Announcement

Collapse
No announcement yet.

China - H7N9 Human Isolates on Deposit at GISAID

Collapse
This is a sticky topic.
X
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • NS1
    replied
    Re: China - H7N9 Human Isolates on Deposit at GISAID

    Please review the attached preliminary GeneWurx overview of the H7N9 Emergent Human sequences filed Sunday at GISAID for details concerning Rare and Novel antigenic Hemagglutinin polymorphisms and the relationships suggested to the currently circulating human pH1N1.
    Attached Files
    Last edited by NS1; June 26, 2013, 11:17 PM. Reason: Detail revision Shanghai1;Citation augmentation;Add links; new version

    Leave a comment:


  • sharon sanders
    replied
    Re: China - H7N9 Human Isolates on Deposit at GISAID

    hat tip NS1 at Genewurx

    These H7N9 HA segments are unrelated genetically to the previous human H7N7 fatality:

    . . . . NetherlandsTeeffelen219_57M_2003_04_17_f (
    . . . . . . . . GISAID HA EPI234814
    . . . . . . . . GISAID Isolate EPI_ISL_67238

    The H7N9 human sequences under investigation do NOT show the H7N7 fatality polybasic extended cleavage area, 'aagaggaggaggaga'/'KRRRR'. The H7N9 human sequences demonstrate a typical H7N9 cleavage area.

    Nor do any of the H7N9 human sequences carry any of the HA amino polymorphisms found on the H7N7 Fatality (I13S, A143T, K416R). They each are unremarkable at those 3 amino acid positions.

    However, a significant quantity and positioning of HA variation from existing H7N9 avian sequences, including antigenic areas, do exist and will be reported after numbering pattern resolution.

    Administration Note:

    Until sample dates are received, we are logically imputing sample dates from the female as the onset date (known previous male deaths promote swabbing) and from the males as the date of death (post-mortem tissue). We are also imputing, until further data is released, that the Shanghai1 sequence represents the first death, 87M; ergo, Shanghai2 arises from the 27 year old male.

    ? AnhuiChuzhouCity1_E1_35F _2013_03_15_s onset 2013-03-15
    ? Shanghai2_E1_27M_2013_03_03_10_f onset 2013-02-19
    ? Shanghai1_E1_87M_2013_03_04_f onset 2013-02-19

    Leave a comment:


  • sharon sanders
    replied
    Re: China - H7N9 Human Isolates on Deposit at GISAID

    hat tip NS1 at Genewurx

    Initial GeneWurx Impressions

    This event is not unprecedented as to H7 classification. A higher interest will occur if the epidemiology demonstrates relationships among the human victims.

    Recall that H7 is the only other primarily Avian hosted HA classification outside of H5 that has human fatality confirmed?

    H7N7 Netherlands from Veterinarian Post-Mortem Lung Tissue

    . . . . NetherlandsTeeffelen219_57M_2003_04_17_f (
    . . . . . . . . GISAID HA EPI234814
    . . . . . . . . GISAID Isolate EPI_ISL_67238


    Also recall that human H7 infection is on record (Netherlands and UK) and that large groups of human poultry workers have fallen ill from H7N7, including during the initial Scherpenzeel outbreak. Eye infection is generally the presenting symptom.

    Avian H7N7 and H7N3 are widespread. H7N7, in particular, hosts significant and increasing homology to current pH1N1 genetic acquisition. We, at GeneWurx, consider H7N7 to be an important candidate as one of several zoonotic sub-segment donators to pH1N1.

    The H7N9 Anhui HA is listed as most similar to avian H7N3 (95%, 1617/1685nu) and H7N7 (95%, 1601/1682nu) according to current deposits / software at GISAID, an initial signal of moderate-to-low potential for reassortment. With no exact match, that potential reassortment obviously does not occur from any sample on record. The H7N9 Anhui NA GISAID BLAST-based evaluation shows homology to most HxN9 serotypes, again with no exact matches.

    Due to the inherent limitations of the software design, BLAST is generally inconclusive on these types of 'Ultimate Origin' matters unless an exact match is found in the database.
    Attached Files

    Leave a comment:


  • mixin
    replied
    Re: China - H7N9 Human Isolates on Deposit at GISAID

    First I need to say that I have no experience with reading H7N9 sequences and a disclaimer that I am not a sequencer, virologist, etc..

    When I aligned the HA amino acids, Anhui and Shanghai/2 are identical but Shanghai/1 has a number of differences. These sequences surprise me often; I would have thought the 2 from Shanghai would have been identical.

    I then decided to align the humans with some of the more recent birds and here is a list of the ones that have HAs:

    A/wild bird/Korea/A14/11 2011/02/01 EPI_ISL_120868 | AH7N9 | HA
    A/spot-billed duck/Korea/447/11 2011/04/01 EPI_ISL_120871 | AH7N9 | HA
    A/wild bird/Korea/A3/11 2011/02/01 EPI_ISL_120869 | AH7N9 | HA
    A/wild bird/Korea/A9/11 2011/02/01 EPI_ISL_120881 | AH7N9 | HA
    A/goose/Nebraska/17097-4/2011 2011/04/05 EPI_ISL_130360 | AH7N9 | HA
    A/guinea fowl/Nebraska/17096-1/2011 2011/04/05 EPI_ISL_130362 | AH7N9 | HA
    A/northern shoverl/Mississippi/11OS145/2011 2011/01/08 EPI_ISL_135036 | AH7N9 | HA
    A/Shanghai/1/2013 2013/01/01 EPI_ISL_138737 | AH7N9 | HA
    A/Shanghai/2/2013 2013/01/01 EPI_ISL_138738 | AH7N9 | HA
    A/Anhui/1/2013 2013/01/01 EPI_ISL_138739 | AH7N9 | H

    In the HA nucleotides, we clearly have 3 separate groups; the Asian birds, the US birds and the humans.

    I see the humans have S31N in the amino acid M2 gene.

    I'm sorry I'm lacking the ability to see any reassortment. Maybe JJackson will come along and take a look.

    Leave a comment:


  • sharon sanders
    started a topic China - H7N9 Human Isolates on Deposit at GISAID

    China - H7N9 Human Isolates on Deposit at GISAID

    hat tip Mixin


    A/Anhui/1/2013
    EPI_ISL_138739
    Submitted by WHO Chinese National Influenza Center

    A/Shanghai/2/2013
    EPI_ISL_138738
    Submitted by WHO Chinese National Influenza Center

    A/Shanghai/1/2013
    EPI_ISL_138737
    Submitted by WHO Chinese National Influenza Center


    We would like to remind our posters that GISAID does not allow any public posting of any information about data from their database.



    FluTrackers News and Data thread on this subject:

    China - Three confirmed cases of human infection with H7N9 avian influenza - Two fatalities
Working...
X