to expand...

I know, I know this is not random.

But I mean the NP gene of americans Dog's H3N8 is highly similar to the NP gene of the Quigai strains or any H5N1 strains & recombination NP to NP is very frequent & plausible in a dual infection.

Also, because the A->T change in the AACGGGCA(T)A section is silent, there will have no selective pressure on it ( no repercussion on the protein )

So this polymorphism can spread in a H5N1 strain if H5N1 & H3N8 met each other here in america.

Since the time a H5N1 have this AACGGGCTA section in his NP gene, there will have an internal recombination risk with the H5 gene.
There will be no need for a dual infection, the donnor & the acceptor will be there in every cells.

Thanks Sonny, that was exactly the article who gave me this kind of Idea.

The H5 gene with AACGGGCTA instead of AACGGGCAA will code for L226 instead of Q226; this one will not be a silent change.

This recombination result could not be amplify if there is no selective pressure on it ( while the virus is in birds ) but could be there to happen opportunistically when the virus is replicating in human or in mammals ( positive selective pressure )

So again Dr.Niman, is it possible ?
Is there a constraint in your recombination laws that go against this possibility ?
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

Here is my alignement.

View attachment recomb.bmp

note that the two sequences below the recombination probe are HA gene while the others are NP genes
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

Mingus said:
I know, I know this is not random.

But I mean the NP gene of americans Dog's H3N8 is highly similar to the NP gene of the Quigai strains or any H5N1 strains & recombination NP to NP is very frequent & plausible in a dual infection.

Also, because the A->T change in the AACGGGCA(T)A section is silent, there will have no selective pressure on it ( no repercussion on the protein )

So this polymorphism can spread in a H5N1 strain if H5N1 & H3N8 met each other here in america.

Since the time a H5N1 have this AACGGGCTA section in his NP gene, there will have an internal recombination risk with the H5 gene.
There will be no need for a dual infection, the donnor & the acceptor will be there in every cells.

Thanks Sonny, that was exactly the article who gave me this kind of Idea.

The H5 gene with AACGGGCTA instead of AACGGGCAA will code for L226 instead of Q226; this one will not be a silent change.

This recombination result could not be amplify if there is no selective pressure on it ( while the virus is in birds ) but could be there to happen opportunistically when the virus is replicating in human or in mammals ( positive selective pressure )

So again Dr.Niman, is it possible ?
Is there a constraint in your recombination laws that go against this possibility ?
Click to expand...

I have focused on stretches of 10 or more exact matches. It is possible that less can be used, but once the number gets too low, there will be many competing possibilities. Since flu is segemented, there could be jumping without dual infections, and there are small regions of identity on multiple genes, which could be involved in packaging.

Most acquired polymoprhisms however, can easily be found with the 10 BP minimum.
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

niman said:
I have focused on stretches of 10 or more exact matches. It is possible that less can be used, but once the number gets too low, there will be many competing possibilities. Since flu is segemented, there could be jumping without dual infections, and there are small regions of identity on multiple genes, which could be involved in packaging.

Most acquired polymoprhisms however, can easily be found with the 10 BP minimum.
Click to expand...

Thank you Dr.Niman, I take this as a yes.

So now, it would be interesting to monitor this section of the NP gene in H5N1 and to closely watch for dog's H3N8 signature.

You know, It would also produce an interesting experience in a laboratory that would bring conclusives proof of recombination in H5N1 to those who do not consider the idea.

A H5N1 strain with the (706C 708G 711T) segment in the NP gene sequence would give rise to a 226L in H5 protein in less MDCK cells passage than a regular H5N1 strain who may never achieve that. ( Due to the recombination possibility & the selective pressure in MDCK cells to amplify the new born in the mix )

A positive result would strongly support the copy-choice recombination theory.
A negative result would only suggest that the "rules" are more complex than expected.
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

also in Chile some years ago:
H7N3 "recombined" (non-homologuous insertion) in the HA-cleavage site with a 30-nucleotides portion from its NP-gene.
http://www.cdc.gov/ncidod/EID/vol10no4/03-0396.htm


But for a single mutation Q226L, recombination with NP would
probably not
be required. We see a few such point-mutations in almost every human H5N1 isolate. And these mutations usually differ in different isolates.

So, considering the large amount of viruses in a host, I assume
that hundreds or thousands of single-point mutations are "tested"
in one infection. Most will be less viable, but if Q226L were more
viable, I think it has a good chance to evolve by "normal"
methods.
This may include short recombinations with NP or whatever,
which has the effect of just one nucleotide changing.
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

gsgs said:
also in Chile some years ago:
H7N3 "recombined" (non-homologuous insertion) in the HA-cleavage site with a 30-nucleotides portion from its NP-gene.
http://www.cdc.gov/ncidod/EID/vol10no4/03-0396.htm


But for a single mutation Q226L, recombination with NP would
probably not
be required. We see a few such point-mutations in almost every human H5N1 isolate. And these mutations usually differ in different isolates.

So, considering the large amount of viruses in a host, I assume
that hundreds or thousands of single-point mutations are "tested"
in one infection. Most will be less viable, but if Q226L were more
viable, I think it has a good chance to evolve by "normal"
methods.
This may include short recombinations with NP or whatever,
which has the effect of just one nucleotide changing.
Click to expand...

Random muations are rare. They are not "normal". They are largely nonsense.
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

Here is another example

Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the haemagglutinin gene of an influenza virus.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2544809&dopt=Abstract
Nature. 1989 Jul 13;340(6229):156-7
Khatchikian D, Orlich M, Rott R.

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

The haemagglutinin glycoprotein HA of influenza viruses is responsible for the attachment of the virus to neuraminic acid-containing receptors at the cell surface and subsequent penetration by triggering fusion of the viral envelope with cellular membranes. To express full activity of the newly synthesized precursor, HA has to be modified by post-translational proteolytic cleavage into the polypeptides HA1 and HA2 by cellular enzymes. If proteases suitable for cleavage are not present in the host cell, the resulting virus particles are non-infectious. During adaptation of the apathogenic influenza virus A/turkey/Oregon/71 to chicken embryo cells, which are not permissive for HA cleavage, we obtained an infectious virus variant with increased pathogenicity. Sequence analysis revealed that during adaptation 54 nucleotides were inserted into the HA gene; their sequence corresponds to a region of the 28S ribosomal RNA (= Host RNA). This insertion is probably responsible for increased cleavability of HA, as well as for infectivity and pathogenicity of the adapted virus.

PMID: 2544809 [PubMed - indexed for MEDLINE]
Click to expand...
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

My My, Ganseerpeel you find an outstanding example. In this case the recombination came from the host ribosomal RNA. Nature is full of resources.

You whant something else...

This week while I wasw occuied with PRRSv sequencing ( swine virus ) I had the Idea to probe some of their polymorphism into los alamos flu data bank just to see.

Most of the time the polymorphism did not find matchs with influenza, but when a match was done most of the time it was a travel log including many swines sequences... and only of north american or asiatic sequences ... the north american type of PRRSV is not present in europe.

In the diagnostic routine, it is not rare to see PRRSV & SIV positives swines. Both of theses virus are RNA virus.

Are theses inter-virus recombination frequent ?
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

is there a database of PRRSV viruses, so we can test it ?
 
Re: Recombination possibility - My Question to Niman in sequences lingo...

Mingus said:
My My, Ganseerpeel you find an outstanding example. In this case the recombination came from the host ribosomal RNA. Nature is full of resources.

You whant something else...

This week while I wasw occuied with PRRSv sequencing ( swine virus ) I had the Idea to probe some of their polymorphism into los alamos flu data bank just to see.

Most of the time the polymorphism did not find matchs with influenza, but when a match was done most of the time it was a travel log including many swines sequences... and only of north american or asiatic sequences ... the north american type of PRRSV is not present in europe.

In the diagnostic routine, it is not rare to see PRRSV & SIV positives swines. Both of theses virus are RNA virus.

Are theses inter-virus recombination frequent ?
Click to expand...

I had previously noted a 18 BP region of identity between flu and Ebola

http://www.recombinomics.com/News/07240505/H5N1_Sichuan_Ebola.html

What made the observation more intersting was the fact that all of the flu matches were H5, and the match was in the envelope gene of both viruses.

The exact match was between Zaire, 1976 and European versions of H5. A little sequence homology goes a long way
 
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