Rhiza Labs FluTracker Forum

The recent WHO report on pandemic vaccines includes an HA tree for clade 2.2. All new human cases (four in 2011 which were not amoung the 2011 sequences listed in Sept 2011 tree) are clade 2.2.1 G (with 3 BP deletion).

http://www.who.int/influenza/vaccines/v ... update.pdf

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New sequences
A/Egypt/N10621/2011
A/Egypt/N09966/2011
A/Egypt/N11126/2011
A/Egypt/N11470/2011

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Full list of clade 2.2.1 G on latest tree
A/Egypt/N03072/2010
A/Egypt/N09539/2009
A/Egypt/N01982/2010
A/Egypt/N10621/2011
A/Egypt/N09966/2011
A/Egypt/N7562/2011
A/Egypt/N6828/2011
A/Egypt/N11126/2011
A/Egypt/N11470/2011
A/Egypt/N6322/2011
A/Egypt/N6774/2011
A/Egypt/N7724/2011
A/Egypt/N0544/2011
A/Egypt/N0423/2011

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Table 1. Influenza A(H5N1) activity reported from 20 September 2011 to 22 February 2012
Country, area or territory Host Genetic clade
Bangladesh Poultry
Wild birds
2.2.2/2.3.2.1
2.3.2.1
Bhutan Poultry unknown
Cambodia Poultry
Wild birds
Human (1)*
1.1
1.1
1.1
China Poultry
Human (2)
2.3.2.1
2.3.2.1/2.3.4.2
China, Hong Kong SAR Poultry
Wild birds
2.3.2.1
2.3.2.1
Egypt Poultry 2.2.1/2.2.1.1
Humans (9) 2.2.1 [5]#
India Poultry
Wild bird
unknown
unknown
Indonesia Poultry unknown
Humans (7) 2.1.3.2 [2]
Iran (Islamic Republic of) Poultry 2.3.2.1
Nepal Poultry
Wild birds
2.3.2.1
2.3.2.1
Viet Nam Poultry
Humans (2)
1.1/2.3.2.1
1.1 [2]
*number in parentheses denotes number of reported cases during this period
#number in brackets denotes the number of viruses for which genetic information is available

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Most recent sequences.

A/Egypt/N00269/2010
A/Egypt/N00270/2010
A/Egypt/N01360/2010
A/Egypt/N01644/2010
A/Egypt/N01982/2010
A/Egypt/N02038/2010
A/Egypt/N02127/2010
A/Egypt/N02554/2010
A/Egypt/N02770/2010
A/Egypt/N03071/2010
A/Egypt/N03072/2010
A/Egypt/N04434/2010
A/Egypt/N05912/2009
A/Egypt/N07908/2009
A/Egypt/N08835/2009
A/Egypt/N09174/2009
A/Egypt/N09539/2009
A/Egypt/N11981/2009
A/Egypt/N15262/2009

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The above sequences were from isolates collected between 06/16/2009 and 03/31/2010. All were clade 2.2.1 G.

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The only other sequence in earlier trees was A/Egypt/N10360/10. Thus, public human cases include the 19 most recent sequences, one 2010, and eleven 2011 dislayed on WHO trees for a total of 31/31 clade 2.2.1 G.

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Commentary
http://www.recombinomics.com/News/02241 ... _2011.html

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EPI348150 A/chicken/Egypt/11VIR4453-138/VRLCU/2011 (A/H5N1) segment 4 (HA) 3136.7 0.000000e+00 1698/1698 (100%)
EPI340131 A/chicken/Egypt/1117/2011 (A/H5N1) segment 4 (HA) 3118.3 0.000000e+00 1695/1698 (99%)
EPI340122 A/chicken/Egypt/1128/2011 (A/H5N1) segment 4 (HA) 3118.3 0.000000e+00 1695/1698 (99%)
EPI340099 A/duck/Egypt/1153/2011 (A/H5N1) segment 4 (HA) 3107.2 0.000000e+00 1693/1698 (99%)
EPI348152 A/chicken/Egypt/11VIR4453-268/2010 (A/H5N1) segment 4 (HA) 3090.6 0.000000e+00 1691/1699 (99%)
EPI340138 A/duck/Egypt/1125S/2011 (A/H5N1) segment 4 (HA) 3090.6 0.000000e+00 1691/1699 (99%)
EPI348153 A/chicken/Egypt/11VIR4453-266/2010 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1690/1699 (99%)
EPI340151 A/chicken/Egypt/10513S/2010 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1690/1699 (99%)
EPI340135 A/chicken/Egypt/1113/2011 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1690/1699 (99%)
EPI338733 A/duck/Egypt/M2583B/2010 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1690/1699 (99%)
EPI338732 A/duck/Egypt/M2583C/2010 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1690/1699 (99%)
EPI338616 A/duck/Egypt/M2583D/2010 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1690/1699 (99%)
EPI348160 A/chicken/Egypt/11VIR4453-267/2010 (A/H5N1) segment 4 (HA) 3083.2 0.000000e+00 1689/1698 (99%)
EPI348156 A/chicken/Egypt11VIR4453-269/2010 (A/H5N1) segment 4 (HA) 3083.2 0.000000e+00 1689/1699 (99%)
EPI348151 A/chicken/Egypt/11VIR4453-270/2010 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1689/1699 (99%)
EPI340133 A/goose/Egypt/1117SF/2011 (A/H5N1) segment 4 (HA) 3079.5 0.000000e+00 1689/1699 (99%)
EPI340103 A/chicken/Egypt/111766V/2011 (A/H5N1) segment 4 (HA) 3079.5 0.000000e+00 1689/1699 (99%)
EPI340101 A/chicken/Egypt/1112AF/2011 (A/H5N1) segment 4 (HA) 3079.5 0.000000e+00 1689/1699 (99%)
EPI340087 A/duck/Egypt/11193SF/2011 (A/H5N1) segment 4 (HA) 3079.5 0.000000e+00 1689/1699 (99%)
EPI340085 A/chicken/Egypt/1118AF/2011 (A/H5N1) segment 4 (HA) 3079.5 0.000000e+00 1689/1699 (99%)
EPI338615 A/duck/Egypt/Q2645C/2010 (A/H5N1) segment 4 (HA) 3079.5 0.000000e+00 1689/1699 (99%)
EPI340165 A/duck/Egypt/10228SF/2010 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1688/1699 (99%)
EPI340154 A/duck/Egypt/10118/2010 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1688/1699 (99%)
EPI340141 A/chicken/Egypt/112SG/2011 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1688/1699 (99%)
EPI340104 A/chicken/Egypt/117AD/2011 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1688/1699 (99%)
EPI340092 A/chicken/Egypt/1155/2011 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1688/1699 (99%)
EPI340091 A/duck/Egypt/11117SS/2011 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1688/1699 (99%)
EPI338731 A/goose/Egypt/M2794E/2011 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1688/1699 (99%)
EPI338613 A/goose/Egypt/M2788A/2011 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1688/1699 (99%)
EPI338612 A/goose/Egypt/M2788E/2011 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1688/1699 (99%)
EPI338611 A/goose/Egypt/M2794A/2011 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1688/1699 (99%)
EPI348157 A/chicken/Egypt/11VIR4453-15/VRLCU/2010 (A/H5N1) segment 4 (HA) 3072.1 0.000000e+00 1687/1698 (99%)
EPI340118 A/chicken/Egypt/1158SF/2011 (A/H5N1) segment 4 (HA) 3072.1 0.000000e+00 1690/1702 (99%)
EPI340152 A/duck/Egypt/10290SF/2010 (A/H5N1) segment 4 (HA) 3068.4 0.000000e+00 1687/1699 (99%)
EPI340147 A/chicken/Egypt/10132/2010 (A/H5N1) segment 4 (HA) 3068.4 0.000000e+00 1687/1699 (99%)
EPI340094 A/duck/Egypt/1116AF/2011 (A/H5N1) segment 4 (HA) 3068.4 0.000000e+00 1687/1699 (99%)
EPI338614 A/chicken/Egypt/M2773A/2011 (A/H5N1) segment 4 (HA) 3068.4 0.000000e+00 1687/1699 (99%)
EPI338610 A/duck/Egypt/M3075B/2011 (A/H5N1) segment 4 (HA) 3068.4 0.000000e+00 1687/1699 (99%)
EPI336862 A/turkey/Jenin/341/2011 (A/H5N1) segment 4 (HA) 3068.4 0.000000e+00 1687/1699 (99%)
EPI348158 A/chicken/Egypt/11VIR4453-109/VRLCU/2011 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340173 A/chicken/Egypt/1021AD/2010 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340160 A/chicken/Egypt/10250SF/2010 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340136 A/chicken/Egypt/1112/2011 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340126 A/chicken/Egypt/112AF/2011 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340124 A/chicken/Egypt/114AF/2011 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340121 A/chicken/Egypt/1146SF/2011 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340119 A/duck/Egypt/1148SF/2011 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340107 A/chicken/Egypt/11184S/2011 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340102 A/chicken/Egypt/1134SD/2011 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340100 A/duck/Egypt/11211S/2011 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI340082 A/quail/Egypt/1171SG/2011 (A/H5N1) segment 4 (HA) 3062.9 0.000000e+00 1686/1699 (99%)
EPI348155 A/chicken/Egypt/11VIR4453-68/VRLCU/2011 (A/H5N1) segment 4 (HA) 3057.3 0.000000e+00 1676/1686 (99%)
EPI340149 A/duck/Egypt/10336SF/2010 (A/H5N1) segment 4 (HA) 3057.3 0.000000e+00 1685/1699 (99%)
EPI340129 A/chicken/Egypt/1174S/2011 (A/H5N1) segment 4 (HA) 3057.3 0.000000e+00 1685/1699 (99%)
EPI340127 A/chicken/Egypt/111AF/2011 (A/H5N1) segment 4 (HA) 3057.3 0.000000e+00 1685/1699 (99%)
EPI340123 A/chicken/Egypt/115AF/2011 (A/H5N1) segment 4 (HA) 3057.3 0.000000e+00 1685/1699 (99%)
EPI340115 A/duck/Egypt/1174SF/2011 (A/H5N1) segment 4 (HA) 3057.3 0.000000e+00 1685/1699 (99%)
EPI340106 A/duck/Egypt/1110AF/2011 (A/H5N1) segment 4 (HA) 3057.3 0.000000e+00 1685/1699 (99%)
EPI338729 A/chicken/Egypt/S3093A/2011 (A/H5N1) segment 4 (HA) 3057.3 0.000000e+00 1685/1699 (99%)
EPI338609 A/chicken/Egypt/S3280B/2011 (A/H5N1) segment 4 (HA) 3057.3 0.000000e+00 1685/1699 (99%)
EPI348154 A/chicken/Egypt/11VIR4453-264/2010 (A/H5N1) segment 4 (HA) 3055.5 0.000000e+00 1684/1699 (99%)
EPI340109 A/chicken/Egypt/111640V/2011 (A/H5N1) segment 4 (HA) 3051.8 0.000000e+00 1684/1699 (99%)
EPI340096 A/chicken/Egypt/111945V/2011 (A/H5N1) segment 4 (HA) 3051.8 0.000000e+00 1684/1699 (99%)
EPI255398 A/Egypt/N09174/2009 (A/H5N1) segment 4 (HA) 3051.8 0.000000e+00 1684/1699 (99%)
EPI348159 A/chicken/Egypt/11VIR4453-137/VRLCU/2011 (A/H5N1) segment 4 (HA) 3048.1 0.000000e+00 1677/1690 (99%)
EPI348148 A/chicken/Egypt/11VIR4453-59/VRLCU/2011 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1672/1683 (99%)
EPI340150 A/duck/Egypt/10331SF/2010 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1683/1699 (99%)
EPI340146 A/chicken/Egypt/10347SF/2010 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1683/1699 (99%)
EPI340134 A/duck/Egypt/1113SD/2011 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1683/1699 (99%)
EPI340116 A/chicken/Egypt/116AF/2011 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1684/1700 (99%)
EPI340110 A/goose/Egypt/11162S/2011 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1683/1699 (99%)
EPI340097 A/duck/Egypt/11221S/2011 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1683/1699 (99%)
EPI340081 A/chicken/Egypt/11529S/2011 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1683/1699 (99%)
EPI338730 A/chicken/Egypt/S2938A/2011 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1683/1699 (99%)
EPI338608 A/chicken/Egypt/S3280D/2011 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1683/1699 (99%)
EPI255371 A/Egypt/N02127/2010 (A/H5N1) segment 4 (HA) 3046.2 0.000000e+00 1683/1699 (99%)
EPI348162 A/chicken/Egypt/11VIR4453-7/VRLCU/2010 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1681/1697 (99%)
EPI255367 A/Egypt/N01982/2010 (A/H5N1) segment 4 (HA) 3042.6 0.000000e+00 1682/1699 (98%)
EPI338187 A/harrier/Israel/531/2011 (A/H5N1) segment 4 (HA) 3040.7 0.000000e+00 1682/1699 (98%)
EPI283791 A/chicken/Egypt/1034/2010 (A/H5N1) segment 4 (HA) 3040.7 0.000000e+00 1682/1699 (98%)
EPI348165 A/chicken/Egypt/11VIR4453-203/VRLCU/2011 (A/H5N1) segment 4 (HA) 3035.2 0.000000e+00 1668/1680 (99%)
EPI340144 A/chicken/Egypt/10413SF/2010 (A/H5N1) segment 4 (HA) 3035.2 0.000000e+00 1681/1699 (98%)
EPI340090 A/chicken/Egypt/1117AF/2011 (A/H5N1) segment 4 (HA) 3035.2 0.000000e+00 1681/1699 (98%)
EPI340089 A/duck/Egypt/11312S/2011 (A/H5N1) segment 4 (HA) 3035.2 0.000000e+00 1681/1699 (98%)
EPI287352 A/chicken/Egypt/1553-15/2010 (A/H5N1) segment 4 (HA) 3035.2 0.000000e+00 1681/1699 (98%)
EPI283813 A/duck/Egypt/1068s/2010 (A/H5N1) segment 4 (HA) 3035.2 0.000000e+00 1681/1699 (98%)
EPI283811 A/goose/Egypt/1057/2010 (A/H5N1) segment 4 (HA) 3035.2 0.000000e+00 1681/1699 (98%)
EPI340128 A/chicken/Egypt/1155AG/2011 (A/H5N1) segment 4 (HA) 3029.6 0.000000e+00 1654/1660 (99%)
EPI340114 A/chicken/Egypt/117AF/2011 (A/H5N1) segment 4 (HA) 3029.6 0.000000e+00 1680/1699 (98%)
EPI340111 A/chicken/Egypt/119AF/2011 (A/H5N1) segment 4 (HA) 3029.6 0.000000e+00 1680/1699 (98%)
EPI340098 A/duck/Egypt/11106SF/2011 (A/H5N1) segment 4 (HA) 3029.6 0.000000e+00 1681/1700 (98%)
EPI340093 A/chicken/Egypt/11124SF/2011 (A/H5N1) segment 4 (HA) 3029.6 0.000000e+00 1681/1700 (98%)
EPI340086 A/goose/Egypt/11350S/2011 (A/H5N1) segment 4 (HA) 3029.6 0.000000e+00 1680/1699 (98%)
EPI283815 A/duck/Egypt/106d/2010 (A/H5N1) segment 4 (HA) 3029.6 0.000000e+00 1680/1699 (98%)
EPI255400 A/Egypt/N09539/2009 (A/H5N1) segment 4 (HA) 3029.6 0.000000e+00 1680/1699 (98%)
EPI340113 A/chicken/Egypt/118AF/2011 (A/H5N1) segment 4 (HA) 3024.1 0.000000e+00 1679/1699 (98%)
EPI283821 A/duck/Egypt/1063s/2010 (A/H5N1) segment 4 (HA) 3024.1 0.000000e+00 1679/1699 (98%)
EPI283782 A/chicken/Egypt/091317s/2009 (A/H5N1) segment 4 (HA) 3024.1 0.000000e+00 1679/1699 (98%)
EPI214881 A/chicken/Egypt/0920-NLQP/2009 (A/H5N1) segment 4 (HA) 3024.1 0.000000e+00 1679/1699 (98%)
EPI184804 A/Egypt/N00585/2009 (A/H5N1) segment 4 (HA) 3024.1 0.000000e+00 1679/1699 (98%)

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All late 2011 and 2012 poultry isolates from Egypt are clade 2.2.1 G.

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