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PostPosted: Wed Mar 30, 2011 7:55 am 
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Location: Pittsburgh, PA USA
Dingo wrote:
niman wrote:
Dingo wrote:
To my untrained eye, this flu in Mexico and Venezuela spreads easily/quickly, produces a high number of pneumonia cases and is deadly.

Is just say S188T seen previously but in central/south America? Or is it something else, something new, maybe a combo with D225G?

I suspect it is more.


Any thoughts? Maybe it's picked up something from one of the strains of bird flu?

The sequences can't come out soon enough.

The strange thing about these reports, two years on, is that they sound like the start of a pandemic, not after the end* of one.

End = WHO idiocy

There are many candidate polymorphisms already in human sequences which originate in swine. S165N traces back to the Hudson county fair in Ohio in 2007. It is in multiple 2011 isolates in the US as well as several isolates in Spain. Recombination allows this change, which is not far from changes at positions 156-159 which produce low reactors, to be palced on an S188T background. Similarly, a sequence from Kentucky had S188T, G158E, and D225G. There are multiple candidates in human H1N1 - but H changes in pandemic H1N1 almost always trace back to SWINE.

Here is the pedigree of S165N at Genbank

CY086912.1 Influenza A virus (A/swine/Minnesota/226128/2010(H1N1)) hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY084226.1 Influenza A virus (A/South Carolina/AF21803/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY084223.1 Influenza A virus (A/Ohio/AF21800/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY084219.1 Influenza A virus (A/North Carolina/AF21796/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY084216.1 Influenza A virus (A/New Jersey/AF21791/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY084206.1 Influenza A virus (A/Florida/AF21772/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY084205.1 Influenza A virus (A/Florida/AF21771/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY084204.1 Influenza A virus (A/District of Columbia/AF21769/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY084203.1 Influenza A virus (A/Arizona/AF21768/2011(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
JF312070.1 Influenza A virus (A/swine/Iowa/A01057153/2010(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
GU721155.2 Influenza A virus (A/swine/Korea/VD03/2009(H1N1)) segment 4 hemagglutinin gene, partial cds; and HA gene, complete sequence 28.2 28.2 100% 1.4 100%
HQ880591.1 Influenza A virus (A/Denmark/111/2010(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
HQ378741.1 Influenza A virus(A/swine/Missouri/46519-5/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
HQ378729.1 Influenza A virus(A/swine/Iowa/46519-1/2007(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY075596.1 Influenza A virus (A/Boston/672/2009(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
HQ190941.1 Influenza A virus (A/Habana/7374/2010(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY073126.1 Influenza A virus (A/Mexico City/WRAIR1773T/2010(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY072526.1 Influenza A virus (A/Tallinn/INS374/2010(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
CY072310.1 Influenza A virus (A/Warsaw/INS316/2009(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
HM461778.1 Influenza A virus (A/swine/Ohio/02026/2008(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
HM461810.1 Influenza A virus (A/swine/Missouri/02060/2008(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
HM461818.1 Influenza A virus (A/swine/North Carolina/02023/2008(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY071650.1 Influenza A virus (A/Quito/WR1589N/2009(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY071111.1 Influenza A virus (A/Wurzburg/INS381/2009(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
CY070773.1 Influenza A virus (A/Japan/AF2287/2009(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY070762.1 Influenza A virus (A/Japan/AF2276/2009(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY070040.1 Influenza A virus (A/Germany/AF2210/2010(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY070037.1 Influenza A virus (A/Germany/AF2207/2010(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
HM804853.1 Influenza A virus (A/swine/SD/1/2010(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY066471.1 Influenza A virus (A/California/VRDL4/2010(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
HM570051.1 Influenza A virus (A/swine/Minnesota/03025/2010(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY064987.1 Influenza A virus (A/California/VRDL6/2010(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
HM193851.1 Influenza A virus (A/swine/Iowa/02999/2010(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY063011.1 Influenza A virus (A/Tallinn/INS183/2010(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
CY062635.1 Influenza A virus (A/Mexico City/014/2009(H1N1)) segment 4, complete sequence 28.2 28.2 100% 1.4 100%
HM165185.1 Influenza A virus (A/Haishu/SWL110/2010(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
GU968918.2 Influenza A virus (A/Beijing/SE2649/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
GU984384.1 Influenza A virus (A/swine/OR/10-004060/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
GU817056.1 Influenza A virus (A/swine/Minnesota/02951/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
GU817055.1 Influenza A virus (A/swine/Minnesota/02950/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
GU817054.1 Influenza A virus (A/swine/Minnesota/02949/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
GU451271.1 Influenza A virus (A/Milan/324/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%
CY054584.1 Influenza A virus (A/Catalonia/S2151/2009(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY052026.1 Influenza A virus (A/Catalonia/NS7362/2009(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY051949.1 Influenza A virus (A/Catalonia/S1687/2009(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
GQ484355.1 Influenza A virus (A/swine/Kansas/77778/2007(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
CY040510.1 Influenza A virus (A/swine/Ohio/63607-32/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040509.1 Influenza A virus (A/swine/North Carolina/63607-9/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040508.1 Influenza A virus (A/swine/North Carolina/63607-8/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040505.1 Influenza A virus (A/swine/North Carolina/63607-37/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040503.1 Influenza A virus (A/swine/North Carolina/63607-27/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040502.1 Influenza A virus (A/swine/North Carolina/63607-25/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040500.1 Influenza A virus (A/swine/North Carolina/63607-14/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040497.1 Influenza A virus (A/swine/North Carolina/225-6/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040496.1 Influenza A virus (A/swine/North Carolina/225-2/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040495.1 Influenza A virus (A/swine/North Carolina/225-13/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040493.1 Influenza A virus (A/swine/Missouri/63607-16/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040490.1 Influenza A virus (A/swine/Minnesota/63607-40/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040486.1 Influenza A virus (A/swine/Minnesota/63607-31/2008 (H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040485.1 Influenza A virus (A/swine/Minnesota/63607-30/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040483.1 Influenza A virus (A/swine/Minnesota/63607-26/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040480.1 Influenza A virus (A/swine/Minnesota/63607-15/2008 (H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040479.1 Influenza A virus (A/swine/Minnesota/63607-12/2008 (H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040477.1 Influenza A virus (A/swine/Minnesota/225-5/2008 (H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040476.1 Influenza A virus (A/swine/Minnesota/225-4/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040468.1 Influenza A virus (A/swine/Iowa/63607-1/2008 (H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040466.1 Influenza A virus (A/swine/Iowa/225-8/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
CY040461.1 Influenza A virus (A/swine/Illinois/225-1/2008(H1N1)) segment 4 sequence 28.2 28.2 100% 1.4 100%
FJ986621.1 Influenza A virus (A/Ohio/02/2007(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
FJ986620.1 Influenza A virus (A/Ohio/01/2007(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
EU604689.1 Influenza A virus (A/swine/OH/511445/2007(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds 28.2 28.2 100% 1.4 100%
EU409948.1 Influenza A virus (A/swine/Ohio/24366/2007(H1N1)) hemagglutinin (HA) gene, partial cds 28.2 28.2 100% 1.4 100%

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PostPosted: Wed Mar 30, 2011 8:06 am 
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Location: Pittsburgh, PA USA
Dingo wrote:
niman wrote:
Dingo wrote:
To my untrained eye, this flu in Mexico and Venezuela spreads easily/quickly, produces a high number of pneumonia cases and is deadly.

Is just say S188T seen previously but in central/south America? Or is it something else, something new, maybe a combo with D225G?

I suspect it is more.


Any thoughts? Maybe it's picked up something from one of the strains of bird flu?

The sequences can't come out soon enough.

The strange thing about these reports, two years on, is that they sound like the start of a pandemic, not after the end* of one.

End = WHO idiocy

Yes, WHO is beyond clueless when it comes to influenza evolution. They still think changes are due to RANDOM mutations and can't be predicted. When the prediction of D225G was made for Ukraine, they withheld the data and claimed there were no significant changes. When D225G was confirmed, they put out the nonsense report (claiming no clustering) at the end of 2009 and then again in February, 2010, just before the sequences from autopsy lung in Ukraine came out, showing widespread D225G and D225N clustered in Ukraine. The use a HEAVILY manipulated "antigen characterization" test to claim matches for mismatches on vaccine targets, and of course have recommended California/7 for the southern hemisphere in 2011 and northern hemisphere in 2011/2012.
Pandemic H1N1 is swine jumped to humans, and now it is starting to evolve more quickly (with MANY versions back in swine ready to jump again).
The WHO August proclamation of an end to the pandemic, followed by the recommendation to leave the vaccine unchanged reflects the outdated views of their "experts", who are clearly hazardous to the world's health.

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PostPosted: Wed Mar 30, 2011 8:09 am 
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Mill Hill has just released a series of 2011 sequences (at GISAID) from Europe.

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PostPosted: Wed Mar 30, 2011 8:13 am 
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niman wrote:
Mill Hill has just released a series of 2011 sequences (at GISAID) from Europe.

The new sequences are dominated by 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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PostPosted: Wed Mar 30, 2011 9:01 am 
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niman wrote:
There are many candidate polymorphisms already in human sequences which originate in swine. S165N traces back to the Hudson county fair in Ohio in 2007. It is in multiple 2011 isolates in the US as well as several isolates in Spain. Recombination allows this change, which is not far from changes at positions 156-159 which produce low reactors, to be palced on an S188T background. Similarly, a sequence from Kentucky had S188T, G158E, and D225G. There are multiple candidates in human H1N1 - but H changes in pandemic H1N1 almost always trace back to SWINE.



Thanks. Interesting the swine connection - this could be end up being a movable feast of the flu jumping into swine, then back out with never ending antigen shift, and the consequences therein.


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PostPosted: Wed Mar 30, 2011 9:02 am 
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Dingo wrote:
niman wrote:
There are many candidate polymorphisms already in human sequences which originate in swine. S165N traces back to the Hudson county fair in Ohio in 2007. It is in multiple 2011 isolates in the US as well as several isolates in Spain. Recombination allows this change, which is not far from changes at positions 156-159 which produce low reactors, to be palced on an S188T background. Similarly, a sequence from Kentucky had S188T, G158E, and D225G. There are multiple candidates in human H1N1 - but H changes in pandemic H1N1 almost always trace back to SWINE.



Thanks. Interesting the swine connection - this could be end up being a movable feast of the flu jumping into swine, then back out with never ending antigen shift, and the consequences therein.

The newly released sequences from 2011 isolates in Europe are dominated by changes at positions 156-159, which produce LOW REACTORS, and also are found in swine.

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PostPosted: Wed Mar 30, 2011 9:04 am 
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niman wrote:
Yes, WHO is beyond clueless when it comes to influenza evolution. They still think changes are due to RANDOM mutations and can't be predicted. When the prediction of D225G was made for Ukraine, they withheld the data and claimed there were no significant changes. When D225G was confirmed, they put out the nonsense report (claiming no clustering) at the end of 2009 and then again in February, 2010, just before the sequences from autopsy lung in Ukraine came out, showing widespread D225G and D225N clustered in Ukraine. The use a HEAVILY manipulated "antigen characterization" test to claim matches for mismatches on vaccine targets, and of course have recommended California/7 for the southern hemisphere in 2011 and northern hemisphere in 2011/2012.
Pandemic H1N1 is swine jumped to humans, and now it is starting to evolve more quickly (with MANY versions back in swine ready to jump again).
The WHO August proclamation of an end to the pandemic, followed by the recommendation to leave the vaccine unchanged reflects the outdated views of their "experts", who are clearly hazardous to the world's health.


I find it morbidly fascinating that the stunning technology we have eg sequencing is no match for the human stupidity of authorities like the WHO. I just hope they are held to account if the **** hits the fan.


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PostPosted: Wed Mar 30, 2011 9:33 am 
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Dingo wrote:
niman wrote:
Yes, WHO is beyond clueless when it comes to influenza evolution. They still think changes are due to RANDOM mutations and can't be predicted. When the prediction of D225G was made for Ukraine, they withheld the data and claimed there were no significant changes. When D225G was confirmed, they put out the nonsense report (claiming no clustering) at the end of 2009 and then again in February, 2010, just before the sequences from autopsy lung in Ukraine came out, showing widespread D225G and D225N clustered in Ukraine. The use a HEAVILY manipulated "antigen characterization" test to claim matches for mismatches on vaccine targets, and of course have recommended California/7 for the southern hemisphere in 2011 and northern hemisphere in 2011/2012.
Pandemic H1N1 is swine jumped to humans, and now it is starting to evolve more quickly (with MANY versions back in swine ready to jump again).
The WHO August proclamation of an end to the pandemic, followed by the recommendation to leave the vaccine unchanged reflects the outdated views of their "experts", who are clearly hazardous to the world's health.


I find it morbidly fascinating that the stunning technology we have eg sequencing is no match for the human stupidity of authorities like the WHO. I just hope they are held to account if the **** hits the fan.

They are WELL into the clueless beyond belief category. They think all of these predictable changes are "coincidences"!!!!!!!

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PostPosted: Wed Mar 30, 2011 10:13 am 
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Posts: 149
Location: Florida
niman wrote:
Dingo wrote:
niman wrote:
Yes, WHO is beyond clueless when it comes to influenza evolution. They still think changes are due to RANDOM mutations and can't be predicted. When the prediction of D225G was made for Ukraine, they withheld the data and claimed there were no significant changes. When D225G was confirmed, they put out the nonsense report (claiming no clustering) at the end of 2009 and then again in February, 2010, just before the sequences from autopsy lung in Ukraine came out, showing widespread D225G and D225N clustered in Ukraine. The use a HEAVILY manipulated "antigen characterization" test to claim matches for mismatches on vaccine targets, and of course have recommended California/7 for the southern hemisphere in 2011 and northern hemisphere in 2011/2012.
Pandemic H1N1 is swine jumped to humans, and now it is starting to evolve more quickly (with MANY versions back in swine ready to jump again).
The WHO August proclamation of an end to the pandemic, followed by the recommendation to leave the vaccine unchanged reflects the outdated views of their "experts", who are clearly hazardous to the world's health.


I find it morbidly fascinating that the stunning technology we have eg sequencing is no match for the human stupidity of authorities like the WHO. I just hope they are held to account if the **** hits the fan.

They are WELL into the clueless beyond belief category. They think all of these predictable changes are "coincidences"!!!!!!!


I guess that is what happens when science is infected (pun intended) with politics, especially international politics.

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PostPosted: Wed Mar 30, 2011 10:43 am 
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Jim wrote:
niman wrote:
Dingo wrote:
I find it morbidly fascinating that the stunning technology we have eg sequencing is no match for the human stupidity of authorities like the WHO. I just hope they are held to account if the **** hits the fan.

They are WELL into the clueless beyond belief category. They think all of these predictable changes are "coincidences"!!!!!!!


I guess that is what happens when science is infected (pun intended) with politics, especially international politics.

16 of the 32 European sequences have a change at positions 156-159 and 10 of the 16 have G158E, which has been shown to be a LOW REACTOR change by multiple labs, including CDC data on H1N1 sequences from isolates OUTSIDE of the US.

This is pure politics disigned to show that mismatches are matches, and the propaganda is fed to MD's on the vaccine recommendation committees and reporters who are spoon fed utter nonsense, which is passed on to anyone who will listen (and multiple message boards act as propaganda propagators).

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