Rhiza Labs FluTracker Forum

Mill Hill has released a series including 32 HA H1N1 sequences from isolates that are largely from Europe collected in late 2010 and 2011. At least 26 of the 32 sequences have S188T.

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Recent sequences at GISAID with S188T

EPI309689 A/Trikala GR/199/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309685 A/Slovenia/234/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309683 A/Slovenia/167/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309681 A/Slovenia/158/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309679 A/Slovenia/146/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309677 A/Slovenia/1195/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309675 A/Slovenia/1098/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309673 A/Poitiers/33/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309671 A/Paris/2301/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309669 A/Northern Ireland/2/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309667 A/LarissaGR/332/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309663 A/Ireland/72392/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309659 A/Iasi/47707/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309655 A/Georgia/3/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309653 A/Geneva/4203654/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309647 A/Geneva/4194183/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309645 A/England/404/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309643 A/England/375/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309641 A/England/334/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309639 A/Egypt/73/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309637 A/Denmark/120/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309635 A/Denmark/115/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309633 A/Croatia/18576-1/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309631 A/Croatia/17897-2/2010 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309629 A/Athens/351/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500
EPI309627 A/Athens/230/2011 (A/H1N1 swl) segment 4 (HA) 27.0 6.17500

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These sequences are dominated by changes at positions 156-159. Most are mixtures with wild type and the most common is G158E, but there are examples of changes at all four positions, which produce LOW REACTORS in antigen characterization tests.

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Additional changes include D225G, D225N, Q226R.

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How frequent?

3 with D225G, 1 with D225N, 3 with Q226R. Remember, this is in just 32 sequences, so most have S188T plus at least one of the key changes (RBD or low reactor region). H1N1 clearly knows how to evolve, while vaccine target, California/7/2009, remains UNCHANGED.

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Thanks. 20%!

So we've gone from when even finding one low reactor was big news to them being found all over the place, and marrying up with changes at D225?

This is not good news. In hindsight, perhaps 2009 -2010 will equal 1917?

Sequences with changes at positions 156-159 are 1,2,10,3 (so 16 of the sequence have LOW REACTOR changes), and those with G158E are clustering, signaling transmission.

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EXACTLY and we are all protected with a 2009 vaccine!

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It is also worth noting that in the 2009/2010 season the only US low reactors noted by the CDC were position 159 changes, and this season they claim that there is only ONE low reactor.

2009 Influenza A (H1N1) [240]

•Two hundred thirty-nine (99.6%) of the 240 tested were characterized as A/California/7/2009-like, the influenza A (H1N1) component of the 2010-11 influenza vaccine for the Northern Hemisphere. One virus (0.4%) of the 240 tested showed reduced titers with antiserum produced against A/California/7/2009.

http://www.cdc.gov/flu/weekly/

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