A/Shanghai/60T/2009(H1N1) released 6/22

[HenryN]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

Well, I understand this. Obviously a silent mutation has a greater chance for survival than a random change in phenotype.

Still, it's a funny one, and problem is I've encountered many such oddities while going into the details. It seems a bit odd that two closely related strains would develop the very same mutation independently, while it is silent and doesn't confer any benefit/selective advantage. Moreover those two strains (tx/15 and south carolina) hasn't diverged so much as to make the occurrence of having the same random mutation happen concurrently likely - but it's not impossile either.

I'll look for some more.

They are easy to find. You can fine one here

http://precedings.nature.com/documents/459/version/4

Briefly it is a synonymous change (no obvious selection) on NA of H5N1 in Egypt. In 2006 a clade 2.2 polymorphism G743A (transition at third base position) was almost exclusively found in closely related sequences in southern Germany, Switzerland and France.

In early 2007 it appear on two distinct sequences in Egypt. Same location and same time. One of the isolates, which was a clear mixture was cloned. Over 40 isolates were sequenced and the mixture was in a 3:1 ratio and were easily distinguished (polymorphisms at 11 NA positions) - also had 22 differences in HA. Thus, the sequences were oviously different, but both acquired G743A at the same time (it was on all clones). In the next few weeks, the same change appeared on two more Egyptian backgrounds (in all cases earlier sequences without G743A were identified). Moreover, the same change was on clade 2.2.3 in Moscow and a very different clade 2.2.3 in Kuwait. Moreover, in addition to the sequences in Ghana, there were distinct sequences in Nigeria. In all cases, closley related sequences from 2006 were available, which did not have G743A.

Thus, the same polymorphism was appended onto something like 10 different clade 2.2 H5N1 genetic backgrounds in early 2007, which was obviously NOT a coincidence.

[gsgs]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

...the airplane strain

[Mamabird]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

More coincidences!!!!

What I do not think is a coincidence is a set of related isolates within the consensus group, including SC/09. The following have unique mutations in the three polymerase genes. The simultaneous mutations are:

PB2 E677G
PB1 K353R
PA D3G

The isolates that share these mutations are:

SC/09 collected 4/26
NY/3177
NY/3181 collected 4/28
Eng/195 4/28
Paris/2580 4/30
Paris/2592 5/01

Quite a travel log, I'd say.

[gsgs]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

if it (E627K etc.) is(was) a mixture, then they should(would) post both variants
or use these additional letters at those positions

we would be interested, how they achieved it, how well it grew
(but they won't tell us...)

[gsgs]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

Cyril, make a statistic how often this
happens and compare with what is expected ! (will you...)

Maybe I did it before (years ago), I don't remember

Another thing that I'm still uncomfortable with is, how much
selection pressure is there on synonymous mutations ?
(A-G,C-T at position 3 in a codon)
Clearly less than for other mutations.
But not zero either.

[HenryN]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

that's good news, isn't it ?

How did it happen ? While they grew the virus in the lab ?

They likely have a mixture and are repalcing the variant with wild type. H1N1 really doesn't care what is at Genbank or GISAID.

[gsgs]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

that's good news, isn't it ?

How did it happen ? While they grew the virus in the lab ?

[Cyril]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

OK, I localized your mutations in PB2 (segment 1).
I think it's a coincidence that South Carolina/09 developed the same
mutation. There are not so many mutations available (13000 in total,
but some are much preferred, e.g. 3rd position A-G,C-T, so basically
~5000)
There are also biological constraints which favour some mutations over others

Well, I understand this. Obviously a silent mutation has a greater chance for survival than a random change in phenotype.

Still, it's a funny one, and problem is I've encountered many such oddities while going into the details. It seems a bit odd that two closely related strains would develop the very same mutation independently, while it is silent and doesn't confer any benefit/selective advantage. Moreover those two strains (tx/15 and south carolina) hasn't diverged so much as to make the occurrence of having the same random mutation happen concurrently likely - but it's not impossile either.

I'll look for some more.

[Mamabird]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

Speaking of PB2 and coincidences, China has switched E627K back to wildtype!

It is still E627K at GISAID, but 4 of the 5 polymorphisms on PB2 have been switch to wild type at Genbank. Several other genes were also switch. I suspect there is a mixture and they found a wild type clone (sounds a lot like Hong Kong and their recombinant H5N1 isolates) and now are replacing the novel sequence with a much more generic sequence.

China deposited TWO PB2 sequences at GISAID last week, and both had (and at least one, if not both STILL have, E627K).

GISAID has two 71T isolates from Shanghai. The original passage still has E627K in PB2, while the C2 passage does not. The C1 passage that was in GISAID previously apparently has been removed.

[HenryN]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

OK, I localized your mutations in PB2 (segment 1).
I think it's a coincidence that South Carolina/09 developed the same
mutation. There are not so many mutations available (13000 in total,
but some are much preferred, e.g. 3rd position A-G,C-T, so basically
~5000)
There are also biological constraints which favour some mutations over others

Speaking of PB2 and coincidences, China has switched E627K back to wildtype!

It is still E627K at GISAID, but 4 of the 5 polymorphisms on PB2 have been switch to wild type at Genbank. Several other genes were also switch. I suspect there is a mixture and they found a wild type clone (sounds a lot like Hong Kong and their recombinant H5N1 isolates) and now are replacing the novel sequence with a much more generic sequence.

China deposited TWO PB2 sequences at GISAID last week, and both had (and at least one, if not both STILL have, E627K).

[HenryN]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

OK, I localized your mutations in PB2 (segment 1).
I think it's a coincidence that South Carolina/09 developed the same
mutation. There are not so many mutations available (13000 in total,
but some are much preferred, e.g. 3rd position A-G,C-T, so basically
~5000)
There are also biological constraints which favour some mutations over others

More coincidences!!!!

[gsgs]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

OK, I localized your mutations in PB2 (segment 1).
I think it's a coincidence that South Carolina/09 developed the same
mutation. There are not so many mutations available (13000 in total,
but some are much preferred, e.g. 3rd position A-G,C-T, so basically
~5000)
There are also biological constraints which favour some mutations over others

[Mamabird]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

Well for instance Texas/15.
I was considering building lineages and thought every isolate would fall into place until I stumbled upon such cases.

Texas/15 shares 406CAG with isolates from nearby California (+one in NY). The three isolates from California (but not the one in NY) bear an additional marker (624GCC).

Texas/15 also shares 317TTA with South Carolina/09, which otherwise has itself the markers of a wildly distributed variant that spans America, Europe, China...

If it's not for recombination I can't explain why this latter mutation appears in both a member of a well-established lineage and this Texas/15 isolate that bears a marker from the California variant.

But again I don't pretend this is a correct explanation - it's basically the only explanation I could come up with myself. It might just show the limitation in my understanding.

Texas/15 is a consensus virus and genetically distint from the two variants that include the CA viruses. The earliest known source for TX/15 is Mex/4115.

[Cyril]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

Well for instance Texas/15.
I was considering building lineages and thought every isolate would fall into place until I stumbled upon such cases.

Texas/15 shares 406CAG with isolates from nearby California (+one in NY). The three isolates from California (but not the one in NY) bear an additional marker (624GCC).

Texas/15 also shares 317TTA with South Carolina/09, which otherwise has itself the markers of a wildly distributed variant that spans America, Europe, China...

If it's not for recombination I can't explain why this latter mutation appears in both a member of a well-established lineage and this Texas/15 isolate that bears a marker from the California variant.

But again I don't pretend this is a correct explanation - it's basically the only explanation I could come up with myself. It might just show the limitation in my understanding.

[gsgs]

Re: A/Shanghai/60T/2009(H1N1) released 6/22

> I've encountered some instances of segments that bear the
> markers of different, not immediately related lineages.
> Only explanation I could come up with (for what it's worth) is for
> them to be recombinant. I just don't know better - they only
> seem to defy logic otherwise.

give an example