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A/Shanghai/71T/2009 acquired E627K

Re: A/Shanghai/71T/2009 acquired E627K

gsgs said:
so maybe a reassorted strain with E627K is circulating in NY
many hospitalizations and deaths recently in NY, although
the level of ILI is almost back to normal
Click to expand...

And the New York epidemic is winding down.., ;)

But, the issues does sound like a recombinatin event to me rather than a reassortment.

Is there an exact match in some strain for the PB2 gene in this isolate from Shanghai?
 
Re: A/Shanghai/71T/2009 acquired E627K

Blue said:
She wore a mask on the plane. Maybe not an N95...
Hard to eat or drink with a mask on. It's a long flight from NYC to China.
Click to expand...

Might need a gallon of Purell on a long flight like that to not involve fomites somewhere along the way.
 
Re: A/Shanghai/71T/2009 acquired E627K

Auburn Boy said:
It's been a while, and my memory fails me..,

Which changes do we recognize as being possible contributors to human versus avian sialic acid recptors at the bindimg domain region?

Thanks.
Click to expand...

Primarily E190D and G225D in the HA segment. Swine Flu has had both from the get go.
 
Re: A/Shanghai/71T/2009 acquired E627K

I took a little look at the HA of a few SE Asian samples. Look at the differences in position 220 - part of the RBD, or that is, behind the pocket per article referencing a change in that area.

Code: 
Positions from 181 till 240
 Consensus sequence   S Y I N D K G K E V L V L W G I H H P S T S A D Q Q S L Y Q N A D A Y V F V G S S R Y S K K F K P E I A I R P K V R D Q 
ACR54974  A/Shanghai/1/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . . . . . 
ACR83538  A/Guangdong/03/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . . . . . 
ACR54045  A/Guangdong/05/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . . . . . 
ACS45017  A/Nanjing/1/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . K . . . . . . . . . . . . . . . . . . 
ACR18920  A/Hong Kong/01/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
ACR46991  A/Osaka/1/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
ACR78154  A/Philippines/2009/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . . . . . 
ACQ84451  A/Korea/01/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
ACR24230  A/Nonthaburi/104/2009(H1N1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

In the actual alignment all the "T"s actually align under position 220.

Might this be part of the explanation for virulence differences?

.
 
Last edited:
Re: A/Shanghai/71T/2009 acquired E627K

AlaskaDenise said:
I took a little look at the HA of a few SE Asian samples. Look at the differences in position 220 - part of the RBD, or that is, behind the pocket per article referencing a change in that area.



In the actual alignment all the "T"s actually align under position 220.

Might this be part of the explanation for virulence differences?

.
Click to expand...

Your alignment of the sequences may be a bit off. The "T's" are usually associated with the S206T mutation thata separates CDC's variant "iv" from the other four variants. Are these all lined up properly?
 
Re: A/Shanghai/71T/2009 acquired E627K

Mamabird said:
Your alignment of the sequences may be a bit off. The "T's" are usually associated with the S206T mutation thata separates CDC's variant "iv" from the other four variants. Are these all lined up properly?
Click to expand...

Not here - I can't get a true copy from the NCBI alignment program.

On the program output, starting below the label 220, they line up as this:

220... ------(location)
SSRYSK-----(censensus)
T.....
T.....
T.....
..K...
......
......
T.....
......
......

Hope this goes through okay.

.
 
Re: A/Shanghai/71T/2009 acquired E627K

AlaskaDenise said:
Not here - I can't get a true copy from the NCBI alignment program.

On the program output, starting below the label 220, they line up as this:

220... ------(location)
SSRYSK-----(censensus)
T.....
T.....
T.....
..K...
......
......
T.....
......
......

Hope this goes through okay.

.
Click to expand...

Yea, that's better. The "T's" represent CDC's variant "iv", complements of New York.
 
Re: A/Shanghai/71T/2009 acquired E627K

gsgs said:
the virus is the Cancun-strain, but it misses 2 of the 11 Cancun markers (C1408T(4),A742G(6)),
the same as Korea/1 and the Japan viruses.
However those have not the other 6 Cancun markers which 71T has.

That could indicate reassortment ?!? 123578 from Cancun,
46 from Japan/Korea
Click to expand...

I made a mistake, Korea/1 nd Japan match in NA, but not in HA,
the 2 mutations there are reversed.
In fact 71T has a new, unique combination of markers in HA.
That makes the reassortment claim less likely, only the
marker in NA would indicate this
 
Re: A/Shanghai/71T/2009 acquired E627K

93 PB2s from New York at genbank, but none since 4.May !

Latest PB2 from the New York / Cancun strain is Guangdong/05 from 29.May
Maybe we'll get Moscow/03 from 4.June
 
Re: A/Shanghai/71T/2009 acquired E627K

Has anyone seen any MSM stories on this sequence & the implications?

Perhaps, they're waiting to see if there are more similar cases.

.
 
Re: A/Shanghai/71T/2009 acquired E627K

AlaskaDenise said:
Has anyone seen any MSM stories on this sequence & the implications?

Perhaps, they're waiting to see if there are more similar cases.

.
Click to expand...

I'd be shocked and thrilled if reporters had any clue what this means. They will wait until some scientist connects the dots in some scientific paper or announcement by CDC or a similar body.
 
Re: A/Shanghai/71T/2009 acquired E627K

AlaskaDenise said:
Has anyone seen any MSM stories on this sequence & the implications?

Perhaps, they're waiting to see if there are more similar cases.

.
Click to expand...

I haven't seen anything in our papers. Chinaview ran this article on Tuesday and there was a Tweet on it by one of the EU guys.

http://news.xinhuanet.com/english/2009-06/17/content_11555550.htm
[snips]
BEIJING, June 17 (Xinhua) -- China's top epidemiologist said Tuesday that the country is closely monitoring any possible new mutation of the A/H1N1 flu virus.

"We are well prepared for the battle against any possible new mutation of the flu virus," said Zeng Guang, chief epidemiologist of the Chinese Center for Disease Control and Prevention, on the sideline of a seminar in Beijing.

He said there is no need to panic. "Although the mutant A/H1N1 virus newly discovered by Japanese scientists reported higher chances of infection, there is no significant change in its nature compared with the original, because its fatality rate remains the same," Zeng said.

"I believe that the major concern for the countries affected by the spreading flu will possibly be virus mutation."

"There is no need to panic. With what we have done, I do not think the current flu epidemic will be as horrible as the one in 1918, which claimed around 40 million lives around the globe," he said. (I hope he's right!)
 
Re: A/Shanghai/71T/2009 acquired E627K

>> but circumstances and details remain secret.
> Only to those who don't look.

> Please:
> Isolate properties
> ...

so, where did you get that ? It's not in the genbank record, nor can it be found
with google. Will you tell us ??? (or someone else, who did look)

I looked and found some info about the case in the newspapers, see below.
 
Re: A/Shanghai/71T/2009 acquired E627K

mixin said:
I haven't seen anything in our papers. Chinaview ran this article on Tuesday and there was a Tweet on it by one of the EU guys.

http://news.xinhuanet.com/english/2009-06/17/content_11555550.htm
[snips]
BEIJING, June 17 (Xinhua) -- China's top epidemiologist said Tuesday that the country is closely monitoring any possible new mutation of the A/H1N1 flu virus.

"We are well prepared for the battle against any possible new mutation of the flu virus," said Zeng Guang, chief epidemiologist of the Chinese Center for Disease Control and Prevention, on the sideline of a seminar in Beijing.

He said there is no need to panic. "Although the mutant A/H1N1 virus newly discovered by Japanese scientists reported higher chances of infection, there is no significant change in its nature compared with the original, because its fatality rate remains the same," Zeng said.

"I believe that the major concern for the countries affected by the spreading flu will possibly be virus mutation."

"There is no need to panic. With what we have done, I do not think the current flu epidemic will be as horrible as the one in 1918, which claimed around 40 million lives around the globe," he said. (I hope he's right!)
Click to expand...
The above story is not about E627K.
 
Re: A/Shanghai/71T/2009 acquired E627K

he must have been aware of the E627K mutation when he said this
 
Re: A/Shanghai/71T/2009 acquired E627K

niman said:
The above story is not about E627K.
Click to expand...
Well, I wasn't sure but when it mentioned "newly discovered", I thought it might be. The sequence has been around long enough that someone over there would have likely noticed the mutation.
 
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