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Tracking known mutations in H1N1 for dummies

Re: Tracking known mutations in H1N1 for dummies

Looks like what you see are differences in relation to other known sequences - so the shanghai sequence lists all other sequences as different at position 627.
 
Re: Tracking known mutations in H1N1 for dummies

looks nice, but I don't understand it yet...
 
Re: Tracking known mutations in H1N1 for dummies

OK, here is how it works. First you click on the link http://mammalia.gsc.riken.jp/swine_influenza/ . Then you scroll down until you get a list of H1N1 sequences. The listing on top shows wich proteins, the numbers are acession numbers in the database. If you click for example on the Latest PB2 sequence added (GQ283485) you get another window. If you go to the bottom right panel, you can scroll down and will see the differences between your PB2 sequence (the one you selected) and the others in the databse. Scroll down and you will see only one other sequence that differs from this one at position 627, GQ253501. This is the shanghai sequence. you can check that by going back to the sequence list and go to june 11 where you will see that the acession number matches with (A/Shanghai/71T/2009(H1N1)). The same thing can be done for other proteins, eg to track the Tamiflu resistance or the HA binding site mutations. The only thing you have to look out for is that you have a full length sequence that has the non mutated sequence as a start. I tried PB2 from a few old isolates (eg Guangdong GQ221691 )and there the Shanghai sequence does not pop up. I guessed that that is because not the entire PB2 was sequenced in the sequence that I used as start, however it seems to be a full length sequence. Maybe someone who has more knowledge can check what happened here ? You can check if the sequence is full length or partial at pubmed by clicking on the acession number : http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html

This is as far as I get with it.
 
Re: Tracking known mutations in H1N1 for dummies

PB2..........
 

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Re: Tracking known mutations in H1N1 for dummies

The 3D diagram does not highlight the different amino acids, so the pictures are the same.
 
Re: Tracking known mutations in H1N1 for dummies

Thanks so much Toaster!

I took Mamabird's list (#2) of important mutations that novel A/H1N1 is missing and used the Shanghai/71T sequence to see if it contained any of those mutations.

There were 2 of the mutations on her list.

NP/G16D was in Texas/15 and NP/L283P was in South Dakota/05.

So this sequence is slightly more humanized.

.
 
Re: Tracking known mutations in H1N1 for dummies

So this is what we are looking for

Temperature sensitivity to 33 C: Neuraminidase 274 H to Y AA substitution
NA H274Y (Riken numbering: H222Y)

NA sequence 271-280
PNYHYEECSCY
PNYYYEECSCY

Tamiflu resistance: PB2 627 E to K AA substitution
HA E627K (Riken numbering E627K)

HA sequence 625-635
PPEQSRMQFSS
PPKQSRMQFSS


Nice catch: the E627K in the Shanghai sequence has been changed back to E627, so probably a sequencing mistake. The mutation has not occurred-see comment to the sequence:



COMMENT [WARNING] On Jun 24, 2009 this sequence was replaced by
gi:241914528. GenBank Accession Numbers GQ253497-GQ253504 represent sequences from the 8 segments of Influenza A virus (A/Shanghai/71T/2009(H1N1)).
 
Last edited:
Re: Tracking known mutations in H1N1 for dummies

Toaster2 said:
So this is what we are looking for

Temperature sensitivity to 33 C: Neuraminidase 274 H to Y AA substitution
NA H274Y (Riken numbering: H222Y)

NA sequence 271-280
PNYHYEECSCY
PNYYYEECSCY

Tamiflu resistance: Haemagglutinin 627 E to K AA substitution
HA E627K (Riken numbering E627K)

HA sequence 625-635
PPEQSRMQFSS
PPKQSRMQFSS


Nice cath: the E627K in the Shanghai sequence has been changed back to E627, so probably a sequencing mistake. The mutation has not occurred-see comment to the sequence:



COMMENT [WARNING] On Jun 24, 2009 this sequence was replaced by
gi:241914528. GenBank Accession Numbers GQ253497-GQ253504 represent sequences from the 8 segments of Influenza A virus (A/Shanghai/71T/2009(H1N1)).
Click to expand...

One minor correction to the above. The E627K mutation relates to the PB2 segment, not HA.
 
Re: Tracking known mutations in H1N1 for dummies

Mamabird said:
One minor correction to the above. The E627K mutation relates to the PB2 segment, not HA.
Click to expand...

Thanks mamabird ! I corrected the post. I don't know how I made the mistake, probably been looking too much at HA mutations in H5N1 in the past :)
 
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