Rhiza Labs FluTracker Forum

WHO has released an update on pandemic vaccine targets which included phylogenetic analysis of human H5N1 cases in Egypt. All 2011 cases listed were clade 2.2.1 G (discussed on earlier thread viewtopic.php?f=5&t=7985 ). Clade 2.2.1 G has a 3 BP deletion and prior analysis noted similarities with seasonal H1N1. That sub-clade has now become dominant in Egypt. A vaccine resistant sub-clade (2.2.1 F) emerged in late 2007 in vaccinated flocks, and was prominent in 2009 and 2010. However, the only reported human case was in 2008 (A/Egypt-NAMRU3/2008 and designated clade 2.2.1.1 in WHO tree).
In contrast, the 19 most recent (collected between June 2009 and March 2010) human H5N1 sequences from Egypt have been clade 2.2.1 G (designated clade 2.2.1 in WHO tree), which is true for the 12 subsequent sequences listed on WHO trees (1 from 2010 and 11 from 2011). Clade 2.2.1 F has been crowded out by clade 2.2.1 G (as seen in public poultry sequences, including a small sub-set on the last WHO tree which has no 2011 clade 2.2.1 F sequences). However, the human H5N1 clade 2.2.1 G are forming clusters, as seen in the 11 2011 sequences in the latest WHO tree.

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www.twitter.com/hniman

In 2011 there were 39 H5N1 confirmed cases (15 fatal) and 11 are listed in the latest WHO tree. Although the sequences and associated demographic information (age, gender, location) have been withheld by NARMU-3 / CDC, the samples are numbered sequentially for each calendar year, so time gaps between collections can be approximated by sample number gaps, which are included in the name of the isolates.

One sequence cluster is created by A/Egypt/N0544/2011, A/Egypt/N6774/2011, A/Egypt/N7724/2011, which includes an isolate from the beginning of 2011 as well as two collections from the spring / summer.

These three human sequences are on a branch with two poultry sequences, A/chicken/Egypt/11506sf/2011 and A/chicken/Egypt/VIR4453-138/VRLCU/2011. The sequence for the latter is at GISAID and the H5 sequence has two recently acquired non-synonymous changes (R143K and D454N), which are unlikely to significantly affect receptor binding. However, this clustering of sequences from samples collected over a long time frame in 2011 raises concerns that this sub-clade is transmitting human to human.

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www.twitter.com/hniman

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%)

_________________
www.twitter.com/hniman

In addition to the above sequence clade 2.2.1 G clsuter from early 2011, the two most recent isolates on the tree, A/Egypt/11126/2011 and A/Egypt/11470/2011, have sequences which are IDENTICAL, even though the sample numbers indicate they were collected weeks apart near the end of 2011, supporting human to human transmission.

_________________
www.twitter.com/hniman

The above two sequences are a concern because they form a branch with no poultry isolates and the length of the branch stem signals multiple changes, yet the two sequences are IDENTICAL.
The WHO tree only has 11 of the 39 confirmed cases, so it is unclear if this cluster is larger than the above two cases, or if there are closely related avian sequences, which is why the full set of 2011/2012 sequeces should be immediately released by the CDC or NAMRU-3, who clearly have much more data than is indicated on the tree in the WHO update.

_________________
www.twitter.com/hniman

Closest public sequences at GISAID
EPI338733 A/duck/Egypt/M2583B/2010 (A/H5N1) segment 4 (HA) 3142.3 0.000000e+00 1701/1701 (100%)
EPI338732 A/duck/Egypt/M2583C/2010 (A/H5N1) segment 4 (HA) 3142.3 0.000000e+00 1701/1701 (100%)
EPI338616 A/duck/Egypt/M2583D/2010 (A/H5N1) segment 4 (HA) 3142.3 0.000000e+00 1701/1701 (100%)
EPI348153 A/chicken/Egypt/11VIR4453-266/2010 (A/H5N1) segment 4 (HA) 3127.5 0.000000e+00 1698/1701 (99%)
EPI348152 A/chicken/Egypt/11VIR4453-268/2010 (A/H5N1) segment 4 (HA) 3125.7 0.000000e+00 1698/1701 (99%)
EPI340138 A/duck/Egypt/1125S/2011 (A/H5N1) segment 4 (HA) 3125.7 0.000000e+00 1698/1701 (99%)
EPI338610 A/duck/Egypt/M3075B/2011 (A/H5N1) segment 4 (HA) 3125.7 0.000000e+00 1698/1701 (99%)
EPI340154 A/duck/Egypt/10118/2010 (A/H5N1) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI340151 A/chicken/Egypt/10513S/2010 (A/H5N1) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI340135 A/chicken/Egypt/1113/2011 (A/H5N1) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI340107 A/chicken/Egypt/11184S/2011 (A/H5N1) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI348156 A/chicken/Egypt11VIR4453-269/2010 (A/H5N1) segment 4 (HA) 3118.3 0.000000e+00 1696/1701 (99%)
EPI348160 A/chicken/Egypt/11VIR4453-267/2010 (A/H5N1) segment 4 (HA) 3116.4 0.000000e+00 1695/1699 (99%)
EPI340133 A/goose/Egypt/1117SF/2011 (A/H5N1) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI340103 A/chicken/Egypt/111766V/2011 (A/H5N1) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI340101 A/chicken/Egypt/1112AF/2011 (A/H5N1) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI340087 A/duck/Egypt/11193SF/2011 (A/H5N1) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI340085 A/chicken/Egypt/1118AF/2011 (A/H5N1) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI338615 A/duck/Egypt/Q2645C/2010 (A/H5N1) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI348151 A/chicken/Egypt/11VIR4453-270/2010 (A/H5N1) segment 4 (HA) 3110.9 0.000000e+00 1693/1698 (99%)
EPI340165 A/duck/Egypt/10228SF/2010 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1695/1701 (99%)
EPI340141 A/chicken/Egypt/112SG/2011 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1695/1701 (99%)
EPI340131 A/chicken/Egypt/1117/2011 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1695/1701 (99%)
EPI340122 A/chicken/Egypt/1128/2011 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1695/1701 (99%)
EPI340104 A/chicken/Egypt/117AD/2011 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1695/1701 (99%)
EPI340092 A/chicken/Egypt/1155/2011 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1695/1701 (99%)
EPI340091 A/duck/Egypt/11117SS/2011 (A/H5N1) segment 4 (HA) 3109.0 0.000000e+00 1695/1701 (99%)
EPI348157 A/chicken/Egypt/11VIR4453-15/VRLCU/2010 (A/H5N1) segment 4 (HA) 3105.3 0.000000e+00 1693/1699 (99%)
EPI340118 A/chicken/Egypt/1158SF/2011 (A/H5N1) segment 4 (HA) 3105.3 0.000000e+00 1697/1704 (99%)
EPI340116 A/chicken/Egypt/116AF/2011 (A/H5N1) segment 4 (HA) 3103.5 0.000000e+00 1694/1701 (99%)
EPI340094 A/duck/Egypt/1116AF/2011 (A/H5N1) segment 4 (HA) 3103.5 0.000000e+00 1694/1701 (99%)
EPI338614 A/chicken/Egypt/M2773A/2011 (A/H5N1) segment 4 (HA) 3103.5 0.000000e+00 1694/1701 (99%)
EPI336862 A/turkey/Jenin/341/2011 (A/H5N1) segment 4 (HA) 3103.5 0.000000e+00 1694/1701 (99%)
EPI340173 A/chicken/Egypt/1021AD/2010 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI340160 A/chicken/Egypt/10250SF/2010 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI340136 A/chicken/Egypt/1112/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI340126 A/chicken/Egypt/112AF/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI340124 A/chicken/Egypt/114AF/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI340121 A/chicken/Egypt/1146SF/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI340119 A/duck/Egypt/1148SF/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI340102 A/chicken/Egypt/1134SD/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI340082 A/quail/Egypt/1171SG/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI338731 A/goose/Egypt/M2794E/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI338613 A/goose/Egypt/M2788A/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI338612 A/goose/Egypt/M2788E/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI338611 A/goose/Egypt/M2794A/2011 (A/H5N1) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI348158 A/chicken/Egypt/11VIR4453-109/VRLCU/2011 (A/H5N1) segment 4 (HA) 3096.1 0.000000e+00 1692/1700 (99%)
EPI340152 A/duck/Egypt/10290SF/2010 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1692/1701 (99%)
EPI340149 A/duck/Egypt/10336SF/2010 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1692/1701 (99%)
EPI340147 A/chicken/Egypt/10132/2010 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1692/1701 (99%)
EPI340129 A/chicken/Egypt/1174S/2011 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1692/1701 (99%)
EPI340127 A/chicken/Egypt/111AF/2011 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1692/1701 (99%)
EPI340123 A/chicken/Egypt/115AF/2011 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1692/1701 (99%)
EPI340106 A/duck/Egypt/1110AF/2011 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1692/1701 (99%)
EPI340100 A/duck/Egypt/11211S/2011 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1692/1701 (99%)
EPI340099 A/duck/Egypt/1153/2011 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1692/1701 (99%)
EPI338609 A/chicken/Egypt/S3280B/2011 (A/H5N1) segment 4 (HA) 3092.4 0.000000e+00 1692/1701 (99%)
EPI348154 A/chicken/Egypt/11VIR4453-264/2010 (A/H5N1) segment 4 (HA) 3090.6 0.000000e+00 1691/1701 (99%)
EPI340109 A/chicken/Egypt/111640V/2011 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1691/1701 (99%)
EPI340098 A/duck/Egypt/11106SF/2011 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1691/1701 (99%)
EPI340096 A/chicken/Egypt/111945V/2011 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1691/1701 (99%)
EPI340093 A/chicken/Egypt/11124SF/2011 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1691/1701 (99%)
EPI255398 A/Egypt/N09174/2009 (A/H5N1) segment 4 (HA) 3086.9 0.000000e+00 1691/1701 (99%)
EPI348155 A/chicken/Egypt/11VIR4453-68/VRLCU/2011 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1682/1688 (99%)
EPI348150 A/chicken/Egypt/11VIR4453-138/VRLCU/2011 (A/H5N1) segment 4 (HA) 3085.0 0.000000e+00 1690/1699 (99%)
EPI340134 A/duck/Egypt/1113SD/2011 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1690/1701 (99%)
EPI340115 A/duck/Egypt/1174SF/2011 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1690/1701 (99%)
EPI340097 A/duck/Egypt/11221S/2011 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1690/1701 (99%)
EPI338730 A/chicken/Egypt/S2938A/2011 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1690/1701 (99%)
EPI338729 A/chicken/Egypt/S3093A/2011 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1690/1701 (99%)
EPI338608 A/chicken/Egypt/S3280D/2011 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1690/1701 (99%)
EPI255371 A/Egypt/N02127/2010 (A/H5N1) segment 4 (HA) 3081.3 0.000000e+00 1690/1701 (99%)
EPI255367 A/Egypt/N01982/2010 (A/H5N1) segment 4 (HA) 3077.6 0.000000e+00 1689/1701 (99%)
EPI348162 A/chicken/Egypt/11VIR4453-7/VRLCU/2010 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1687/1698 (99%)
EPI338187 A/harrier/Israel/531/2011 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1689/1701 (99%)
EPI283791 A/chicken/Egypt/1034/2010 (A/H5N1) segment 4 (HA) 3075.8 0.000000e+00 1689/1701 (99%)
EPI348148 A/chicken/Egypt/11VIR4453-59/VRLCU/2011 (A/H5N1) segment 4 (HA) 3073.9 0.000000e+00 1678/1685 (99%)
EPI348159 A/chicken/Egypt/11VIR4453-137/VRLCU/2011 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1680/1689 (99%)
EPI340150 A/duck/Egypt/10331SF/2010 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1688/1701 (99%)
EPI340146 A/chicken/Egypt/10347SF/2010 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1688/1701 (99%)
EPI340144 A/chicken/Egypt/10413SF/2010 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1688/1701 (99%)
EPI340110 A/goose/Egypt/11162S/2011 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1688/1701 (99%)
EPI340089 A/duck/Egypt/11312S/2011 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1688/1701 (99%)
EPI340081 A/chicken/Egypt/11529S/2011 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1688/1701 (99%)
EPI287352 A/chicken/Egypt/1553-15/2010 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1688/1701 (99%)
EPI283813 A/duck/Egypt/1068s/2010 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1688/1701 (99%)
EPI283811 A/goose/Egypt/1057/2010 (A/H5N1) segment 4 (HA) 3070.3 0.000000e+00 1688/1701 (99%)
EPI340088 A/duck/Egypt/11175SF/2011 (A/H5N1) segment 4 (HA) 3064.7 0.000000e+00 1688/1702 (99%)
EPI283815 A/duck/Egypt/106d/2010 (A/H5N1) segment 4 (HA) 3064.7 0.000000e+00 1687/1701 (99%)
EPI255400 A/Egypt/N09539/2009 (A/H5N1) segment 4 (HA) 3064.7 0.000000e+00 1687/1701 (99%)
EPI340090 A/chicken/Egypt/1117AF/2011 (A/H5N1) segment 4 (HA) 3059.2 0.000000e+00 1686/1701 (99%)
EPI283821 A/duck/Egypt/1063s/2010 (A/H5N1) segment 4 (HA) 3059.2 0.000000e+00 1686/1701 (99%)
EPI283782 A/chicken/Egypt/091317s/2009 (A/H5N1) segment 4 (HA) 3059.2 0.000000e+00 1686/1701 (99%)
EPI214881 A/chicken/Egypt/0920-NLQP/2009 (A/H5N1) segment 4 (HA) 3059.2 0.000000e+00 1686/1701 (99%)
EPI184804 A/Egypt/N00585/2009 (A/H5N1) segment 4 (HA) 3059.2 0.000000e+00 1686/1701 (99%)
EPI340128 A/chicken/Egypt/1155AG/2011 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1657/1659 (99%)
EPI340114 A/chicken/Egypt/117AF/2011 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1685/1701 (99%)
EPI340111 A/chicken/Egypt/119AF/2011 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1685/1701 (99%)
EPI340086 A/goose/Egypt/11350S/2011 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1685/1701 (99%)
EPI283820 A/chicken/Egypt/1021L/2010 (A/H5N1) segment 4 (HA) 3053.6 0.000000e+00 1685/1701 (99%)

_________________
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Closest public sequences at Genbank
CY099589.1 Influenza A virus (A/duck/Egypt/M2583B/2010(H5N1)) hemagglutinin (HA) gene, complete cds 3068 3068 100% 0.0 100%
CY099590.1 Influenza A virus (A/duck/Egypt/M2583C/2010(H5N1)) hemagglutinin (HA) gene, complete cds 3068 3068 100% 0.0 100%
CY099580.1 Influenza A virus (A/duck/Egypt/M2583D/2010(H5N1)) hemagglutinin (HA) gene, complete cds 3068 3068 100% 0.0 100%
CY099578.2 Influenza A virus (A/duck/Egypt/M2583A/2010(H5N1)) hemagglutinin (HA) gene, complete cds 3054 3054 100% 0.0 99%
JN807810.1 Influenza A virus (A/duck/Egypt/1125S/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3054 3054 100% 0.0 99%
CY099586.1 Influenza A virus (A/duck/Egypt/M3075B/2011(H5N1)) hemagglutinin (HA) gene, complete cds 3054 3054 100% 0.0 99%
JN807841.1 Influenza A virus (A/chicken/Egypt/11184S/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3050 3050 100% 0.0 99%
JN807813.1 Influenza A virus (A/chicken/Egypt/1113/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3050 3050 100% 0.0 99%
JN807797.1 Influenza A virus (A/chicken/Egypt/10513S/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3050 3050 100% 0.0 99%
JN807794.1 Influenza A virus (A/duck/Egypt/10118/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3050 3050 100% 0.0 99%
JN807863.1 Influenza A virus (A/chicken/Egypt/1118AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3045 3045 100% 0.0 99%
JN807861.1 Influenza A virus (A/duck/Egypt/11193SF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3045 3045 100% 0.0 99%
JN807847.1 Influenza A virus (A/chicken/Egypt/1112AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3045 3045 100% 0.0 99%
JN807845.1 Influenza A virus (A/chicken/Egypt/111766V/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3045 3045 100% 0.0 99%
JN807815.1 Influenza A virus (A/goose/Egypt/1117SF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3045 3045 100% 0.0 99%
CY099581.1 Influenza A virus (A/duck/Egypt/Q2645C/2010(H5N1)) hemagglutinin (HA) gene, complete cds 3045 3045 100% 0.0 99%
JN807857.1 Influenza A virus (A/duck/Egypt/11117SS/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3041 3041 100% 0.0 99%
JN807856.1 Influenza A virus (A/chicken/Egypt/1155/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3041 3041 100% 0.0 99%
JN807844.1 Influenza A virus (A/chicken/Egypt/117AD/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3041 3041 100% 0.0 99%
JN807826.1 Influenza A virus (A/chicken/Egypt/1128/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3041 3041 100% 0.0 99%
JN807817.1 Influenza A virus (A/chicken/Egypt/1117/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3041 3041 100% 0.0 99%
JN807807.1 Influenza A virus (A/chicken/Egypt/112SG/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3041 3041 100% 0.0 99%
JN807783.1 Influenza A virus (A/duck/Egypt/10228SF/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3041 3041 100% 0.0 99%
JN807830.1 Influenza A virus (A/chicken/Egypt/1158SF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3039 3039 100% 0.0 99%
JN807854.1 Influenza A virus (A/duck/Egypt/1116AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3036 3036 100% 0.0 99%
JN807832.1 Influenza A virus (A/chicken/Egypt/116AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3036 3036 100% 0.0 99%
CY099582.1 Influenza A virus (A/chicken/Egypt/M2773A/2011(H5N1)) hemagglutinin (HA) gene, complete cds 3036 3036 100% 0.0 99%
JN582043.1 Influenza A virus (A/turkey/Jenin/341/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3036 3036 100% 0.0 99%
JN807866.1 Influenza A virus (A/quail/Egypt/1171SG/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
JN807846.1 Influenza A virus (A/chicken/Egypt/1134SD/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
JN807829.1 Influenza A virus (A/duck/Egypt/1148SF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
JN807827.1 Influenza A virus (A/chicken/Egypt/1146SF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
JN807824.1 Influenza A virus (A/chicken/Egypt/114AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
JN807822.1 Influenza A virus (A/chicken/Egypt/112AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
JN807812.1 Influenza A virus (A/chicken/Egypt/1112/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
JN807788.1 Influenza A virus (A/chicken/Egypt/10250SF/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
JN807775.1 Influenza A virus (A/chicken/Egypt/1021AD/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
CY099583.1 Influenza A virus (A/goose/Egypt/M2788A/2011(H5N1)) hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
CY099584.1 Influenza A virus (A/goose/Egypt/M2788E/2011(H5N1)) hemagglutinin (HA) gene, complete cds
CY099585.1 Influenza A virus (A/goose/Egypt/M2794A/2011(H5N1)) hemagglutinin (HA) gene, complete cds
CY099591.1 Influenza A virus (A/goose/Egypt/M2794E/2011(H5N1)) hemagglutinin (HA) gene, complete cds 3032 3032 100% 0.0 99%
JN807849.1 Influenza A virus (A/duck/Egypt/1153/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3027 3027 100% 0.0 99%
JN807848.1 Influenza A virus (A/duck/Egypt/11211S/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3027 3027 100% 0.0 99%
JN807842.1 Influenza A virus (A/duck/Egypt/1110AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3027 3027 100% 0.0 99%
JN807825.1 Influenza A virus (A/chicken/Egypt/115AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3027 3027 100% 0.0 99%
JN807821.1 Influenza A virus (A/chicken/Egypt/111AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3027 3027 100% 0.0 99%
JN807819.1 Influenza A virus (A/chicken/Egypt/1174S/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3027 3027 100% 0.0 99%
JN807801.1 Influenza A virus (A/chicken/Egypt/10132/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3027 3027 100% 0.0 99%
JN807799.1 Influenza A virus (A/duck/Egypt/10336SF/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3027 3027 100% 0.0 99%
JN807796.1 Influenza A virus (A/duck/Egypt/10290SF/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3027 3027 100% 0.0 99%
CY099587.1 Influenza A virus (A/chicken/Egypt/S3280B/2011(H5N1)) hemagglutinin (HA) gene, complete cds 3027 3027 100% 0.0 99%
JN807855.1 Influenza A virus (A/chicken/Egypt/11124SF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3023 3023 100% 0.0 99%
JN807852.1 Influenza A virus (A/chicken/Egypt/111945V/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3023 3023 100% 0.0 99%
JN807850.1 Influenza A virus (A/duck/Egypt/11106SF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3023 3023 100% 0.0 99%
JN807839.1 Influenza A virus (A/chicken/Egypt/111640V/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3023 3023 100% 0.0 99%
CY062455.1 Influenza A virus (A/Egypt/N09174/2009(H5N1)) segment 4 sequence 3023 3023 100% 0.0 99%
JN807851.1 Influenza A virus (A/duck/Egypt/11221S/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3018 3018 100% 0.0 99%
JN807833.1 Influenza A virus (A/duck/Egypt/1174SF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3018 3018 100% 0.0 99%
JN807814.1 Influenza A virus (A/duck/Egypt/1113SD/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3018 3018 100% 0.0 99%
CY099593.1 Influenza A virus (A/chicken/Egypt/S3093A/2011(H5N1)) hemagglutinin (HA) gene, complete cds 3018 3018 100% 0.0 99%
CY099592.1 Influenza A virus (A/chicken/Egypt/S2938A/2011(H5N1)) hemagglutinin (HA) gene, complete cds 3018 3018 100% 0.0 99%
CY099588.1 Influenza A virus (A/chicken/Egypt/S3280D/2011(H5N1)) hemagglutinin (HA) gene, complete cds 3018 3018 100% 0.0 99%
CY062476.1 Influenza A virus (A/Egypt/N02127/2010(H5N1)) segment 4 sequence 3018 3018 100% 0.0 99%
CY062472.1 Influenza A virus (A/Egypt/N01982/2010(H5N1)) segment 4 sequence 3016 3016 100% 0.0 99%
JN600467.1 Influenza A virus (A/harrier/Israel/531/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3014 3014 100% 0.0 99%
HQ198263.2 Influenza A virus (A/chicken/Egypt/1034/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3014 3014 100% 0.0 99%
JN807867.1 Influenza A virus (A/chicken/Egypt/11529S/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3009 3009 100% 0.0 99%
JN807859.1 Influenza A virus (A/duck/Egypt/11312S/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3009 3009 100% 0.0 99%
JN807838.1 Influenza A virus (A/goose/Egypt/11162S/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3009 3009 100% 0.0 99%
JN807804.1 Influenza A virus (A/chicken/Egypt/10413SF/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3009 3009 100% 0.0 99%
JN807802.1 Influenza A virus (A/chicken/Egypt/10347SF/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3009 3009 100% 0.0 99%
JN807798.1 Influenza A virus (A/duck/Egypt/10331SF/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3009 3009 100% 0.0 99%
HQ198283.2 Influenza A virus (A/goose/Egypt/1057/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3009 3009 100% 0.0 99%
HQ198285.1 Influenza A virus (A/duck/Egypt/1068s/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3009 3009 100% 0.0 99%
JN807860.1 Influenza A virus (A/duck/Egypt/11175SF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3005 3005 100% 0.0 99%
HQ198287.2 Influenza A virus (A/duck/Egypt/106d/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3005 3005 100% 0.0 99%
CY062457.1 Influenza A virus (A/Egypt/N09539/2009(H5N1)) segment 4 sequence 3005 3005 100% 0.0 99%
JN807858.1 Influenza A virus (A/chicken/Egypt/1117AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3000 3000 100% 0.0 99%
HQ198293.2 Influenza A virus (A/duck/Egypt/1063s/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3000 3000 100% 0.0 99%
HQ198254.1 Influenza A virus (A/chicken/Egypt/091317s/2009(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3000 3000 100% 0.0 99%
GU002700.1 Influenza A virus (A/chicken/Egypt/0920-NLQP/2009(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 3000 3000 100% 0.0 99%
CY041910.1 Influenza A virus (A/Egypt/N00585/2009(H5N1)) segment 4 sequence 3000 3000 100% 0.0 99%
JN807862.1 Influenza A virus (A/goose/Egypt/11350S/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2996 2996 100% 0.0 99%
JN807837.1 Influenza A virus (A/chicken/Egypt/119AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2996 2996 100% 0.0 99%
JN807834.1 Influenza A virus (A/chicken/Egypt/117AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2996 2996 100% 0.0 99%
HQ198292.2 Influenza A virus (A/chicken/Egypt/1021L/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2996 2996 100% 0.0 99%
HQ198279.2 Influenza A virus (A/duck/Egypt/1020sd/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2996 2996 100% 0.0 99%
HQ198271.2 Influenza A virus (A/duck/Egypt/1011d/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2996 2996 100% 0.0 99%
HQ198261.1 Influenza A virus (A/chicken/Egypt/1029/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2996 2996 100% 0.0 99%
CY062480.1 Influenza A virus (A/Egypt/N02770/2010(H5N1)) segment 4 sequence 2996 2996 100% 0.0 99%
JN807835.1 Influenza A virus (A/chicken/Egypt/118AF/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2991 2991 100% 0.0 99%
HQ198264.2 Influenza A virus (A/chicken/Egypt/1035/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2991 2991 100% 0.0 99%
CY062453.1 Influenza A virus (A/Egypt/N08835/2009(H5N1)) segment 4 sequence 2991 2991 100% 0.0 99%
CY062451.1 Influenza A virus (A/Egypt/N07908/2009(H5N1)) segment 4 sequence 2991 2991 100% 0.0 99%
CY062447.1 Influenza A virus (A/Egypt/N05912/2009(H5N1)) segment 4 sequence 2991 2991 100% 0.0 99%
GU002672.1 Influenza A virus (A/chicken/Egypt/092-NLQP/2009(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2991 2991 100% 0.0 99%
JN807809.1 Influenza A virus (A/chicken/Egypt/115/2011(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2987 2987 100% 0.0 99%
JN807791.1 Influenza A virus (A/turkey/Egypt/10453F/2010(H5N1)) segment 4 hemagglutinin (HA) gene, complete cds 2987 2987 100% 0.0 99%
CY062482.1 Influenza A virus (A/Egypt/N03071/2010(H5N1)) segment 4 sequence 2987 2987 100% 0.0 99%
GU002696.1 Influenza A virus (A/duck/Egypt/0990SM-NLQP/2009(H5N1)) segment 4 hemagglutinin (HA) gene, partial cds 2987 2987 100% 0.0 99%
EF535826.1 Influenza A virus (A/Egypt/2621-NAMRU3/2007(H5N1)) hemagglutinin (HA) gene, complete cds 2987 2987 100% 0.0 99%
JN807820.1 Influenza A virus (A/chicken/Egypt/1155AG/2011(H5N1)) segment 4 hemagglutinin (HA) gene, partial cds 2984 2984 97% 0.0 99%

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Commentry
http://www.recombinomics.com/News/02251 ... uster.html

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Commentary
http://www.recombinomics.com/News/02251 ... ntity.html

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The failure of NAMRU-3 (US Navy) and CDC (who gets samples from NAMRU-3) to release 2010/2011/2012 sequences raises serious pandemic concerns. Egypt had 39 confirmed H5N1 human cases in 2011, and the WHO report only has 11 of these sequences, yet these sequences form 2 clusters, including the 2 most recent sequences, which are IDENTICAL in spite of a significant time gap in collection dates.

In Egypt, only cases with a poultry link are tested for H5N1, and therefore human to human transmission will be largely missed. Detection is heavily dependent on sequences clusters, when testing is severely restricted.

Therefore, full sequences from all 2011 and 2012 cases should be released immediately.

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