Rhiza Labs FluTracker Forum

The place to discuss the flu
It is currently Wed Jun 19, 2013 9:12 pm

All times are UTC - 5 hours [ DST ]




Post new topic Reply to topic  [ 91 posts ]  Go to page Previous  1, 2, 3, 4, 5 ... 10  Next
Author Message
PostPosted: Thu Jan 06, 2011 7:45 pm 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 28249
Location: Pittsburgh, PA USA
stephensons wrote:
niman wrote:
niman wrote:
The phyogenic tree has 41 HA sequences from recent cases in the UK including the 4 sets released at GISAID from August through November. The three sequences without S188T were from fatal cases. However, the sequences from the other 37 cases, most of which were from December, have not been made public.

Of the 21 sequences with S188T, 4 were from fatal cases and four more were from severe cases, including two IDENTICAL sequences with D225G, which is appended onto the S188T genetic background.


Just had a look at the phylogenetic tree. Correct me if I'm wrong we have 2 cases of D225G (coded D222G) and are they transmitting, like Ukraine in 2009?

You are correct. The two sequences are IDENTICAL and both cases are SEVERE.

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Thu Jan 06, 2011 7:51 pm 
Offline

Joined: Fri Jan 08, 2010 3:22 pm
Posts: 5180
Location: East of London
Quote:
Just had a look at the phylogenetic tree. Correct me if I'm wrong we have 2 cases of D225G (coded D222G) and are they transmitting, like Ukraine in 2009


Quote:
You are correct. The two sequences are IDENTICAL and both cases are SEVERE


Ty.

_________________
Praemonitus, Praemunitus..Forewarned is Forearmed.


Top
 Profile  
 
PostPosted: Thu Jan 06, 2011 8:00 pm 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 28249
Location: Pittsburgh, PA USA
Commentary

http://www.recombinomics.com/News/01061 ... Clade.html

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Thu Jan 06, 2011 9:33 pm 
Offline

Joined: Wed Oct 07, 2009 5:01 am
Posts: 15
Location: USA
stephensons wrote:
Quote:
Just had a look at the phylogenetic tree. Correct me if I'm wrong we have 2 cases of D225G (coded D222G) and are they transmitting, like Ukraine in 2009


Quote:
You are correct. The two sequences are IDENTICAL and both cases are SEVERE


Ty.


The patterning on the two separate emergent sub-clades from the Southern Hemisphere is quite evident.

_________________
http://genewurx.com/
Independent Primary Research on Viral Genetics and the
Host-Pathogen Immune Dynamics of Zoonotic Influenza Reservoirs


Top
 Profile  
 
PostPosted: Thu Jan 06, 2011 10:01 pm 
Offline

Joined: Wed Oct 07, 2009 5:01 am
Posts: 15
Location: USA
stephensons wrote:
Quote:
Just had a look at the phylogenetic tree. Correct me if I'm wrong we have 2 cases of D225G (coded D222G) and are they transmitting, like Ukraine in 2009


Quote:
You are correct. The two sequences are IDENTICAL and both cases are SEVERE


Ty.


Notice that the branch polymorphisms are not labeled from that point upwardly. The numbering system employed in our analyses adds 3 to the amino acid positions indicated in the UK chart.

The accumulation of 100N, 188T, 377K, 225G and 454N patterns onto the OzBrisbane209_51F_2010_08_09 sequence from the late winter in the Southern Hemisphere. Though parameters are adjustable for the phylogenetic chart, the top section may indicate one or more additional branches past the suspected 225G joint.

Are these strictly indicative of the high variability head and tail changes being seen frequently (under aa100, over aa499)?

GeneWurx_UK_December_Emerging_Genetics_v3.xls

Is it probable that no instance of change at any amino acid position from 156 to 159 has been elucidated from this wide inspection of the severe wave?

Second sub-clade:

By chart appearances, the accumulation of 128D onto the more established backgrounds with 100N and 377K (lower section) creates a fatality risk similar to more recognised severity markers. The bottom fatal sequence designated on the lower branch as A/England/4780352/2010 is identified as UKWhiteChapel4780352_5M_2010_10_26_f in v3 of the GeneWurx Emerging Genetics spreadsheet within column AY and carries three additional silent (synonymous) changes at syn58C, syn131S and syn210S.

_________________
http://genewurx.com/
Independent Primary Research on Viral Genetics and the
Host-Pathogen Immune Dynamics of Zoonotic Influenza Reservoirs


Top
 Profile  
 
PostPosted: Thu Jan 06, 2011 10:23 pm 
Offline

Joined: Wed Oct 07, 2009 5:01 am
Posts: 15
Location: USA
All four of the earlier released sequences that had no clinical outcomes at initial release are noted as fatal on this chart if we are reading correctly.

The four cases are each genetically divergent.

Three share the common 377K. No individual change appears on all four fatal sequences. In fact, no two of the four share any other polymorphism than the three sharing 377K.

_________________
http://genewurx.com/
Independent Primary Research on Viral Genetics and the
Host-Pathogen Immune Dynamics of Zoonotic Influenza Reservoirs


Top
 Profile  
 
PostPosted: Thu Jan 06, 2011 10:41 pm 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 28249
Location: Pittsburgh, PA USA
Commentary

http://www.recombinomics.com/News/01071 ... ecomb.html

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Thu Jan 06, 2011 10:54 pm 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 28249
Location: Pittsburgh, PA USA
NS1 wrote:
All four of the earlier released sequences that had no clinical outcomes at initial release are noted as fatal on this chart if we are reading correctly.

The four cases are each genetically divergent.

Three share the common 377K. No individual change appears on all four fatal sequences. In fact, no two of the four share any other polymorphism than the three sharing 377K.

3 out of 4 were fatal. They were early and representative. Now S188T is dominant.

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Fri Jan 07, 2011 12:33 am 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 28249
Location: Pittsburgh, PA USA
S188T is a receptor binding domain change that was in 22 of the 41 sequences from the UK. However, a second receptor binding domain change S186P was present in 14 more of the sequences. Thus, as was seen in seasonal H1N1, changes flanking position 190 are driving the newly emerging sequences.

S186P pedigree
EPI295396 A/SAGA/90/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI295385 A/SAGA/85/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI295384 A/CHIBA/23/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI294682 A/England/118/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI294040 A/NAGANO/2181/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI294029 A/YOKOHAMA/84/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI288179 A/Belgorod/RII4/2009 (A/H1N1) segment 4 (HA) 27.0 5.73352
EPI286652 A/Stockholm/5/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI284314 A/Myanmar/M536/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280326 A/Wisconsin/08/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280286 A/Florida/13/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279208 A/CANBERRA/8/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279016 A/GOROKA/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278875 A/India/007/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278516 A/Ukraine/122/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278514 A/Ukraine/123/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI277042 A/Singapore/478/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI273897 A/India/3725/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272842 A/Qingdao/492/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272392 A/CHIBA-C/22/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272008 A/WELLINGTON/1/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI269839 A/turkey/Ontario/FAV114-17/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI269838 A/turkey/Ontario/FAV117-1C/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI259196 A/swine/NC/19646/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257748 A/Jiangxi-Donghu/SWL1172/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256035 A/Thessaloniki/791/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI252354 A/Ontario/25913/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI246200 A/swine/IL/5265-2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI246197 A/swine/IL/5265-1/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI244053 A/swine/Illinois/02957/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI244041 A/KYOTO/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI238359 A/Chernihiv/857/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI237302 A/California/VRDL7/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI230786 A/Ankara/17/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI230497 A/swine/4/Mexico/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI217181 A/Tennessee/17/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI215819 A/DARWIN/2126/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI210034 A/FUKUOKA-C/2/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI252306 A/Ontario/10016/2009 (A/H1N1 swl) segment 4 (HA) 51.0 0.00000
EPI226552 A/YOKOHAMA/1311/2009 (A/H1N1 swl) segment 4 (HA) 51.0 0.00000
EPI244054 A/swine/Illinois/02960/2010 (A/H1N1 swl) segment 4 (HA) 49.1 0.00000

_________________
www.twitter.com/hniman


Top
 Profile  
 
PostPosted: Fri Jan 07, 2011 12:38 am 
Offline

Joined: Fri Sep 11, 2009 8:30 am
Posts: 687
niman wrote:
S188T is a receptor binding domain change that was in 22 of the 41 sequences from the UK. However, a second receptor binding domain change S186P was present in 14 more of the sequences. Thus, as was seen in seasonal H1N1, changes flanking position 190 are driving the newly emerging sequences.

S186P pedigree
EPI295396 A/SAGA/90/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI295385 A/SAGA/85/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI295384 A/CHIBA/23/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI294682 A/England/118/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI294040 A/NAGANO/2181/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI294029 A/YOKOHAMA/84/2010 (A/H1N1 swl) segment 4 (HA) 27.0 5.73352
EPI288179 A/Belgorod/RII4/2009 (A/H1N1) segment 4 (HA) 27.0 5.73352
EPI286652 A/Stockholm/5/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI284314 A/Myanmar/M536/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280326 A/Wisconsin/08/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280286 A/Florida/13/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279208 A/CANBERRA/8/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279016 A/GOROKA/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278875 A/India/007/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278516 A/Ukraine/122/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278514 A/Ukraine/123/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI277042 A/Singapore/478/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI273897 A/India/3725/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272842 A/Qingdao/492/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272392 A/CHIBA-C/22/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272008 A/WELLINGTON/1/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI269839 A/turkey/Ontario/FAV114-17/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI269838 A/turkey/Ontario/FAV117-1C/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI259196 A/swine/NC/19646/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257748 A/Jiangxi-Donghu/SWL1172/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI256035 A/Thessaloniki/791/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI252354 A/Ontario/25913/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI246200 A/swine/IL/5265-2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI246197 A/swine/IL/5265-1/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI244053 A/swine/Illinois/02957/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI244041 A/KYOTO/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI238359 A/Chernihiv/857/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI237302 A/California/VRDL7/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI230786 A/Ankara/17/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI230497 A/swine/4/Mexico/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI217181 A/Tennessee/17/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI215819 A/DARWIN/2126/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI210034 A/FUKUOKA-C/2/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI252306 A/Ontario/10016/2009 (A/H1N1 swl) segment 4 (HA) 51.0 0.00000
EPI226552 A/YOKOHAMA/1311/2009 (A/H1N1 swl) segment 4 (HA) 51.0 0.00000
EPI244054 A/swine/Illinois/02960/2010 (A/H1N1 swl) segment 4 (HA) 49.1 0.00000




And some of us know what this means if you go by historical data.


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 91 posts ]  Go to page Previous  1, 2, 3, 4, 5 ... 10  Next

All times are UTC - 5 hours [ DST ]


Who is online

Users browsing this forum: niman and 51 guests


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
Powered by phpBB® Forum Software © phpBB Group