A/Shanghai/71T/2009 acquired E627K

[HenryN]

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

they isolate these sequences, upload to genbank, but give no
comments on the mutation, not even location,age, travel history,
how they grew it etc.

do I see a new strategy of secrecy here ?

sequences are being uploaded, even all 8 segments from China,
but circumstances and details remain secret.

Please:
Isolate properties



Resistance to adamantines
Unknown

Resistance to oseltamivir
Unknown

Resistance to other drugs
Unknown

Resistance to peramivir
Unknown

Resistance to zanamivir
Unknown

Swine influenza a (h1n1) virus isolated during human swine flu outbreak of 2009
Yes

Publicly accessible in DDBJ/EMBL/GenBank
No

Host properties




Clinical patient status
Recovered

Host age in years
22

Host gender (m, f)
F

Computed annotations




Protein name
M2


Numbering on the reference sequence
31


Sequence of the mutant at the specified location
N


Potential action of the mutation
Antiviral Resistance - Adamantanes


Name of the mutation
S31N



<HR>

Protein name
PB2


Numbering on the reference sequence
627


Sequence of the mutant at the specified location
K


Potential action of the mutation
Human Adaptation <IMG onmouseover='ddrivetip("The mutation potentially affects the host specificity => better adaptation to human","","200")' title="" onmouseout=hideddrivetip() alt=i src="images/icons/icon_info.png" width=12 height=12>


Name of the mutation
E627K



<HR>

Protein name
PB2


Numbering on the reference sequence
701


Sequence of the mutant at the specified location
N


Potential action of the mutation
Human Adaptation <IMG onmouseover='ddrivetip("The mutation potentially affects the host specificity => better adaptation to human","","200")' title="" onmouseout=hideddrivetip() alt=i src="images/icons/icon_info.png" width=12 height=12>


Name of the mutation
D701N

[HenryN]

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

they isolate these sequences, upload to genbank, but give no
comments on the mutation, not even location,age, travel history,
how they grew it etc.

do I see a new strategy of secrecy here ?

sequences are being uploaded, even all 8 segments from China,
but circumstances and details remain secret.

Only to those who don't look.

[mixin]

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

I tried looking at your links. Either my computer is screwy or your links are not working.

[gsgs]

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

http://images.google.com/imgres?imgurl=http://www.esrf.eu/UsersAndScience/Publications/Highlights/2007/SB/fig-71.jpg&imgrefurl=http://www.esrf.eu/UsersAndScience/Publications/Highlights/2007/SB/SB4&usg=__xSeJpyvM7nihRrbCDnq3dTn8rPQ=&h=380&w=464&sz=142&hl=en&start=1&tbnid=T5NeVqkm_OpFCM:&tbnh=105&tbnw=128&prev=/images&#37;3Fq%3Dimportin%2Bpb2%26gbv%3D2%26ndsp%3D20%26hl%3Den%26sa%3DN%26ie%3DUTF-8

> the mutation D701N, observed in some pathogenic strains of influenza including H5N1 infecting
> humans in Vietnam [2], may alter the energetics of this interaction.

http://www.nature.com/nsmb/journal/v14/n3/suppinfo/nsmb1212_S1.html

[HenryN]

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

I tried looking at your links. Either my computer is screwy or your links are not working.

If you are talking about the links in the commentary, you have a computer problem. I clicked on the first 5 and they all worked.

[HenryN]

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

the fact that we have possible reassortment and E627K
in the same virus together with the other 4 mutations
close to 627 in PB2 lets me assume that it's somehow
a lab error.
Or an immunodeficient patient.
Or extensive growth of viruses over several generations.

So many A-nucleotides
So many mutations in total, i.e. Shanghai/37T
Why the T in the name ?

we sometimes see such things with nearby mutations,
I tend to ignore them, they look like errors.


e.g. these Paris-isolates Paris/2590 , Paris/2592 ,...
1059,1062,1080,1317,1329,1330 in NA - what is it ?

Norway/1168,1177 156,159,162 in PB1

Italy/02 in NP

Mexico/47N in NA

Shanghai/37T in NA

Maybe they are NOT "random mutations"! As far as the Shanghai PB2 sequence is concerned, the virus was cloned and sequenced a second time. The sequence from the clone is exactly the same as the original.

While I agree the clustering may represent an "error", the error is NOT in the lab dong the sequencing.

[gsgs]

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

checking PB2s for positions
626,627,628, 677,678,679,680,681, 700,701,702,703,704, 721

PEQ EDPDE EDKRY K   ,3341
PKQ EDPDE EDRRY K   ,2748  - Brevig/1918 - H3N2,2007 - H1N1,2007
PKQ EDPDE EDKRY K   ,389  -  Qinghai(H5N1) - indreflu
PEQ EDPDE ENKRY K   ,156 - 
PEQ EDPDE EDRRY K   ,102
PVQ EDPDE EDKRY K   ,53
PEQ EDPEE EDKRY K   ,49
PEQ DDPDE EDKRY K   ,49
PEQ GDPDE EDKRY K   ,38
PEQ DDPDE EDRRY K   ,36
PEQ KDPDE EDKRY K   ,26
PEQ DDPNE EDRRY K   ,20
PEQ EDPNE EDKRY K   ,18
PKQ ENPNE ENKKY K   ,1   - Shanghai/71T

[AlaskaDenise]

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

Copied from another thread.....Toaster2 posted:

Does anyone know if the PB2 E627K in A/Shanghai/71T/2009 is an event only in a single patient isolate or are there already additional Hong Kong isolates published dating after this isolate (as I understand from about a week ago) that also have it (or that do not have it) ? I did notice a surge in Hong Kong cases - maybe they are related to PB2 E727K taking hold in the population.

.

[Mamabird]

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

As far as we know today, this is the only case. This one incident is based on a review of all the available PB2 sequences posted to both GenBank and GISAID.

As we have discussed on other threads, it would be nice to have some recent results from Australia, or for that matter entire genomes from any of the virus samples that they have been collected in that country. It would make monitoring a bit easier in an area that is really being hit hard with new Swine Flu infections.

[gsgs]

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

By Li Xinran | 2009-6-1 |

SHANGHAI yesterday confirmed its fifth case of swine flu - a 23-year-old female Chinese student from the United States.

The woman, who was studying at a US college, took CX0831 flight from New York to Hong Kong on Thursday and arrived at Pudong International Airport on flight KA870 later that night and was driven home by her family, Chen Qiwei, spokesman for city government, said.

She developed a fever at 5pm on Saturday and went to a branch of Shanghai No.1 People's Hospital in Songjiang District at about 8pm with family members.

She was quarantined at the hospital with a temperature of 38.2 degrees Celsius and reported to the Center for Disease Control and Prevention of Songjiang District.

A test yesterday by the Shanghai Center for Disease Control and Prevention was positive for the H1N1 virus.

The patient was then sent to the Shanghai Public Health Clinic Center, a designated hospital for swine flu cases, and confirmed to be the city's fifth case by experts there.

She is in a stable condition after treatment, Chen said.

She was reported to have worn a mask throughout her journey from the US and passed airport checks.

Eight family members and friends who were her close contacts will be under medical observation for a week. All are healthy and showing no symptoms.

The city's first case, a Chinese passenger from Melbourne, has recovered and discharged from hospital.

The other three patients are still in hospital but are all in a stable condition.

[AlaskaDenise]

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

.............She was reported to have worn a mask throughout her journey from the US and passed airport checks.............

The city's first case, a Chinese passenger from Melbourne, has recovered and discharged from hospital. ...............

Is it possible that the young lady caught the flu immediately after arrival in Shanghai? The PB2/627 mutation should increase infectivity.

Was the Melbourne passenger recently arrived from Melbourne? If so, as Mamabird says, Australian sequences may hold some important clues.

.

[HenryN]

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

they isolate these sequences, upload to genbank, but give no
comments on the mutation, not even location,age, travel history,
how they grew it etc.

do I see a new strategy of secrecy here ?

sequences are being uploaded, even all 8 segments from China,
but circumstances and details remain secret.

What we have here is a failure to communicate. As posted on the FluTracker map of H1N1 cases:

Report Date: 5/31/2009
Reported Location: Songjiang District, Shanghai, China
Confirmed Cases: 1

May 31, found a case of fever clinics, Shanghai imported confirmed cases of influenza type H1N1. At present, Shanghai imported a total of five cases of confirmed cases of influenza type H1N1. The patient was a woman, a Chinese national, 23 years old, attending a university in the United States. She was on May 28 by Long Island CX0831 flights to Hong Kong from the United States, after waiting 1 hour flight KA870 to Beijing by 23 o\'clock that night, arrived in Shanghai Pudong International Airport, takes a car to go home. Patients in at 5:00 p.m. on May 30 found that self-heating temperature, 20, the patients accompanied by family members takes a car to the south of Shanghai First People\'s Hospital out-patient hospital treatment of fever, body temperature measured 38.2 degrees Celsius. First People\'s Hospital, the patient was sent to out-patient observation room heat treatment to isolate and report Songjiang District Center for Disease Control and Prevention. Songjiang District, CDC received a report on epidemiological surveys carried out in patients with and nose throat swab samples collected for testing, results showed that alpha can not rule out the possibility of influenza H1N1. At 7 o\'clock on May 31, Songjiang District, Shanghai, CDC will send samples of the Center for Disease Control and Prevention for testing. Shanghai CDC received the sample immediately after the laboratory testing. 15:30, test results as follows: Type A H1N1 influenza virus nucleic acid positive. Shanghai Municipal Health Bureau, Shanghai CDC immediately epidemiological investigation, and patients with special negative pressure to the city hospitals ambulance Shanghai Public Health Clinical Center. At the same time, city-level expert group to conduct consultations organized in light of the clinical manifestations, epidemiological investigation and laboratory test results, found for the Type A H1N1 influenza cases confirmed cases. Patients after treatment and in stable condition. By epidemiological investigation, the patient by May 28 and CX0831 flight KA870 flight from the United States arrived in Shanghai via Hong Kong, both the whole flight with a mask, the Immigration and Quarantine did not find anything unusual in the family use their private vehicles to take home. The day before sick patients so far have been in close contact with the staff, their family members and friends of eight, the first People\'s Hospital medical staff 8. According to the Ministry of Health criteria of close contacts, with the exception of medical personnel to take protective measures have been in close contact with those who are not included, the patients were in close contact with eight of her relatives and friends, have accepted the focus on a week-long medical observation. Close contacts of patients with good health, no influenza-like symptoms. (Shanghai Municipal Health Bureau feeds)

[HenryN]

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

Map with all of the above

http://flutracker.rhizalabs.com/flu/gmap0906181402.html?lat=32.509761735919426&lon=118.740234375&zoom=6

[AlaskaDenise]

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

If she took her hour-long HK layover off the plane, it would be extremely difficult to trace her contacts there.

.

[Auburn Boy]

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

Once the Swine Flu virus has invaded and infected its human host, it seems to have little problem in replicating in both the lungs and the nose where the alpha 2,6 receptors are readily found. And remember, most of the isolates collected from humans are nasal swabs.

However, with the E627K change, the viral loads in the nose will likely be even higher than they are currently. So the virus will still replicate in both the lungs and nose, but with higher viral loads in the nose, the coughs and sneezes will spread more of the pathogen into the air for all of us to breath.

If you think that the current Swine Flu spreads rapidly, hide and watch what happens when E627K becomes predominant. No country has adequate medical facilities to handle the influz of patients that will unsue.

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.