Rhiza Labs FluTracker Forum

National Institute of Health Research and Development in Jakarta has deposted the HA sequence (at GISAID) from a 2011 (Jan 28) fatality (2M) in West Java, A/Indonesia/NIHRD11073/2011.

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Sequence has receptor binding domain change Q226K.

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Sequence also has R193M (H3 numbering).

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Closest match among WHO reported cases:

The first case is a 2 year old male from Depok City, West Java Province. He developed symptoms on 3 February, was admitted to a private clinic on 5 February and referred to a hospital on 6 February. He died on 6 February. Prior to his illness, sick and dead poultry were reported in his neighborhood.

http://www.who.int/csr/don/2011_03_14/en/index.html

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Commentary

http://www.recombinomics.com/News/11031 ... do_2M.html

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R193M pedigree profile

EPI341332 A/Indonesia/NIHRD11073/2011(H5N1) (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340810 A/chicken/Lampung/BPPVRIII-10-161/2010 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340790 A/bird/Gunung Kidul/BBVW-52-I/2010 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340788 A/chicken/Klaten/BBVW-109-II/2010 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340786 A/chicken/Jombang/BBVW-166-III/2010 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340784 A/chicken/Sleman/BBVW-150-III/2010 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340782 A/chicken/Sleman/BBVW-180-III/2010 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340780 A/chicken/Lamongan/BBVW-170-III/2010 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340778 A/chicken/Temanggung/BBVW-1203d-VIII/2009 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340776 A/chicken/Temanggung/BBVW-1203b-VIII/2009 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340774 A/chicken/Tasikmalaya/BBVW-991-VI/2009 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340768 A/chicken/Kuningan/BBVW-1004-VI/2009 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI340766 A/chicken/Kudus/BBVW-1186-IX/2009 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI324615 A/tree sparrow/Indonesia/D10013/2010 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI324340 A/chicken/Indonesia/D10014/2010 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI321329 A/chicken/Indonesia/Tanggerang_1/2007 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI307911 A/chicken/Indonesia/SmiWN18/2009 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI287380 A/poultry/Egypt/3982-55/2010 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI228556 A/Chicken/Nakornsawan-2-07/2004 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI181390 A/Indonesia/5/2005 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI165824 A/chicken/Nakornsawan/NIAH6-3-0009/2005 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI164763 A/Indonesia/7272/2008 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI164208 A/Indonesia/8228/2008 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI162940 A/Indonesia/7261/2008 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI117660 A/chicken/Nakornsawan/NIAH6-3-0009/2005 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)
EPI100500 A/Chinese pond heron/Hong Kong/18/2005 (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)

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Q226K pedigree

EPI341332 A/Indonesia/NIHRD11073/2011(H5N1) (A/H5N1) segment 4 (HA) 27.0 7.199799e+00 14/14 (100%)

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Top 100 matches

EPI341332 A/Indonesia/NIHRD11073/2011(H5N1) (A/H5N1) segment 4 (HA) 3153.4 0.000000e+00 1707/1707 (100%)
EPI340778 A/chicken/Temanggung/BBVW-1203d-VIII/2009 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1692/1707 (99%)
EPI340776 A/chicken/Temanggung/BBVW-1203b-VIII/2009 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1692/1707 (99%)
EPI164208 A/Indonesia/8228/2008 (A/H5N1) segment 4 (HA) 3064.7 0.000000e+00 1691/1707 (99%)
EPI340810 A/chicken/Lampung/BPPVRIII-10-161/2010 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1690/1708 (98%)
EPI324340 A/chicken/Indonesia/D10014/2010 (A/H5N1) segment 4 (HA) 3048.1 0.000000e+00 1689/1708 (98%)
EPI340774 A/chicken/Tasikmalaya/BBVW-991-VI/2009 (A/H5N1) segment 4 (HA) 3037.0 0.000000e+00 1686/1707 (98%)
EPI162940 A/Indonesia/7261/2008 (A/H5N1) segment 4 (HA) 3037.0 0.000000e+00 1686/1707 (98%)
EPI340790 A/bird/Gunung Kidul/BBVW-52-I/2010 (A/H5N1) segment 4 (HA) 3031.5 0.000000e+00 1686/1708 (98%)
EPI340768 A/chicken/Kuningan/BBVW-1004-VI/2009 (A/H5N1) segment 4 (HA) 3025.9 0.000000e+00 1684/1707 (98%)
EPI340766 A/chicken/Kudus/BBVW-1186-IX/2009 (A/H5N1) segment 4 (HA) 3009.3 0.000000e+00 1681/1707 (98%)
EPI164763 A/Indonesia/7272/2008 (A/H5N1) segment 4 (HA) 2994.5 0.000000e+00 1673/1699 (98%)
EPI324615 A/tree sparrow/Indonesia/D10013/2010 (A/H5N1) segment 4 (HA) 2987.2 0.000000e+00 1677/1707 (98%)
EPI340782 A/chicken/Sleman/BBVW-180-III/2010 (A/H5N1) segment 4 (HA) 2981.6 0.000000e+00 1678/1709 (98%)
EPI55643 A/Indonesia/CDC1031RE2/2007 (A/H5N1) segment 4 (HA) 2981.6 0.000000e+00 1676/1707 (98%)
EPI49264 A/Indonesia/CDC887/2006 (A/H5N1) segment 4 (HA) 2948.4 0.000000e+00 1670/1707 (97%)
EPI49164 A/Indonesia/CDC938E/2006 (A/H5N1) segment 4 (HA) 2948.4 0.000000e+00 1670/1707 (97%)
EPI49145 A/Indonesia/CDC938/2006 (A/H5N1) segment 4 (HA) 2948.4 0.000000e+00 1670/1707 (97%)
EPI120008 A/Indonesia/TLL012/2006 (A/H5N1) segment 4 (HA) 2931.8 0.000000e+00 1667/1707 (97%)
EPI55776 A/Indonesia/CDC1047S/2007 (A/H5N1) segment 4 (HA) 2926.2 0.000000e+00 1666/1707 (97%)
EPI55757 A/Indonesia/CDC1047/2007 (A/H5N1) segment 4 (HA) 2926.2 0.000000e+00 1666/1707 (97%)
EPI55738 A/Indonesia/CDC1046T/2007 (A/H5N1) segment 4 (HA) 2926.2 0.000000e+00 1666/1707 (97%)
EPI55719 A/Indonesia/CDC1046/2007 (A/H5N1) segment 4 (HA) 2920.7 0.000000e+00 1665/1707 (97%)
EPI307911 A/chicken/Indonesia/SmiWN18/2009 (A/H5N1) segment 4 (HA) 2918.8 0.000000e+00 1620/1639 (98%)
EPI41399 A/Indonesia/CDC523/2006 (A/H5N1) segment 4 (HA) 2917.0 0.000000e+00 1664/1707 (97%)
EPI55624 A/Indonesia/CDC1031T2/2007 (A/H5N1) segment 4 (HA) 2915.1 0.000000e+00 1632/1659 (98%)
EPI55605 A/Indonesia/CDC1031T/2007 (A/H5N1) segment 4 (HA) 2915.1 0.000000e+00 1632/1659 (98%)
EPI55586 A/Indonesia/CDC1031/2007 (A/H5N1) segment 4 (HA) 2915.1 0.000000e+00 1632/1659 (98%)
EPI181390 A/Indonesia/5/2005 (A/H5N1) segment 4 (HA) 2909.6 0.000000e+00 1663/1707 (97%)
EPI119998 A/Indonesia/TLL007/2006 (A/H5N1) segment 4 (HA) 2904.1 0.000000e+00 1662/1707 (97%)
EPI116487 A/Indonesia/5/2005 (A/H5N1) segment 4 (HA) 2904.1 0.000000e+00 1662/1707 (97%)
EPI124067 A/Indonesia/5/2005 (A/H5N1) segment 4 (HA) 2898.5 0.000000e+00 1659/1704 (97%)
EPI120006 A/Indonesia/TLL011/2006 (A/H5N1) segment 4 (HA) 2898.5 0.000000e+00 1661/1707 (97%)
EPI120004 A/Indonesia/TLL010/2006 (A/H5N1) segment 4 (HA) 2898.5 0.000000e+00 1661/1707 (97%)
EPI119994 A/Indonesia/TLL005/2006 (A/H5N1) segment 4 (HA) 2898.5 0.000000e+00 1661/1707 (97%)
EPI224608 A/Chicken/West Java/TASIKSOL/2006 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1660/1707 (97%)
EPI124421 A/Indonesia/542H/2006 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1660/1707 (97%)
EPI123831 A/Chicken/Indonesia/Rejang Lebong1631-22/2006 (A/H5N1) segment 4 (HA) 2893.0 0.000000e+00 1658/1704 (97%)
EPI120002 A/Indonesia/TLL009/2006 (A/H5N1) segment 4 (HA) 2891.1 0.000000e+00 1659/1707 (97%)
EPI224706 A/Muscovy Duck/Jakarta/HABWIN/2006 (A/H5N1) segment 4 (HA) 2887.4 0.000000e+00 1659/1707 (97%)
EPI123832 A/Chicken/Indonesia/Lampung1631-23/2006 (A/H5N1) segment 4 (HA) 2887.4 0.000000e+00 1657/1704 (97%)
EPI119996 A/Indonesia/TLL006/2006 (A/H5N1) segment 4 (HA) 2887.4 0.000000e+00 1659/1707 (97%)
EPI119990 A/Indonesia/TLL003/2006 (A/H5N1) segment 4 (HA) 2887.4 0.000000e+00 1659/1707 (97%)
EPI41820 A/Indonesia/CDC669P/2006 (A/H5N1) segment 4 (HA) 2887.4 0.000000e+00 1659/1707 (97%)
EPI41801 A/Indonesia/CDC669/2006 (A/H5N1) segment 4 (HA) 2883.7 0.000000e+00 1658/1707 (97%)
EPI226651 A/Chicken/Murao Jambi/BBPV-II/2005 (A/H5N1) segment 4 (HA) 2881.9 0.000000e+00 1658/1707 (97%)
EPI225050 A/chicken/West Java/TASIKSOB/2006 (A/H5N1) segment 4 (HA) 2881.9 0.000000e+00 1658/1707 (97%)
EPI124217 A/Indonesia/286H/2006 (A/H5N1) segment 4 (HA) 2881.9 0.000000e+00 1658/1707 (97%)
EPI120000 A/Indonesia/TLL008/2006 (A/H5N1) segment 4 (HA) 2881.9 0.000000e+00 1658/1707 (97%)
EPI49202 A/Indonesia/CDC835/2006 (A/H5N1) segment 4 (HA) 2881.9 0.000000e+00 1658/1707 (97%)
EPI119992 A/Indonesia/TLL004/2006 (A/H5N1) segment 4 (HA) 2878.2 0.000000e+00 1657/1707 (97%)
EPI41948 A/Indonesia/CDC759/2006 (A/H5N1) segment 4 (HA) 2878.2 0.000000e+00 1657/1707 (97%)
EPI124201 A/Indonesia/283H/2006 (A/H5N1) segment 4 (HA) 2876.4 0.000000e+00 1657/1707 (97%)
EPI49240 A/Indonesia/CDC836T/2006 (A/H5N1) segment 4 (HA) 2876.4 0.000000e+00 1657/1707 (97%)
EPI49221 A/Indonesia/CDC836/2006 (A/H5N1) segment 4 (HA) 2876.4 0.000000e+00 1657/1707 (97%)
EPI41839 A/Indonesia/CDC699/2006 (A/H5N1) segment 4 (HA) 2876.4 0.000000e+00 1658/1708 (97%)
EPI124475 A/Indonesia/567H/2006 (A/H5N1) segment 4 (HA) 2874.5 0.000000e+00 1646/1691 (97%)
EPI124253 A/Indonesia/304H/2006 (A/H5N1) segment 4 (HA) 2874.5 0.000000e+00 1655/1704 (97%)
EPI321321 A/chicken/Flores Timur/BBVD-256/2007 (A/H5N1) segment 4 (HA) 2870.8 0.000000e+00 1656/1707 (97%)
EPI321318 A/chicken/Denpasar/BBVD-494/2007 (A/H5N1) segment 4 (HA) 2870.8 0.000000e+00 1656/1707 (97%)
EPI321280 A/chicken/Badung/BBVD-175/2007 (A/H5N1) segment 4 (HA) 2870.8 0.000000e+00 1656/1707 (97%)
EPI226652 A/Chicken/Pakun Baru/BPPV-II/2005 (A/H5N1) segment 4 (HA) 2870.8 0.000000e+00 1654/1704 (97%)
EPI41915 A/Indonesia/CDC739/2006 (A/H5N1) segment 4 (HA) 2870.8 0.000000e+00 1657/1708 (97%)
EPI124143 A/Indonesia/195H/2005 (A/H5N1) segment 4 (HA) 2869.0 0.000000e+00 1647/1694 (97%)
EPI321749 A/peaceful dove/Badung/BBVD-493/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321409 A/chicken/Tabanan/BBVD-461/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321408 A/chicken/Tabanan/BBVD-339/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321339 A/chicken/Klungkung/BBVD-417/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321335 A/chicken/Jembrana/BBVD-298b/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321334 A/chicken/Jembrana/BBVD-298/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321333 A/chicken/Jembrana/BBVD-273/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321313 A/chicken/Denpasar/BBVD-291/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321300 A/chicken/Bantul/BBVW-446-24454/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321299 A/chicken/Bantul/BBVW-446-24453/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321298 A/chicken/Bantul/BBVW-446-24452/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321293 A/chicken/Bangli/BBVD-387ab/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321292 A/chicken/Bangli/BBVD-343/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321287 A/chicken/Badung/BBVD-319ac/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321283 A/chicken/Badung/BBVD-219/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321282 A/chicken/Badung/BBVD-216/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI321281 A/chicken/Badung/BBVD-205/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1655/1707 (96%)
EPI234502 A/Swan/Indonesia/Malang1631-61/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1653/1704 (97%)
EPI226718 A/Indonesia/160H/2005 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1653/1704 (97%)
EPI123833 A/Muscovy Duck/Indonesia/Kedri1631-24/2006 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1653/1704 (97%)
EPI55700 A/Indonesia/CDC1032T/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1623/1659 (97%)
EPI55662 A/Indonesia/CDC1032/2007 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1623/1659 (97%)
EPI49183 A/Indonesia/CDC940/2006 (A/H5N1) segment 4 (HA) 2865.3 0.000000e+00 1656/1708 (96%)
EPI321750 A/peaceful dove/Denpasar/BBVD-480/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1654/1707 (96%)
EPI321583 A/duck/Sleman/BBVW-599-33290/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1656/1709 (96%)
EPI321581 A/duck/Sleman/BBVW-599-33288/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1656/1709 (96%)
EPI321579 A/duck/Sleman/BBVW-598-32237/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1656/1709 (96%)
EPI321543 A/duck/Magelang/BBVW-604-44402/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1656/1709 (96%)
EPI321541 A/duck/Magelang/BBVW-604-44401/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1656/1709 (96%)
EPI321520 A/duck/Bantul/BBVW-358-24381/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1654/1707 (96%)
EPI321399 A/chicken/Sleman/BBVW-626-234/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1654/1707 (96%)
EPI321397 A/chicken/Sleman/BBVW-626-233/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1654/1707 (96%)
EPI321366 A/chicken/Magelang/BBVW-662-764/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1654/1707 (96%)
EPI321351 A/chicken/Kulon Progo/BBVW-610-11020/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1654/1707 (96%)
EPI321341 A/chicken/Klungkung/BBVD-484/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1654/1707 (96%)
EPI321337 A/chicken/Klungkung/BBVD-225/2007 (A/H5N1) segment 4 (HA) 2859.7 0.000000e+00 1654/1707 (96%)

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Note that all 100 top matches are clade 2.1 (Indonesia)

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Q226R In H5N1 clade 2.3 in China

http://www.recombinomics.com/News/04030 ... Q226R.html

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