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PostPosted: Wed Aug 03, 2011 2:54 pm 
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CDC has released sequences (at GISAID) of a new construct, A/Minnesota/11/2010 X-203A, signaling the testing of a trH3N2 pandemic vaccine target.

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PostPosted: Wed Aug 03, 2011 2:57 pm 
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niman wrote:
CDC has released new construct, A/Minnesota/11/2010 X-203A, signaling the testing of a trH3N2 vaccine target.

As expected, trH3N2 vaccine target has D225G.

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PostPosted: Wed Aug 03, 2011 3:07 pm 
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Non-synonymous changes in trH3N2 vaccine targets include
S118T
T128N
E153G
H167Y
D140N
A145E
L146Q
N193K
L194I
T203I
D225G
P274H
G276D
N277E
R299K
N445S
K453R
V489I
D492N

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PostPosted: Wed Aug 03, 2011 3:22 pm 
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Top 100 matches

EPI328900 A/Minnesota/11/2010 X-203A (A/H3N2) segment 4 (HA) 3142.3 0.000000e+00 1701/1701 (100%)
EPI328898 A/Minnesota/11/2010 X-203 (A/H3N2) segment 4 (HA) 3136.7 0.000000e+00 1700/1701 (99%)
EPI293965 A/Minnesota/11/2010 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI291898 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 3125.7 0.000000e+00 1698/1701 (99%)
EPI312980 A/Pennsylvania/40/2010 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI317003 A/swine/Indiana/A0109091/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI324857 A/swine/North Carolina/A01049436/2011 (A/H3N2) segment 4 (HA) 3103.5 0.000000e+00 1694/1701 (99%)
EPI291838 A/Minnesota/09/2010 (A/H3N2) segment 4 (HA) 3046.2 0.000000e+00 1667/1676 (99%)
EPI291893 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 2972.4 0.000000e+00 1615/1618 (99%)
EPI222910 A/swine/Minnesota/7931/2007 (A/H3N2) segment 4 (HA) 2931.8 0.000000e+00 1665/1703 (97%)
EPI314335 A/turkey/BC/1529-3/2005 (A/H3N2) segment 4 (HA) 2904.1 0.000000e+00 1659/1702 (97%)
EPI103199 A/swine/Ontario/33853/2005 (A/H3N2) segment 4 (HA) 2904.1 0.000000e+00 1659/1702 (97%)
EPI103127 A/Ontario/RV1273/2005 (A/H3N2) segment 4 (HA) 2904.1 0.000000e+00 1659/1702 (97%)
EPI229372 A/turkey/OH/313053/2004 (A/H3N2) segment 4 (HA) 2898.5 0.000000e+00 1659/1703 (97%)
EPI103181 A/swine/Manitoba/12707/2005 (A/H3N2) segment 4 (HA) 2893.0 0.000000e+00 1657/1702 (97%)
EPI103145 A/swine/Alberta/14722/2005 (A/H3N2) segment 4 (HA) 2893.0 0.000000e+00 1657/1702 (97%)
EPI101389 A/turkey/Ohio/313053/04 (A/H3N2) segment 4 (HA) 2893.0 0.000000e+00 1658/1703 (97%)
EPI289638 A/swine/Minnesota/1300/2007 (A/H3N2) segment 4 (HA) 2881.9 0.000000e+00 1655/1702 (97%)
EPI158876 A/turkey/MN/366767/2005 (A/H3N2) segment 4 (HA) 2881.9 0.000000e+00 1655/1702 (97%)
EPI168645 A/turkey/Minnesota/366767/2005 (A/H3N2) segment 4 (HA) 2865.3 0.000000e+00 1653/1703 (97%)
EPI103217 A/turkey/Ontario/31232/2005 (A/H3N2) segment 4 (HA) 2865.3 0.000000e+00 1653/1703 (97%)
EPI228922 A/turkey/Illinois/2004 (A/H3N2) segment 4 (HA) 2859.7 0.000000e+00 1653/1704 (97%)
EPI227574 A/turkey/NC/353568/2005 (A/H3N2) segment 4 (HA) 2854.2 0.000000e+00 1650/1702 (96%)
EPI168650 A/turkey/North Carolina/353568/2005 (A/H3N2) segment 4 (HA) 2854.2 0.000000e+00 1650/1702 (96%)
EPI166252 A/swine/Minnesota/SG-00234/2005 (A/H3N2) segment 4 (HA) 2846.8 0.000000e+00 1641/1690 (97%)
EPI225756 A/swine/Minnesota/66853/2006 (A/H3N2) segment 4 (HA) 2843.1 0.000000e+00 1649/1703 (96%)
EPI98712 A/swine/MI/PU243/04 (A/H3N1) segment 4 (HA) 2839.4 0.000000e+00 1647/1702 (96%)
EPI182817 A/swine/Quebec/4001/2005 (A/H3N2) segment 4 (HA) 2837.6 0.000000e+00 1647/1702 (96%)
EPI222756 A/swine/Minnesota/1145/2007 (A/H3N2) segment 4 (HA) 2832.0 0.000000e+00 1646/1702 (96%)
EPI128344 A/Ontario/1252/2007 (A/H3N2) segment 4 (HA) 2832.0 0.000000e+00 1646/1702 (96%)
EPI166255 A/swine/Minnesota/SG-00235/2007 (A/H3N2) segment 4 (HA) 2830.2 0.000000e+00 1638/1690 (96%)
EPI166258 A/swine/Minnesota/SG-00236/2007 (A/H3N2) segment 4 (HA) 2828.3 0.000000e+00 1637/1689 (96%)
EPI225758 A/swine/Minnesota/66960/2006 (A/H3N2) segment 4 (HA) 2826.5 0.000000e+00 1646/1703 (96%)
EPI222674 A/swine/Oklahoma/008722/2007 (A/H3N2) segment 4 (HA) 2826.5 0.000000e+00 1646/1703 (96%)
EPI184448 A/swine/North Carolina/R08-001877-D08-013371/2008 (A/H3N2) segment 4 (HA) 2826.5 0.000000e+00 1646/1703 (96%)
EPI314635 A/swine/QC/2108-2/2009 (A/H3N2) segment 4 (HA) 2821.0 0.000000e+00 1645/1703 (96%)
EPI225753 A/swine/Minnesota/65767/2006 (A/H3N2) segment 4 (HA) 2821.0 0.000000e+00 1645/1703 (96%)
EPI222959 A/swine/Minnesota/578/2007 (A/H3N2) segment 4 (HA) 2821.0 0.000000e+00 1645/1703 (96%)
EPI103163 A/swine/British Columbia/28103/2005 (A/H3N2) segment 4 (HA) 2821.0 0.000000e+00 1645/1703 (96%)
EPI222657 A/swine/Minnesota/5947/2007 (A/H3N2) segment 4 (HA) 2815.4 0.000000e+00 1644/1703 (96%)
EPI166278 A/swine/Minnesota/SG-00242/2006 (A/H3N2) segment 4 (HA) 2815.4 0.000000e+00 1637/1693 (96%)
EPI222961 A/swine/Minnesota/761/2007 (A/H3N2) segment 4 (HA) 2804.3 0.000000e+00 1642/1703 (96%)
EPI314679 A/swine/QC/414/2009 (A/H3N2) segment 4 (HA) 2800.6 0.000000e+00 1643/1704 (96%)
EPI309154 A/swine/Pennsylvania/62170-3/2010 (A/H3N2) segment 4 (HA) 2798.8 0.000000e+00 1640/1702 (96%)
EPI309153 A/swine/Pennsylvania/62170-1/2010 (A/H3N2) segment 4 (HA) 2798.8 0.000000e+00 1640/1702 (96%)
EPI222682 A/swine/Oklahoma/011506/2007 (A/H3N2) segment 4 (HA) 2798.8 0.000000e+00 1641/1703 (96%)
EPI312689 A/swine/Minnesota/239105/2009 (A/H3N2) segment 4 (HA) 2793.3 0.000000e+00 1638/1701 (96%)
EPI259504 A/swine/Minnesota/03008/2010 (A/H3N2) segment 4 (HA) 2793.3 0.000000e+00 1642/1705 (96%)
EPI182824 A/mink/Nova Scotia/1055488/2007 (A/H3N2) segment 4 (HA) 2793.3 0.000000e+00 1639/1702 (96%)
EPI317007 A/swine/Iowa/A0109112/2010 (A/H3N2) segment 4 (HA) 2787.7 0.000000e+00 1641/1705 (96%)
EPI291872 A/Pennsylvania/14/2010 (A/H3N2) segment 4 (HA) 2787.7 0.000000e+00 1638/1702 (96%)
EPI291870 A/Pennsylvania/14/2010 (A/H3N2) segment 4 (HA) 2787.7 0.000000e+00 1638/1702 (96%)
EPI291865 A/Pennsylvania/14/2010 (A/H3N2) segment 4 (HA) 2787.7 0.000000e+00 1638/1702 (96%)
EPI318095 A/swine/Iowa/A01049113/2010 (A/H3N2) segment 4 (HA) 2782.2 0.000000e+00 1640/1705 (96%)
EPI314666 A/swine/QC/1698-2/2009 (A/H3N2) segment 4 (HA) 2782.2 0.000000e+00 1639/1704 (96%)
EPI314665 A/swine/QC/1698-1/2009 (A/H3N2) segment 4 (HA) 2782.2 0.000000e+00 1639/1704 (96%)
EPI324849 A/swine/Iowa/A01049254/2010 (A/H3N2) segment 4 (HA) 2776.6 0.000000e+00 1638/1704 (96%)
EPI324844 A/swine/Nebraska/A01049235/2010 (A/H3N2) segment 4 (HA) 2776.6 0.000000e+00 1639/1705 (96%)
EPI314796 A/swine/Pennsylvania/602170-4/2010 (A/H3N2) segment 4 (HA) 2776.6 0.000000e+00 1636/1702 (96%)
EPI314667 A/swine/QC/1698-4/2009 (A/H3N2) segment 4 (HA) 2776.6 0.000000e+00 1638/1704 (96%)
EPI314643 A/swine/QC/382/2009 (A/H3N2) segment 4 (HA) 2776.6 0.000000e+00 1637/1703 (96%)
EPI318106 A/swine/Iowa/A01049185/2010 (A/H3N2) segment 4 (HA) 2771.1 0.000000e+00 1636/1703 (96%)
EPI314668 A/swine/QC/1698-5/2009 (A/H3N2) segment 4 (HA) 2771.1 0.000000e+00 1637/1704 (96%)
EPI324851 A/swine/Iowa/A01049317/2010 (A/H3N2) segment 4 (HA) 2765.6 0.000000e+00 1636/1704 (96%)
EPI316991 A/swine/Iowa/A0109035/2010 (A/H3N2) segment 4 (HA) 2765.6 0.000000e+00 1633/1701 (96%)
EPI316990 A/swine/Iowa/A0109034/2010 (A/H3N2) segment 4 (HA) 2765.6 0.000000e+00 1633/1701 (96%)
EPI307943 A/swine/Iowa/A01057188/2010 (A/H3N2) segment 4 (HA) 2765.6 0.000000e+00 1636/1704 (96%)
EPI314687 A/swine/QC/1840-2/2009 (A/H3N2) segment 4 (HA) 2761.9 0.000000e+00 1633/1701 (96%)
EPI302647 A/swine/Illinois/53612-2/2009 (A/H3N2) segment 4 (HA) 2760.0 0.000000e+00 1635/1704 (95%)
EPI302646 A/swine/Illinois/53612-1/2009 (A/H3N2) segment 4 (HA) 2760.0 0.000000e+00 1635/1704 (95%)
EPI244297 A/Kansas/13/2009 (A/H3N2) segment 4 (HA) 2760.0 0.000000e+00 1635/1704 (95%)
EPI230035 A/swine/Wisconsin/R7c/2001 (A/H3N2) segment 4 (HA) 2754.5 0.000000e+00 1633/1703 (95%)
EPI25393 A/turkey/ Minnesota/764-2/03 (A/H3N2) segment 4 (HA) 2754.5 0.000000e+00 1635/1705 (95%)
EPI314795 A/swine/Pennsylvania/602170-2/2010 (A/H3N2) segment 4 (HA) 2748.9 0.000000e+00 1631/1702 (95%)
EPI314663 A/swine/QC/1685-1/2009 (A/H3N2) segment 4 (HA) 2748.9 0.000000e+00 1632/1703 (95%)
EPI25391 A/turkey/North Carolina/12344/03 (A/H3N2) segment 4 (HA) 2748.9 0.000000e+00 1634/1705 (95%)
EPI219360 A/swine/Kansas/015252/2009 (A/H3N2) segment 4 (HA) 2743.4 0.000000e+00 1630/1702 (95%)
EPI314664 A/swine/QC/1685-5/2009 (A/H3N2) segment 4 (HA) 2737.9 0.000000e+00 1630/1703 (95%)
EPI314695 A/swine/QC/440-A/2009 (A/H3N2) segment 4 (HA) 2728.6 0.000000e+00 1631/1706 (95%)
EPI292016 A/swine/Iowa/H03BF5/2003 (A/H3N2) segment 4 (HA) 2728.6 0.000000e+00 1630/1705 (95%)
EPI302658 A/swine/Illinois/53612-5/2009 (A/H3N2) segment 4 (HA) 2726.8 0.000000e+00 1629/1704 (95%)
EPI318101 A/swine/Iowa/A01049160/2010 (A/H3N2) segment 4 (HA) 2721.2 0.000000e+00 1630/1706 (95%)
EPI314515 A/quail/QC/FAV-10/2008 (A/H3N2) segment 4 (HA) 2721.2 0.000000e+00 1626/1702 (95%)
EPI302653 A/swine/Illinois/53612-4/2009 (A/H3N2) segment 4 (HA) 2721.2 0.000000e+00 1628/1704 (95%)
EPI324850 A/swine/Pennsylvania/A01049256/2010 (A/H3N2) segment 4 (HA) 2717.5 0.000000e+00 1628/1705 (95%)
EPI324852 A/swine/Minnesota/A01049346/2010 (A/H3N2) segment 4 (HA) 2715.7 0.000000e+00 1628/1705 (95%)
EPI307945 A/swine/Illinois/A01057088/2010 (A/H3N2) segment 4 (HA) 2715.7 0.000000e+00 1629/1706 (95%)
EPI219368 A/swine/Oklahoma/001142/2009 (A/H3N2) segment 4 (HA) 2715.7 0.000000e+00 1626/1703 (95%)
EPI98686 A/swine/Minnesota/00395/2004 (A/H3N1) segment 4 (HA) 2715.7 0.000000e+00 1626/1703 (95%)
EPI307944 A/swine/Illinois/A01057087/2010 (A/H3N2) segment 4 (HA) 2710.2 0.000000e+00 1627/1705 (95%)
EPI302659 A/swine/Illinois/53612-6/2010 (A/H3N2) segment 4 (HA) 2710.2 0.000000e+00 1626/1704 (95%)
EPI316988 A/swine/Iowa/A0109031/2010 (A/H3N2) segment 4 (HA) 2704.6 0.000000e+00 1625/1704 (95%)
EPI316989 A/swine/Iowa/A0109032/2010 (A/H3N2) segment 4 (HA) 2700.9 0.000000e+00 1624/1704 (95%)
EPI302664 A/swine/Illinois/53612-7/2010 (A/H3N2) segment 4 (HA) 2699.1 0.000000e+00 1625/1705 (95%)
EPI314161 A/swine/Quebec/1265553/2010 (A/H3N2) segment 4 (HA) 2688.0 0.000000e+00 1616/1695 (95%)
EPI131612 A/swine/Wisconsin/H03HO7/2003 (A/H3N2) segment 4 (HA) 2682.5 0.000000e+00 1621/1704 (95%)
EPI318097 A/swine/Indiana/A01049124/2010 (A/H3N2) segment 4 (HA) 2671.4 0.000000e+00 1621/1706 (95%)
EPI307929 A/swine/Pennsylvania/057108-1/2010 (A/H3N2) segment 4 (HA) 2665.8 0.000000e+00 1618/1704 (94%)
EPI161141 A/Hong Kong/CUHK4147/1997 (A/H3N2) segment 4 (HA) 2665.8 0.000000e+00 1620/1706 (94%)
EPI98728 A/swine/IN/PU542/04 (A/H3N1) segment 4 (HA) 2665.8 0.000000e+00 1618/1704 (94%)

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PostPosted: Wed Aug 03, 2011 5:30 pm 
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Commentary

http://www.recombinomics.com/News/08031 ... ccine.html

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PostPosted: Wed Aug 03, 2011 8:53 pm 
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niman wrote:
CDC has released sequences (at GISAID) of a new construct, A/Minnesota/11/2010 X-203A, signaling the testing of a trH3N2 pandemic vaccine target.

Antigenic characterisation:
Note: 6:2 A/reassortant NYMC X-203A (A/PR8/34 x A/Minnesota/11/2010 H3N2 SOIV)

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PostPosted: Wed Aug 03, 2011 9:12 pm 
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niman wrote:
niman wrote:
CDC has released sequences (at GISAID) of a new construct, A/Minnesota/11/2010 X-203A, signaling the testing of a trH3N2 pandemic vaccine target.

Antigenic characterisation:
Note: 6:2 A/reassortant NYMC X-203A (A/PR8/34 x A/Minnesota/11/2010 H3N2 SOIV)

CDC Test and Isolation Bias Raises H1N1 Pandemic Concerns
Recombinomics Commentary 14:20
May 4, 2011

DR. GELLIN: I am always impressed by what a body of work that is. Two questions. One of them, you had mentioned about the low reactors and the biological issues at the lab in London, is that the same issue for the H1 as well as the H3? Because they showed, I think, that there was a higher percentage of H1 low reactors in the London lab, as well. The question really is that a lab problem or does that signal some other evolution, since they have had more H1 this year?

DR. COX: Yes. What we know for H1N1 viruses is that if you isolate them in a particular cell line, you tend to get more of the variance with changes within that region that I mentioned -- the 153 to 158 region. They had been using the particular cell line that pulls out that particular variant or that selects for that particular variant.

They have subsequently switched to normal MDCK cells. I think what they are seeing is a combination of the two phenomena. Plus, they receive a lot of viruses that have been isolated COT, the special kind of MDCK cells. I think it is a combination of they are receiving viruses with changes that cause that reduction in activity and then having some additional low reactors, but they are scattered throughout the tree.

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PostPosted: Thu Aug 04, 2011 8:17 am 
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niman wrote:
Non-synonymous chnages in trH3N2 vaccine targets include
S118T
T128N
E153G
H167Y
D140N
A145E
L146Q
N193K
L194I
T203I
D225G
P274H
G276D
N277E
R299K
N445S
K453R
V489I
D492N

N193K and L194I are in both vaccine reassortants, but these changes are not present in the original Minnesota/11/2010 sequence (grown on mammalian cells).

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PostPosted: Sun Aug 28, 2011 11:42 pm 
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Related to A/IN/08/11

http://www.recombinomics.com/News/08291 ... IN_H3.html

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