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  • #16
    Re: list of reassortment studies

    http://mbio.asm.org/content/1/1/e00067-10.full

    VN1203=V=A/Vietnam/1203/2004(H5N1)
    CH58=C=A/Ck/Vietnam/C58/2004(H5N1)
    CA09=M=A/California/04/2009(pH1N1)
    NY312=N=A/New York/312/2001(H1N1)
    S09=O=A/green winged teal/Ohio/175/1986(H2N1)
    1918=8=A/Brevig Mission/1/1918(H1N1)

    6=1918-K627E=68888888
    E=NY-K627E=ENNNNNNN
    K=S09-E627K=KOOOOOOO
    CA09-E627K=XMMMMMMM
    CA09-D701N=YMMMMMMM

    rNY312=NY312=NNNNNNNN
    rNY312-K27E=ENNNNNNN
    1918RNP=888N8NNNN
    1918RNP-K627E=688N8NNN
    VN1203RNP=VVVNVNNN
    S09RNP=OOONONNN
    S09RNP-E627K=KOONONNN
    CA09RNP=MMMNMNNN
    CA09RNP-E627K=XMMNMNNN
    CA09RNP-D701N=YMMNMNNN
    =VVVCCCCC
    =CCCVVVVV


    TABLE 1
    Characteristics of viruses evaluated in this study
    Name,Genotype,Nadir weight-change (% of baseline),Lung titer (PFU/g) at 3dpi,at 5dpi, Histopathology
    -----------------------------------------------------------------------------------------------------------------------------------------------
    rNY312,NY312,−0.62%,2.6e3,2.7e3,fif+vrva
    rNY312-K627E,NY312, PB2-K627E,−0.57%,4.1e3,3.5e3,fif+vrva
    1918RNP,1918RNP:NY312,−15.9%,7.7e5,6.5e5,mmnb+abva
    1918RNP-K627E,1918RNP;PB2-K627E;NY312,+0.54%,4.4e4,2.6e5,fif+mbva
    VN1203RNP,VN1203RNP:NY312,−15.7%,4.2e5,2.6e3,mmnb+ abva
    S09RNP,S09RNP:NY312,−4.93%,5.2e4,1.4e2,fa+pava
    S09RNP-E627K,S09RNP;PB2-E627K:NY312,−8.06%,9.9e5,2.3e5,mb+obva
    CA09RNP,CA09RNP:NY312,−4.18%,2.2e5,4.1e4,mfnb+llob va
    CA09RNP-E627K,CA09RNP;PB2-E627K:NY312,−0.83%,1.1e3,4.3e2,fif+vrva
    CA09RNP-D701N,CA09RNP;PB2-D701N:NY312,−1.71%,1.2e4,2.5e3,fif,vrva

    fif:Few inflammatory foci
    vrva:very rare viral antigen
    mmnb:Moderate-marked necrotizing bronchiolitis
    abva:abundant bronchiolar viral antigen
    mbva:minimal bronchiolar viral antigen
    fa:Focal alveolitis
    pava:predominantly alveolar viral antigen
    mb:Mild bronchiolitis
    obva:moderate bronchiolar viral antigen
    mfnb:Mild, focal necrotizing bronchiolitis
    llobva:low levels of bronchiolar viral antigen



    ------------add others to this table, add columns for MDCK,alveolar cells,ferret pathology,ferret transmission,humans
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

    Comment


    • #17
      Re: list of reassortment studies

      Viral RNA polymerase complex promotes optimal growth of 1918 virus in the lower respiratory
      tract of ferrets , Kawaoka et.al. 2008
      Substitution of single genes from the 1918 virus in the genetic background of
      (A/Kawasaki/173/2001; K173) virus did not markedly alter the pattern of infection.
      That is, the reassortants grew well in nasal turbinates, but only sporadically (if
      at all) in the trachea and lungs. One exception was the 1918PB1/K173 reassortant,
      which replicated efficiently in lung tissues as well as the upper respiratory tract.
      A reassortant virus expressing the 1918 viral RNA polymerase complex (PA, PB1, and PB2)
      and nucleoprotein showed virulence properties in the upper and lower
      respiratory tracts of ferrets that closely resembled those of wild-
      type 1918 virus. Our findings strongly implicate the viral RNA
      polymerase complex as a major determinant of the pathogenicity
      of the 1918 pandemic virus. This new insight may aid in identifying
      virulence factors in future pandemic viruses that could be targeted
      with antiviral compounds.
      pathogenesis ? pandemic influenza


      BKKKKKKK
      KBKKKKKK lung
      KKBKKKKK
      KKKBKKKK
      KKKKBKKK
      KKKKKBKK
      KKKKKKBK
      KKKKKKKB
      BBBKBKKK virulent in ferrets

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

      Cited By ...

      Viral RNA polymerase complex promotes optimal growth of 1918 virus in the lower respiratory tract of ferrets
      Tokiko Watanabe, Shinji Watanabe, Kyoko Shinya, Jin Hyun Kim, Masato Hatta, Yoshihiro Kawaoka
      Proc Natl Acad Sci U S A. 2009 January 13; 106(2): 588–592. Published online 2008 December 29. doi: 10.1073/pnas.0806959106
      PMCID:
      PMC2626747
      Article PubReader PDF–877K Supplementary Material
      Is Cited by the Following 24 Articles in this Archive:


      Code:
      A (H1N1) pdm09 HA D222 variants associated with severity and mortality in patients during a second wave in Mexico
      Reconstruction of the 1918 Influenza Virus: Unexpected Rewards from the Past
      Analysis by Single-Gene Reassortment Demonstrates that the 1918 Influenza Virus Is Functionally Compatible with a Low-Pathogenicity Avian Influenza Virus in Mice
      Engineering H5N1 avian influenza viruses to study human adaptation
      Integrated Clinical, Pathologic, Virologic, and Transcriptomic Analysis of H5N1 Influenza Virus-Induced Viral Pneumonia in the Rhesus Macaque
      Restored PB1-F2 in the 2009 Pandemic H1N1 Influenza Virus Has Minimal Effects in Swine
      PB1-F2 Modulates Early Host Responses but Does Not Affect the Pathogenesis of H1N1 Seasonal Influenza Virus
      Mutations in Polymerase Genes Enhanced the Virulence of 2009 Pandemic H1N1 Influenza Virus in Mice
      Decoding the Distribution of Glycan Receptors for Human-Adapted Influenza A Viruses in Ferret Respiratory Tract
      Autopsy series of 68 cases dying before and during the 1918 influenza pandemic peak
      Insights on influenza pathogenesis from the grave
      The pathogenesis of influenza virus infections: the contributions of virus and host factors
      Pathogenesis of the 1918 Pandemic Influenza Virus
      The contribution of animals models to the understanding of the host-range and virulence of influenza A viruses
      PB2 Residue 158 Is a Pathogenic Determinant of Pandemic H1N1 and H5 Influenza A Viruses in Mice 
      The HA and NS Genes of Human H5N1 Influenza A Virus Contribute to High Virulence in Ferrets
      The PB2-E627K Mutation Attenuates Viruses Containing the 2009 H1N1 Influenza Pandemic Polymerase
      MicroRNA Expression and Virulence in Pandemic Influenza Virus-Infected Mice 
      Mechanisms and functional implications of the degradation of host RNA polymerase II in influenza virus infected cells
      Attenuated Strains of Influenza A Viruses Do Not Induce Degradation of RNA Polymerase II 
      Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System
      Emergence and pandemic potential of swine-origin H1N1 influenza virus
      Nuclear Factor 90 Negatively Regulates Influenza Virus Replication by Interacting with Viral Nucleoprotein 
      Adaptive Mutations Resulting in Enhanced Polymerase Activity Contribute to High Virulence of Influenza A Virus in Mice
      I'm interested in expert panflu damage estimates
      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

      Comment


      • #18
        Re: list of reassortment studies

        http://www.ncbi.nlm.nih.gov/pubmed/24131710
        novel transfection based inoculation system to select reassortant viruses under in vivo selective pressure
        risk of reassortment between H9N2 and pH1N1
        ----------------------------------------------------------------
        I'm interested in expert panflu damage estimates
        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

        Comment


        • #19
          Re: list of reassortment studies

          http://www.ncbi.nlm.nih.gov/pubmed/24510170
          February 2014 , Differences in transmissibility and pathogenicity of reassortants
          between H9N2 and 2009 pandemic H1N1 influenza A viruses from humans and swine

          a=A/Swine/Jiangsu/48/2010(pH1N1) [JS48]
          b=A/Swine/Jiangsu/285/2010(pH1N1) [JS285]
          9=A/Swine/Taizhou/5/08(H9N2-9.4.2.5) (TZ5)
          1=A/California/04/2009(pH1N1) [CA04]

          999a9999 ++tgp +pm
          999b9999 ++tgp +pm
          99919999 ++tgp +pm
          999a9a99 +tgp +++pm
          999b9b99 +tgp ++pm
          99919199 +tgp ++pm

          tgp:transmissibility in guinea pigs
          pm:pathogenicity in mice
          +:increased
          ------------------------------------------------------------
          Related Content

          Novel genetic reassortants in H9N2 and their diverse pathogenicity to mice November 2011
          Attenuation of a human H9N2 in mammalian host by reassortment with an avian flu July 2004
          Experimental infection of non-human primates with avian H9N2 October 2013
          Variability of NS1 proteins among H9N2 isolated in Israel during 2000–2009 December 2010
          An NA-deficient pH1N1 mutant can efficiently replicate in cultured cells
          ------------------------------------------------------------------------------
          I'm interested in expert panflu damage estimates
          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

          Comment


          • #20
            Re: list of reassortment studies

            no reassortment (yet) , just 10 passagings in ferrets:
            http://jvi.asm.org/content/early/201...65-13.abstract

            hp H7N1(Italy,2013) + T81I(PB2),V284M(NP),R95K(M1),Q211K(M1),K313R(HA)

            is droplet transmissible in ferrets and virulent


            1978sweu had A284V(5) , bird-index has TARQ , H7N9 has 313V
            I'm interested in expert panflu damage estimates
            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

            Comment


            • #21
              Re: list of reassortment studies

              http://www.ncbi.nlm.nih.gov/pubmed/24429367
              888m8mm8 is transmissable in guinea pigs like m (while 88888888 doesn't transmit at all)
              8:PR8,m=******

              ------m- allows filamentous viruses, enhances NA-activity

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

              http://www.ncbi.nlm.nih.gov/pubmed/24224823
              888888e8 is filamentous

              8:PR8
              e:equine H3N8
              ------------------------------------------------------------------------------------

              ==========edit================
              from post 1:
              Attached Files rspmf3.txt (1.23 MB, 7730 views)

              7730 views is unusual, and it's a big file of 1.23 MB
              I wonder whether it has to do with the DOS-attacks ?!
              I'm interested in expert panflu damage estimates
              my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

              Comment


              • #22
                Re: list of reassortment studies

                [from another thread, I want it here too]

                June 12th, 2014, 06:06 AM
                gsgs
                Registered User Join Date: Feb 2006
                Location: germany
                Posts: 10,542

                Re: Genes found in nature yield 1918-like virus with pandemic potential

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


                Found it here:
                http://www.cell.com/cell-host-microb...2814%2900163-2


                7 amino acid in polymerases and HA conferred
                droplet transmission in ferrets,

                Interestingly, for most viral proteins
                (except for hemagglutinin [HA], neuraminidase [NA], and PB1-
                F2), we found avian influenza virus proteins that differed from
                their 1918 counterparts by only a limited number of amino acids
                (Table S1).

                [that's because of the bird-index (they didn't know that ?!) 1918 flu has
                46=8+7+10+9+7+5 amino-acid differences from the index in the 6 inner segments.]


                PB2 of A/blue-winged teal/Ohio/926/2002 (H3N8), 00,01,04,03,03,01
                PB1 of A/blue-winged teal/Alberta(ALB)/286/77(H3N6), 02,03,--,--,01,--
                PA of A/pintail duck/ALB/219/77 (H1N1), 05,00,03,02,00,05
                HA of A/pintail duck/ALB/238/79 (H1N1), 03,01,06,03,00,02*
                NP of A/blue-winged teal/Ohio/908/2002 (H1N1), 03,04,08,02,02,02
                NA of A/mallard/duck/ALB/46/77 (H1N1), 05,02,01,02,01,00
                M of A/duck/Germany/113/95(H9N2), 02,--,03,05,01,03
                NS of A/canvasback duck/Alberta/102/76 (H3N6), 04,03,--,--,01,03

                -------------------
                -
                N375S,E383D,R584H
                R269K,S400L,K716R,

                V105M,L136M

                T121A
                D209N,R224G,S291N
                -------------------------


                8 , 6, 9 , 7 , 6, 4 amino acids from the 1918 virus.

                [so it has already 0+1+1+2+1+1=6 of the 46 mutations from 1918 in the inner segments (13%),
                which presumably almost randomly appeared in some birds, but not systematically, not together,
                I wished they had taken the pure bird-index-virus plus HA,NA]

                [I remember, Taubenberger et.al. did something similar some years ago,
                they called the bird-index "avian consensus", was it mentioned ? The word
                "consensus" doesn't appear in the Kawaoka paper (57 pages .pdf, 14+suppl.)]

                ================================================== =====

                the Taubenberger paper : (2012)
                http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416129/


                http://www.flutrackers.com/forum/showpost.php?p=489304

                > segments 1,2,3,5,6,7,8, from A/Green Wing Teal/Ohio/175/1986 (H2N1)
                > segment 4 from A/mallard/Ohio/265/1987 (H1N9)
                > similar to the avian influenza virus consensus (see below),


                3,0,7,-,3,-,0,1 A/Green Wing Teal/Ohio/175/1986 (H2N1) [9004]
                4,3,5,-,2,-,0,1 A/mallard/Ohio/265/1987 (H1N9) [10751]
                8,7,10,-,9,-,7,5 A/Brevig Mission/1/1918(H1N1) [3]
                0,0,0,0,0,0,0,0 A/bird-index-a/2000(H3N8) {1]


                ==============================================


                A/blue-winged teal/Ohio/926/2002 (H3N8)
                A/blue-winged teal/Alberta(ALB)/286/77(H3N6)
                A/pintail duck/ALB/219/77 (H1N1)
                ====
                A/blue-winged teal/Ohio/908/2002 (H1N1)
                ====
                A/duck/Germany/113/95(H9N2)
                A/canvasback duck/Alberta/102/76 (H3N6)

                A/pintail duck/ALB/238/79 (H1N1)
                A/mallard/duck/ALB/46/77 (H1N1)
                8,6,9,33,7,31,6,4
                20 (PB1-F2),

                0,1,4,3,3,1
                2,3,-,-,1,-
                5,0,3,2,0,5
                3,1,6,3,0,2
                3,4,8,2,2,2
                5,2,1,2,1,0
                2,1,3,5,1,3
                4,3,-,-,1,3

                -------------------reading the whole paper ...-----------------------
                Interestingly, for most viral proteins
                (except for hemagglutinin [HA], neuraminidase [NA], and PB1-
                F2), we found avian influenza virus proteins that differed from
                their 1918 counterparts by only a limited number of amino acids
                (Table S1).

                grew well in Madin-Darby canine kidney (MDCK) cells and
                embryonated chicken eggs
                growth was comparable to that of the 1918 virus

                intermediate pathogenicity in mice, mild in ferrets

                The 1918 PB2 and HA Genes Contribute to Enhanced
                Pathogenicity and Transmissibility in Ferrets

                We were unable to generate 1918-like avian
                PB2-627K:HA-190D/225D virus in embryonated chicken eggs,

                PB2-627K:HA-89ED/190D/225D virus group and found three
                additional mutations, HA-S113N, PB2-A684D, and PA-V253M


                (E627K and A684D in PB2;
                E89D, S113N, I187T, E190D, G225D, and D265V in HA; V253M
                in PA; and T232I in NP) may be associated with efficient 1918-
                like avian virus transmission in ferrets.


                --------------------------------------------------
                46,>A/Brevig Mission/1/1918(H1N1)
                T108A(1),V114I(1),A199S(1),L475M(1),I539V(1),D567N (1),E627K(1),K702R(1)
                K54R(2),N375S(2),E383D(2),V473L(2),L576I(2),V645M( 2),S654N(2)
                P28L(3),D55N(3),V100A(3),C241Y(3),K312R(3),I322V(3 ),E382D(3),S400L(3),T552S(3),K716R(3)

                G16D(5),V33I(5),R100I(5),V105M(5),L136M(5),L283P(5 ),F313Y(5),Q357K(5),N473S(5)

                T121A(7),L234I(7),G267E(7),E269G(7),K271R(7),S273N (7),Q331K(7)
                E70K(8),I178V(8),D209N(8),E227K(8),S291N(8)
                -----------------------------------------------------------

                ===============================================
                http://www.cidrap.umn.edu/news-persp...irborne-spread
                E627K(1),H99Y(2),H103Y(4),T156A(4),Q222L(4) or G224S(4)
                ================================================== =
                Attached Files
                I'm interested in expert panflu damage estimates
                my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                Comment

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