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A/Hong Kong/2369/2009(H1N1) - H274Y

C

Cyril

Active member
Hope this hasn't been posted already but I check the h1n1 outbreak sequences regularly and found that A/Hong Kong/2369/2009(H1N1) is tagged as having the H274Y polymorphism that "might confer tamiflu resistance".

Has someone checked this?

It seems like a rather common h1n1 sequence otherwise (checked NA & HA).
 
Re: A/Hong Kong/2369/2009(H1N1) - H274Y

Ok silly question - of course someone did check, my bad.
Thanks for the link.
 
Re: A/Hong Kong/2369/2009(H1N1) - H274Y

I have mapped the polymorphisms for this strains in the h1n1 sequences - I believe it's more appropriate in this thread.

I used NewYork/06 as an (arbitrary) consensus sequence.

I included each sequence that shares at least one SNP with HK/2369 that is not "widespread" (ie. that doesn't have more than 6 individuals in my bank).


Code: 
                               HA                                NA
                               006 220 229 239 240 314 391 470   106 158 248 275 291
consensus                      GTA ACA CCG GAT CAA CCG GAG TTA   ATA CTA GAT CAC GTG
marker (Syn, Widespread)       S    W  SW              SW  SW     W  S    W      S
-------------------------------------------------------------------------------------
A/Hong Kong/2369/2009(H1N1)    GTG         GAA     TCG                       TAC GTA
A/New Jersey/01/2009(H1N1)                 GAA                                   GTA
A/Paris/2591/2009(H1N1)            TCA     GAA                       TTA
A/Oklahoma/03/2009(H1N1)           TCA CCT             GAA CTA   GTA     AAT     GTA
A/Finland/553/2009(H1N1)       GTG             CGA
                                                x3


Of the five HK/2369 specific markers, three can be found in other sequences whose correspondence cannot be explained by direct lineage.


I then expanded Finland/553 in a similar fashion to unroll its (non-widespread) 240CGA SNP :

Code: 
                               HA                                            NA
                               006 073 169 220 229 239 240 314 391 470 565   106 158 248 275 291
consensus                      GTA AAC GTT ACA CCG GAT CAA CCG GAG TTA TGT   ATA CTA GAT CAC GTG
marker (Syn, Widespread)       S   S   S    W  SW              SW  SW  S      W  S    W      S
-------------------------------------------------------------------------------------------------
A/Hong Kong/2369/2009(H1N1)    GTG                 GAA     TCG                           TAC GTA
A/New Jersey/01/2009(H1N1)                     GAA                                       GTA
A/Paris/2591/2009(H1N1)                    TCA     GAA                           TTA
A/Oklahoma/03/2009(H1N1)                   TCA CCT             GAA CTA       GTA     AAT     GTA
A/Finland/553/2009(H1N1)       GTG                     CGA
A/Mexico/InDRE4487/2009(H1N1)              TCA         CGA         CTA       GTA     AAT
A/Texas/17/2009(H1N1)              AAT GTC TCA         CGA         CTA TGC   GTA     AAT
A/Texas/37/2009(H1N1)              AAT GTC TCA                     CTA TGC   GTA     AAT

This SNP (240CGA) appears in three individuals on which the marker presence cannot be explained by simple direct lineage.

I have 391 individuals in my bank for HA and 367 for NA (I only use sequences with full coding regions).

Whatever the reason - codon bias, recombination...; something not random is going on here - or it's some very low-entropy kind of random. :)
 
Re: A/Hong Kong/2369/2009(H1N1) - H274Y

Cyril said:
I have mapped the polymorphisms for this strains in the h1n1 sequences - I believe it's more appropriate in this thread.

I used NewYork/06 as an (arbitrary) consensus sequence.

I included each sequence that shares at least one SNP with HK/2369 that is not "widespread" (ie. that doesn't have more than 6 individuals in my bank).


Code: 
                               HA                                NA
                               006 220 229 239 240 314 391 470   106 158 248 275 291
consensus                      GTA ACA CCG GAT CAA CCG GAG TTA   ATA CTA GAT CAC GTG
marker (Syn, Widespread)       S    W  SW              SW  SW     W  S    W      S
-------------------------------------------------------------------------------------
A/Hong Kong/2369/2009(H1N1)    GTG         GAA     TCG                       TAC GTA
A/New Jersey/01/2009(H1N1)                 GAA                                   GTA
A/Paris/2591/2009(H1N1)            TCA     GAA                       TTA
A/Oklahoma/03/2009(H1N1)           TCA CCT             GAA CTA   GTA     AAT     GTA
A/Finland/553/2009(H1N1)       GTG             CGA
                                                x3


Of the five HK/2369 specific markers, three can be found in other sequences whose correspondence cannot be explained by direct lineage.


I then expanded Finland/553 in a similar fashion to unroll its (non-widespread) 240CGA SNP :

Code: 
                               HA                                            NA
                               006 073 169 220 229 239 240 314 391 470 565   106 158 248 275 291
consensus                      GTA AAC GTT ACA CCG GAT CAA CCG GAG TTA TGT   ATA CTA GAT CAC GTG
marker (Syn, Widespread)       S   S   S    W  SW              SW  SW  S      W  S    W      S
-------------------------------------------------------------------------------------------------
A/Hong Kong/2369/2009(H1N1)    GTG                 GAA     TCG                           TAC GTA
A/New Jersey/01/2009(H1N1)                     GAA                                       GTA
A/Paris/2591/2009(H1N1)                    TCA     GAA                           TTA
A/Oklahoma/03/2009(H1N1)                   TCA CCT             GAA CTA       GTA     AAT     GTA
A/Finland/553/2009(H1N1)       GTG                     CGA
A/Mexico/InDRE4487/2009(H1N1)              TCA         CGA         CTA       GTA     AAT
A/Texas/17/2009(H1N1)              AAT GTC TCA         CGA         CTA TGC   GTA     AAT
A/Texas/37/2009(H1N1)              AAT GTC TCA                     CTA TGC   GTA     AAT

This SNP (240CGA) appears in three individuals on which the marker presence cannot be explained by simple direct lineage.

I have 391 individuals in my bank for HA and 367 for NA (I only use sequences with full coding regions).

Whatever the reason - codon bias, recombination...; something not random is going on here - or it's some very low-entropy kind of random. :)
Click to expand...
It is recombination between closely related sequences, which happens at a VERY high frequency (no codon bias required)
 
Re: A/Hong Kong/2369/2009(H1N1) - H274Y

Actually we had a talk about this in this thread :
http://www.flutrackers.com/forum/showthread.php?t=111885&page=2
(thank you again for your explanations, btw).

I'm a programmer with an interest in evolutionary programming techniques and I took the opportunity of studying a live model with the h1n1 sequences.

It quickly became apparent that there wouldn't be a clear-cut way of mapping lineages at the nucleotides level of details because of such SNPs that appear in different backgrounds - and are quite common.

Recombination was my guess (and I'm glad it turned out not to be stupid after all) but I don't have the necessary background to go further or make an assertion - it's just my observation as a computer scientist.
 
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