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  • gsgs
    replied
    Re: list of reassortment studies

    not really about reassortment, but related, since it deals with H7-viruses,
    even H7N9 ones, although from the American lineage.

    > Several high and low pathogenicity H7N3 and H7N9 viruses replicated
    > efficiently in the respiratory tract of mice without prior adaptation following
    > intranasal inoculation, but only MX/7218 virus caused lethal disease in this
    > species. H7N3 and H7N9 viruses were also detected in the mouse eye
    > following ocular inoculation. Virus from both H7N3 and H7N9 subtypes
    > replicated efficiently in the upper and lower respiratory tract of ferrets,
    > however, only MX/7218 virus infection caused clinical signs and symptoms
    > and was capable of transmission to naïve ferrets in a direct contact model.
    > Similar to other highly pathogenic H7 viruses, MX/7218 replicated to high
    > titers in human bronchial epithelial cells, yet downregulated numerous
    > genes related to NF-κB-mediated signaling transduction.

    --------------------------------------------------------------------------------------------
    In the context of recently emerged novel influenza strains through reassortment, avian influenza subtypes such as H5N1, H7N7, H7N2, H7N3 and H9N2 pose a constant threat in terms of their adaptation to the human host. Among these subtypes, it was recently ...

    we have quantitatively characterized the glycan receptor-binding specificity of HAs from representative
    strains of Eurasian (H7N7) and North American (H7N2) lineages that have caused human infection.
    Furthermore, we have demonstrated for the first time that two specific mutations; Gln226→Leu and
    Gly228→Ser in glycan receptor-binding site of H7 HA substantially increase its binding affinity to human
    receptor

    Introducing the double Gln226→Leu/Gly228→Ser mutations on FC (mFC:LS) and CC (mCC:LS) resulted in
    binding to both avian and human receptors
    The FC, CC and NY/107 strains were also previously analyzed for their ability to transmit in the ferret
    animal model NY/107 and the highly pathogenic CC strain showed some transmission via direct
    contact, however the other highly pathogenic strain isolated from fatal case did not show any transmission.
    None of the viruses transmitted via respiratory droplets.
    We previously demonstrated that the human receptor-binding specificity and affinity correlates with
    respiratory droplet transmissibility in ferrets.
    We demonstrated that the double Gln226→Leu/Gly228→Ser mutation (hallmark changes for
    human adaptation of H3 and H2 HA) dramatically increased human receptor-binding affinity
    of FC and CC HA
    (A/Netherlands/230/03 referred to henceforth as CC
    A/Netherlands/219/03 henceforth referred to as FC

    ------------------------------------------------------------

    copy of post 4 from the other thread:
    2 other papers about h9n2 evolution

    Samples of chicken, duck, quail, and pigeon were collected from Jiangsu, Anhui, and Hebei in 2009-2011, and sixteen H9N2 subtype isolates of avian influenza virus (AIV) were identified. The eight full-length genes of 16 AIV isolates were amplified by RT-PCR and sequenced. Genome sequence analysis sh …

    Samples of chicken, duck, quail, and pigeon were collected from Jiangsu, Anhui,
    and Hebei in 2009-2011
    amino acid motif of cleavage sites in the HA gene was P-S-R/K-S-S-R
    Leucine (L) at the amino acid position 226 in the HA
    AIVs originated from F98-like virus as backbone and formed two new genotypes through
    reassortment with HA gene of Y280-like virus and PB2 and M genes of G1-like virus

    ----------------------------------------------------------------------



    there is variable homology among the various NA subtype sequences, especially
    in the N1 and N2 subtypes with the deletion of 4~30 amino acids in the stalk domain [23,1993]
    Meanwhile, the factors that influence NA include deletion of the stalk domain,
    the mutations drug-resistance, as well as the changing of antigen sites or glycosites
    and the variation of the topology of N-glycan structures [28,2011].
    The pattern of stalk domain deletion in N2 NA is distinctive in different combinations of IVs.
    The representative NA sequences in each available N2 subtypes are aligned in the stalk domain.
    As can be observed, the number of deletions varies from 4 to 24 residues,
    causing the loss of one or two potential glycosites.
    9 NA subtypes are concentrated into two evolutionary groups: one group was represented by
    N2 and contains N3, N6, N7, and N9; and another group contains N1, N4, N5, and N8.

    deletion of 3 residues and one corresponding glycosite with the pattern “E-R-61N-3-64T-V-H”
    (meaning 3 residues missing between 61N and 64T, e.g., A/chicken/Zhejiang/611/2011 (H9N2)),
    appeared in most of the NA subtypes of the H9N2 virus.

    ---------------------------------------------------------------
    Last edited by gsgs; April 22, 2013, 01:31 AM. Reason: link to full paper now

    Leave a comment:


  • gsgs
    replied
    Re: list of reassortment studies

    Kimble et.al:
    In 2009, a novel H1N1 influenza (pH1N1) virus caused the first influenza pandemic in 40 y. The virus was identified as a triple reassortant between avian, swine, and human influenza viruses, highlighting the importance of reassortment in the generation ...

    Compatibility of H9N2 avian influenza surface genes and 2009 pandemic H1N1
    internal genes for transmission in the ferret model

    reassortant virus composed of wild-type avian H9N2 surface genes in a
    seasonal human H3N2 backbone could gain efficient respiratory droplet
    transmission in the ferret model.

    Experimentally, H9N2 surface genes reassorted with
    seasonalH3N2internalgeneshaveshownefficienttransmi ssionin
    a ferret model only after adaptation by serial passage and in-
    corporation of amino acid changes on the surface and internal
    genes (15)

    All four viruses were made with the pH1N1 internal
    genes (PB2, PB1, PA, NP, M, and NS) from A/Netherlands/602/
    2009 (H1N1) (20). The surface genes came from either A/guinea
    fowl/Hong Kong/WF10/1999 (H9N2) or from A/ferret/Mary-
    land/P10_UMD/2008 (H9N2), herein referred to as WF10 and
    P10, respectively (15, 21).

    The P10 virus is the result of 10 serial passages in
    ferrets of an avian-human H9N2:H3N2 reassortant containing
    the WF10 surface on a seasonal H3N2 (A/Memphis/14/1998)
    backbone (15).

    (T189A in HA1 and G192R in HA2) and one in the NA (I28V)
    compared with the WF10

    These amino acid changes were shown
    to be crucial for efficient and reproducible respiratory droplet
    transmission in ferrets (15). The four viruses generated in this
    report had P10 HA and NA (2P10), P10 HA and pH1N1 NA
    (1P10), WF10 HA and NA, (2WF10) or WF10 HA and pH1N1
    NA (1WF10) (Fig. 1A).

    2P10:
    1P10:
    2WF10:
    1WF10:


    Sorrell EM, Wan H, Araya Y, Song H, Perez DR (2009) Minimal molecular constraints
    for respiratory droplet transmission of an avian-human H9N2 influenza A virus. Proc
    Natl Acad Sci USA 106:7565–7570

    ------------------------------------------------------

    . Sun Y, et al. (2011) High genetic compatiblity and increased pathologenicity of
    reassortants derived from avian H9N2 and pandemic H1N1/2009 influenza viruses.
    Proc Natl Acad Sci USA 108:4164–4169.


    people in China, ranging from 13.7% to 37.2%, might have ev-
    idence of prior infections of the H9N2 virus (11, 12).

    A/chicken/Hebei/LC/2008, HB08) and a pan-
    demic H1N1 influenza virus (A/Beijing/16/2009, BJ09)



    the virus is very poultry-adapted
    in the inner segments. As was the 1997
    Hong Kong virus, a reassortant from chickens.
    It was not in wild birds and they could wipe
    it out. The ~2002 recurrent H5N1 was not so
    much a poultry virus (#amino acid mutations in segment 8 etc.), it was in wild birds and did
    spread and still persists. I think chances are good that they can wipe out this H7N9.
    Testing must be increased since it's LP, but they can do that.

    Leave a comment:


  • gsgs
    replied
    Re: list of reassortment studies


    (1:H1N1pdn,2009 , 5:H5N1,1997)
    increased replication of 11151111 in epithelial cells ,(others 7+1 reduced) , 100% lethal to mice
    Serial passage of 11111111 or 11151111 in cells increased pathogenicity
    Serial passage of 55555555 attenuated

    Coinfection of MDCK cells with 1 and 5 gave singlegene reassortants in vitro
    single-gene reassortment is common among H1N1 and H3N2 i.e. with HA

    tested in MDCK cells ,human A549 cells ,normal human bronchial epithelial cells (NHBE)

    11111111 was mild in mice with <10% weightloss , also 51111111,15111111,11511111,11115111,11111115
    11151111 and 55555555 100% lethal
    11111511 and 11111151 : no weithloss

    serially passaged 3 times in differentiated NHBE cells cultured at the air-liquid interface
    11111111 and 11151111 replicated to high titers , 55555555 attenuated after passage 2
    11151111 100 fold of 11111111

    11111111(p3,3 passages) 11151111(p3) more weight loss than p0.
    11111111 transmits in ferrets 11151111 and 55555555 not
    Octaviani et al. found that 15555555,51555555,11555555 had enhanced growth in A549-M2 cells
    transmissibility is a multigenic trait, involving the PB2

    -------------------------------------------------------
    Kawaoka et.al.
    Experimental adaptation of an influenza H5 HA
    confers respiratory droplet transmission to a
    reassortant H5 HA/H1N1 virus in ferrets

    11151111 + --> droplet in ferrets

    avian H3 Q226L
    avian H5 Q226L not
    Q226L and G228S, increased
    Q226L and N224K yes (2,6)

    E119G/V152I/N224K/Q226L
    -------------------------------------------------

    Dec.2009,guinea pigs,701(PB2),158-160(HA)
    ---------------------------------------------------------

    Leave a comment:


  • gsgs
    replied
    Re: list of reassortment studies

    Highly pathogenic avian influenza H5N1 viruses have devastated the poultry industry in many countries of the eastern hemisphere. Occasionally H5N1 viruses cross the species barrier and infect humans, sometimes with a severe clinical outcome. When this ...

    Reassortment between Avian H5N1 and Human Influenza Viruses
    Is Mainly Restricted to the Matrix and Neuraminidase Gene Segments
    H1N1, H3N2 and pandemic H1N1
    human NA and MP were preferentially selected by H5
    these H5 reassortants did not show a marked increase in replication
    in MDCK cells and human bronchial epithelial cells.
    In ferrets, inoculation with a mixture of H5N1-pandemic H1N1 reassortant
    viruses resulted in outgrowth of (aaaaahha) viruses
    This virus was not transmitted via aerosols or respiratory droplets
    to na&#239;ve recipient ferrets.
    -------------------------------------------------------
    In 2009, a novel H1N1 influenza (pH1N1) virus caused the first influenza pandemic in 40 y. The virus was identified as a triple reassortant between avian, swine, and human influenza viruses, highlighting the importance of reassortment in the generation ...

    Compatibility of H9N2 avian influenza surface genes and 2009 pandemic H1N1 internal
    genes for transmission in the ferret model
    (33393933) could gain efficient respiratory droplet transmission ferrets
    1P10:111p11111 (best)
    2P10:111p1p111 ok
    1wf10:111w1111 no
    2wf10:111w1w111 a bit
    1:A/NL/602/09(H1N1),p:A/ferret/MD/P10-UMD/08(H9N2),w:A/guinea fowl/HK/WF10/00(H9N2)
    ---------------------------------------------------------------
    H9N2 influenza viruses have been circulating worldwide in multiple avian species and repeatedly infecting mammals, including pigs and humans, posing a significant threat to public health. The coexistence of H9N2 and pandemic influenza H1N1/2009 viruses ...



    Both H9N2 avian influenza and 2009 pandemic H1N1 viruses (pH1N1) are able to infect humans and swine, which has raised concerns that novel reassortant H9 viruses with pH1N1 genes might be generated in these hosts by reassortment. Although previous studies have demonstrated that reassortant H9 viruse …

    99999999 (G1) bad in pigs
    11111111 good in pigs
    11191111 good in pigs
    11191911 good in pigs

    Leave a comment:


  • gsgs
    replied
    Re: list of reassortment studies

    hey, I didn't know that you can easily download all the abstracts from pubmed !
    72002 influenza abstracts in 88MB

    779524 hits for "virus" , that could be~ 1GB
    21286702 hits for "journal"

    eassort : 1537
    eassort,H7 : 96
    eassort,H9 : 136
    eassort,N9 : 17
    eassort,N2 : 662 (presumably because of H3N2)

    I attach the 3 smaller files
    Attached Files

    Leave a comment:


  • gsgs
    replied
    Re: list of reassortment studies

    counts of seroptypes mentioned in that file of 725 abstracts:

    Code:
        183,H
          3,H0N1
    
         62,H1
          1,H1pdm 
        825,H1N1
         35,H1N1pdm
          1,H1N1pps
          2,H1N1s 
         15,H1N1v 
        126,H1N2
          1,H1N3
          2,H1N8
          1,H1N9 
    
         18,H2 
          1,H2H2
          2,H2N1 
         53,H2N2
          9,H2N3
          2,H2N5 
    
         48,H3
         12,H3N1
        483,H3N2
          1,H3N2s
          5,H3N2v
          5,H3N6
         30,H3N8
    
          9,H4
          1,H41P 
          1,H4N
          1,H4N1 
         10,H4N2
         14,H4N6
          4,H4N8
          3,H4N9
    
        102,H5
        656,H5N1
         61,H5N2
         16,H5N3
          3,H5N5
          1,H5N8
          8,H5N9
    
         44,H6
         24,H6N1
         34,H6N2
          3,H6N5
          5,H6N6
         12,H6N8
          1,H6N9 
    
         63,H7 
         10,H7N1
          5,H7N2
         18,H7N3
         39,H7N7 
    
          2,H8N4
    
         42,H9
          4,H9N1 
        290,H9N2 
          1,H9N6 
          8,H9N8
          2,H10 
          3,H10N3 
         12,H10N7
          2,H10N8 
    
          3,H11
          3,H11N1
          2,H11N2
          4,H11N3
          1,H11N6
          5,H11N9
    
          1,H12N3 
    
         12,H13 
          9,H13N2
          2,H13N6 
          1,H13N8
          1,H13N9 
    
         10,H14 
    
          4,H15
          2,H15N4
    
          3,H16
          4,H16N3
          1,H16N6 
    
          1,H17

    Leave a comment:


  • gsgs
    started a topic list of reassortment studies

    list of reassortment studies

    who helps with that pubmed reassortment meta-study ?
    making a list of the viruses,species,(lab),reassorted segments,dates, from the studies

    motivation is, of course, to get a feeling for what we can expect with H7N9,
    when we can see first experiments and results

    I managed to create and attach a file with the 725 abstracts to this post !




    pubmed reassortment influenza 725 hits


    pubmed reassortment influenza ferret(s) 37(36) hits


    pubmed reassortment influenza mouse(mice) 83(81) hits


    pubmed reassortment influenza guinea 7 hits


    pubmed reassortment influenza pig(s)[swine] 225(238)[216] hits


    pubmed reassortment influenza horse(s) 14(14) hits


    pubmed reassortment influenza cell culture(s) 16(10) hits


    pubmed reassortment influenza chicken(s) 119(86) hits


    pubmed reassortment influenza mallard(s) 12(9) hits


    pubmed reassortment influenza duck(s) 106(78) hits




    --------------------------------------------------------------------
    reassortment studies with ******:

    Mar.2011 http://www.ncbi.nlm.nih.gov/pubmed/21195732 cell culture,WI
    Feb.2011 http://www.ncbi.nlm.nih.gov/pubmed/21291589 ferrets,NL, H1N2
    July 2011 http://www.ncbi.nlm.nih.gov/pubmed/21730147 ferrets,MD, H9N2
    Mar 2013 http://www.ncbi.nlm.nih.gov/pubmed/23302886 ferrets,MD,H1N2
    July 2011 http://www.ncbi.nlm.nih.gov/pubmed/21507962 mice,Korea,H3N2,H5N1
    July 2011 http://www.ncbi.nlm.nih.gov/pubmed/21799774 mice,Beijin,guinea pigs,triple
    Sept.2011 http://www.ncbi.nlm.nih.gov/pubmed/21849283 mice,TW,H1N1(PA!)
    May 2012 http://www.ncbi.nlm.nih.gov/pubmed/22323532 mice,UK,H3N2,PR34
    Feb.2013 http://www.ncbi.nlm.nih.gov/pubmed/23221570 mice,JP,Mex

    -------------------------------------------------------------------


    threads in this subforum (not so easy to make it clickable)

    Code:
    VJ: Experimental infection with a Thai reassortant swine influenza virus of pandemic     H1N1 origin induced disease     tetano March 16th, 2013
    Characterization of influenza virus reassortants based on new donor strain   A/HK/1/68/162/35(H3N2)    tetano March 16th, 2013
    A comprehensive analysis of reassortment in influenza A virus    tetano March 10th, 2013
    Reassortment Complements Spontaneous Mutation in Influenza A Virus NP and    M1 genes to Accelerate Adaptation to a New Host    tetano February 2nd, 2013
    In vivo selection of H1N2 influenza virus reassortants in the ferret model    tetano January 12th, 2013
    New approaches for unravelling reassortment pathways      tetano January 5th, 2013
    Possible outcomes of reassortment in vivo between wild type and live attenuated   influenza vaccine strains   tetano October 17th, 2012
    Pathogenicity and transmissibility of reassortant H9 influenza viruses with genes   from pandemic H1N1 virus   tetano August 11th, 2012
    Viral reassortment as an information exchange between viral segments    tetano Feb 18th, 2012
    An influenza reassortant with polymerase of pH1N1 and NS gene of H3N2 influenza A virus   is attenuated in vivo     February 11th, 2012  by tetano
    Polymerase activity of hybrid ribonucleoprotein complexes generated from reassortment    between 2009 pandemic H1N1 and seasonal H3N2 influenza A viruses   tetano Dec 12th, 2011
    A Novel Reassortant Canine H3N1 Influenza Virus between Pandemic H1N1 and   Canine H3N2 Influenza Viruses in Korea   tetano December 5th, 2011
    Palindromes drive the re-assortment in Influenza A    tetano December 4th, 2011
    Reassortment and mutation of the avian influenza polymerase PA subunit overcomes   species barriers  tetano November 18th, 2011
    Novel genetic reassortants in H9N2 influenza A viruses and their diverse pathogenicity   to mice    tetano November 4th, 2011
    Reassortant H9N2 Influenza Viruses Containing H5N1-Like PB1 Genes Isolated from    Black-Billed Magpies in Southern China    tetano October 10th, 2011
    H9N2 avian influenza viruses and pH1N1 virus can reassort and generate novel    viruses with respiratory transmission potential in mammals  Gert van der Hoek Sep 18th, 2011
    Increased pathogenicity of a reassortant 2009 pandemic H1N1 influenza virus containing   an H5N1 hemagglutinin   tetano September 16th, 2011
    Altered Pathogenicity for Seasonal Influenza Virus by Single Reassortment of the RNP   Genes Derived From the 2009 Pandemic Influenza Virus   tetano August 20th, 2011
    When Flu Strains 'Hook Up,' Dangerous Progeny Can Result    tetano July 14th, 2011
    Reassortment between seasonal H1N1 and pandemic (H1N1) 2009 influenza viruses   is restricted by limited compatibility among polymerase subunits   tetano June 22nd, 2011
    ProMed: H3N2/H1N1 REASSORTANT ex PATIENT    Tonka June 9th, 2011 06:52 PM
    reassortment database    gsgs May 29th, 2011
    Reassortant Pandemic (H1N1) 2009 Virus in Pigs, United Kingdom    tetano May 25th, 2011 08:35 PM
    Virulence and genetic compatibility of polymerase reassortant viruses derived from the pandemic (H1N1) 2009 virus and circulating influenza A viruses   tetano April 23rd, 2011
    N-Glycans from Porcine Trachea and Lung: Predominant NeuAc╬▒2-6Gal Could Be a Selective Pressure for Influenza Variants in Favor of Human-Type Receptor   tetano February 26th, 2011
    germany/ reassortant H1N1 in pigs   Anne February 12th, 2011
    Possible Increased Pathogenicity of Pandemic (H1N1) 2009 Influenza Virus upon Reassortment   tetano February 5th, 2011
    The nonadaptive nature of the H1N1 2009 Swine Flu pandemic contrasts with the adaptive facilitation of transmission to a new host   tetano January 8th, 2011
    Reassortment between seasonal and swine-origin H1N1 influenza viruses generates viruses with enhanced growth capability in cell culture   tetano January 5th, 2011
    Reassortment of Ancient Neuraminidase and Recent Hemagglutinin in Pandemic (H1N1) 2009 Virus,   tetano September 30th, 2010
    Genetic characterization of 2008 reassortant influenza A virus (H5N1), Thailand   tetano September 16th, 2010
    Scientists prove humans can have two flus at once   tetano September 16th, 2010
    Reassortant between Human-Like H3N2 and Avian H5 Subtype Influenza A Viruses in Pigs: A Potential Public Health Risk   tetano September 15th, 2010
    Reassortment of pandemic H1N1/2009 influenza A virus in swine   tetano August 10th, 2010
    Kawaoka: hybridization of H1N1 and H5N1   tetano August 5th, 2010
    Evidence Obtained from anova to Reason Cross-species Infection and Cross-subtype Mutation in Neuraminidases of Influenza A Viruses   tetano June 17th, 2010
    A phylogenetic approach to detecting reassortments in viruses with segmented genomes   tetano June 17th, 2010
    Viral reassortment and transmission after coinfection of pigs with classical H1N1 and triple reassortant H3N2 swine influenza viruses   tetano May 21st, 2010
    Chinese study: a case of H1N1-H3N2 (seasonal) hybrid virus   tetano May 13th, 2010
    graphics of evolution of PB1 since 1968   gsgs December 16th, 2009
    will newflu reassort with oldflu ?   gsgs August 26th, 2009
    Reassortment Patterns in Swine Influenza Viruses  sharon sanders August 22nd, 2009
    seasonal H1N1, 2006/7  gsgs August 22nd, 2009
    Reassortment of the Influenza Virus Genome    Chuck July 7th, 2009
    Reassortment between avian H5N1 and human H3N2 influenza viruses in ferrets   Anne June 6th, 2009
    what reassortments can we expect in pandemic flu now ?   gsgs June 1st, 2009
    reassortments in swine  gsgs June 1st, 2009
    5% have 2 viruses   gsgs May 30th, 2009
    H1N1 Related to Virus Born on Hog Factories in 1998   Veg May 3rd, 2009
    |A STUDY: Deviation from the random distribution pattern of influenza A virus...|_   Giuseppe Michieli April 19th, 2008
    Reassortant Avian Influenza Virus (H5N1) in Poultry, Nigeria, 2007  sharon sanders March 26th, 2008
    Bird flu genes found in new swine flu  Coleman December 22nd, 2007
    similarity of the 16 HAs   gsgs August 29th, 2007
    H3N2, 1976   gsgs April 2nd, 2007
    The use of the word, "reassortment".  GaudiaRay November 9th, 2006
    New data show how bird flu quickly spreads  Harriet August 19th, 2006
    Tests suggest bird flu hybrids not big threat  Snowy Owl August 1st, 2006
    
    
    ...
    Attached Files
    Last edited by gsgs; July 21, 2013, 10:20 AM. Reason: transmission added
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