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  • #61
    Re: 225G Preliminary Worldwide Tracking & Evaluation

    Originally posted by Florida1 View Post
    The D225G change in 2009 H1N1 influenza virus is not a concern

    by Vincent Racaniello on <abbr class="published" title="2009-11-24">24 November 2009</abbr>





    The Norwegian Institute of Public Health recently identified a mutation in 2009 H1N1 influenza virus isolated from two patients who died and one with severe disease. It has been suggested that this mutation, which causes a change from the amino acid aspartic acid to glycine at position 225 of the viral HA protein (D225G), could make the virus more likely to infect deeper in the airways and cause more severe disease. What is the basis for this concern and does it have merit?


    Attachment of all influenza A virus strains to cells requires sialic acids. There are a number of chemically different forms of sialic acids, and influenza virus strains vary in their affinity for them. Human influenza A strains bind preferentially to sialic acids linked to galactose by an alpha(2,6) bond, while avian and equine strains prefer alpha(2,3) linked sialic acids.


    The type of sialic acid preferred by influenza viruses is controlled by amino acids in the HA protein. Amino acids 190 and 225 are important determinants of receptor binding specificity of the 1918 H1 hemagglutinin. The HA of the 1918 strain A/South Carolina/1/18 prefers alpha(2,3) linked sialic acids; the New York variant, isolated in September 1918, binds both alpha(2,3) and alpha(2,6) sialic acids. These two H1 hemagglutinins differ only by a single amino acid, position 225, which is aspartic acid (D) in the South Carolina strain and glycine (G) in the NY strain. When amino acid 190, which is D in both strains, is changed to E in the NY HA, the virus (AV18) preferentially binds alpha(2,3) sialic acids. These findings are summarized in the table.
    Different isolates of the 2009 H1N1 influenza virus have D at HA at amino acid 190 and mostly D at amino acid 225. The virus prefers to bind to alpha(2,3) linked sialic acids. The amino acid change D225G would be expected to produce a virus with preference for both alpha(2,3) and alpha(2,6) linked sialic acids.


    In the human respiratory tract, alpha(2,6) linked sialic acids are dominant on epithelial cells in the nasal mucosa, paranasal sinuses, pharynx, trachea, and bronchi. Alpha(2,3) linked sialic acids are found on nonciliated bronchiolar cells at the junction between the respiratory bronchiole and alveolus, and on type II cells lining the alveolar wall.


    Based on these considerations, it could be hypothesized that the D225G change would allow the 2009 H1N1 virus to replicate deeper in the respiratory tract. But 2009 H1N1 virus without this amino acid change can already replicate deep in the respiratory tract of ferrets, and probably also in humans. Cells with alpha(2,6) linked sialic acids are present in the lower respiratory tract of humans. So it?s not clear if any effect on virulence would be conferred by the ability of the 2009 H1N1 strain to bind alpha(2,3) linked sialic acids.


    An important consideration is that the D225G amino acid change has a negative impact on transmission. The change from D to G at amino acid 225 of the 1918 HA significantly impairs transmission among ferrets. When both D225G and D190E are present, transmission is abolished. These changes do not impair viral replication or virulence in the respiratory tract of inoculated animals.


    Transmissibility is clearly a positive selection factor for viral evolution. There may be selection for increased virulence only if there is no negative impact on viral transmission. Given these considerations, the choice between an H1 HA amino acid at position 225 that allows efficient transmission (D225) or one that impairs transmission and might or might not allow multiplication deeper in the lung (D225G) seems obvious.


    Tumpey, T., Maines, T., Van Hoeven, N., Glaser, L., Solorzano, A., Pappas, C., Cox, N., Swayne, D., Palese, P., Katz, J., & Garcia-Sastre, A. (2007). A Two-Amino Acid Change in the Hemagglutinin of the 1918 Influenza Virus Abolishes Transmission Science, 315 (5812), 655-659 DOI: 10.1126/science.1136212
    Shen J, Ma J, & Wang Q (2009). Evolutionary Trends of A(H1N1) Influenza Virus Hemagglutinin Since 1918. PloS one, 4 (11) PMID: 19924230
    from NS1 via email -

    "We appreciate and agree with Dr. Racaniello?s astute analysis on 225G. We are slightly more cautious about assigning ?low? transmissibility based on the limited evidence we have, though the ferret studies and current lack of defined human clusters compel one toward an initial evaluation of low transmissibility. The absence of evidence is not always negational. More data points will define the matter soon."

    Comment


    • #62
      Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

      <o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="stockticker"></o:smarttagtype><!--[if gte mso 9]><xml> <o:OfficeDocumentSettings> <o:RelyOnVML/> <o:AllowPNG/> </o:OfficeDocumentSettings> </xml><![endif]--><!--[if gte mso 9]><xml> <w:WordDocument> <w:View>Normal</w:View> <w:Zoom>0</w:Zoom> <w:Compatibility> <w:BreakWrappedTables/> <w:SnapToGridInCell/> <w:WrapTextWithPunct/> <w:UseAsianBreakRules/> </w:Compatibility> </w:WordDocument> </xml><![endif]--><!--[if !mso]><object classid="clsid:38481807-CA0E-42D2-BF39-B33AF135CC4D" id=ieooui></object> <style> st1\:*{behavior:url(#ieooui) } </style> <![endif]--><!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman";} </style> <![endif]--> I would like to add an addendum to my earlier post (#55). When I wrote it I had not read NS1’s full post at #49 just the extract in Tropical’s post #53. When taken with the rest of the post NS1’s dismissal of the cytokine storm makes more sense as what he/she is rejecting is a wide spread cytokine storm and not a localised one which is also what I think is happening. His argument regarding the role of NS1 is appealing and nicely fits theory but I have not seen any evidence to directly support it (not that that means there isn’t any and I have not read others of his posts). When infected the host cell produces an interferon (INF) which is an intracellular cytokine and is major player in the immune systems attempts to prevent viral replication. The non structural protein NS1 is involved in blocking INF’s activities. Another INF role is in the presentation of viral antigen on the cell surface and in programmed cell death (PCD) - both of which I touched on before.
      <o:p> </o:p>
      So it is very plausible that NS1 is suppressing INF activity which leads to ( => )
      => to a failure to present antigen via <st1:stockticker>MHC</st1:stockticker> (which then can't initiate T-cell antibody production) and a failure to initiate apoptosis (Apoptosis includes the shutting down of protein manufacture so would also stop viral production)
      => lyses of a large amount of viral protein and other cell contents (which would have been broken-down as part of PCD)
      => massive localised immune response in the area of lyses i.e. the lungs (AKA cytokine storm)
      => ARDS and the kind of post mortem reports we have been getting showing extreme tissue damages in and around the lungs.
      <o:p> </o:p>
      It is the compound effects of cells killed from the inside by replicating virus and from the outside killed by the toxicity of the immune response that proves too much for some. If all this is true then it is those with weak immune systems who will not be able to cope with the massive release of new virons once the cells begin to lyse so will suffer from many more infected cells. The young and fit, who suffered so badly in 1918/19, will produce a powerful response and end up damaging, or killing, healthy cell. (The results from Australian ECMO centres does show a good prognosis for patients with ARDS and horrendous X-rays if they can be helped through the critical period of total lung failure – which again fits theory nicely but is not a proof). Mama bears balanced reaction contains spread without going all ‘bull in the china shop’.
      <o:p> </o:p>
      I liked Vincent Racaniello’s post at #63 – excellent as always – but with one caveat. He is talking about the observed behaviour of certain protein substitutions on some 1918 H1N1 virii. This does not mean the same changes would have the same effects on a H1N1(2009) background. The opening post in this thread is a research paper on changes at 225 and in post #2 at the time of its release in June I wrote
      <o:p> </o:p>
      Otherwise the paper is reinforcing the conclusion that all the coded for proteins work as a functional set and just because a particular mutation has a given effect in one strain it does not ensure similar effects unless all the other proteins are also identical. There seem to be many ways of achieving the same end.
      <o:p> </o:p>
      I believed that to be true then and now.
      Last edited by JJackson; December 3, 2009, 12:28 PM. Reason: trying to add some clarity

      Comment


      • #63
        Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

        Originally posted by Florida1 View Post
        from NS1 via email -

        "We appreciate and agree with Dr. Racaniello?s astute analysis on 225G. We are slightly more cautious about assigning ?low? transmissibility based on the limited evidence we have, though the ferret studies and current lack of defined human clusters compel one toward an initial evaluation of low transmissibility. The absence of evidence is not always negational. More data points will define the matter soon."
        That's my gut feeling, too. If D225G was nasty, transmissible, and as widespread as we suspect it is, you'd be seeing large clusters of deaths all over the world. That isn't happening.

        Comment


        • #64
          Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

          Originally posted by JJackson View Post
          <o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="stockticker"></o:smarttagtype><!--[if gte mso 9]><xml> <o:OfficeDocumentSettings> <o:RelyOnVML/> <o:AllowPNG/> </o:OfficeDocumentSettings> </xml><![endif]--><!--[if gte mso 9]><xml> <w:WordDocument> <w:View>Normal</w:View> <w:Zoom>0</w:Zoom> <w:Compatibility> <w:BreakWrappedTables/> <w:SnapToGridInCell/> <w:WrapTextWithPunct/> <w:UseAsianBreakRules/> </w:Compatibility> </w:WordDocument> </xml><![endif]--><!--[if !mso]><object classid="clsid:38481807-CA0E-42D2-BF39-B33AF135CC4D" id=ieooui></object> <style> st1\:*{behavior:url(#ieooui) } </style> <![endif]--><!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman";} </style> <![endif]--> I would like to add an addendum to my earlier post (#55). When I wrote it I had not read NS1?s full post at #49 just the extract in Tropical?s post #53. When taken with the rest of the post NS1?s dismissal of the cytokine storm makes more sense as what he/she is rejecting is a wide spread cytokine storm and not a localised one which is also what I think is happening. His argument regarding the role of NS1 is appealing and nicely fits theory but I have not seen any evidence to directly support it (not that that means there isn?t any and I have not read others of his posts). When infected the host cell produces an interferon (INF) which is an intracellular cytokine and is major player in the immune systems attempts to prevent viral replication. The non structural protein NS1 is involved in blocking INF?s activities. Another INF role is in the presentation of viral antigen on the cell surface and in programmed cell death (PCD) - both of which I touched on before.
          <o:p> </o:p>
          So it is very plausible that NS1 is suppressing INF activity which leads to ( => )
          => to a failure to present antigen via <st1:stockticker>MHC</st1:stockticker> and a failure to initiate apoptosis (Apoptosis includes the shutting down of protein manufacture so would also stop viral production)
          => lyses of a large amount of viral protein and other cell contents (which would have been broken-down as part of PCD)
          => massive localised immune response in the area of lyses i.e. the lungs (AKA cytokine storm)
          => ARDS and the kind post mortem reports we have been getting showing extreme tissue damages in and around the lungs.
          <o:p> </o:p>
          It is the compound effects of cells killed from the inside by replicating virus and from the outside killed by the toxicity of the immune response that proves too much for some. If all this is true then it is those with weak immune systems who will not be able to cope with the massive release of new virons once the cells begin to lyse so will suffer from many more infected cells. The young and fit, who suffered so badly in 1918/19, will produce a powerful response and end up damaging, or killing, healthy cell. (The results from Australian ECMO centres does show a good prognosis for patients with ARDS and horrendous X-rays if they can be helped through the critical period of total lung failure ? which again fits theory nicely but is not a proof). Mama bears balanced reaction contains spread without going all ?bull in the china shop?.
          <o:p> </o:p>
          I liked Vincent Racaniello?s post at #63 ? excellent as always ? but with one caveat. He is talking about the observed behaviour of certain protein substitutions on some 1918 H1N1 virii. This does not mean the same changes would have the same effects on a H1N1(2009) background. The opening post in this thread is a research paper on changes at 225 and in post #2 at the time of its release in June I wrote
          <o:p> </o:p>
          <o:p> </o:p>
          I believed that to be true then and now.

          NS1 has made an edit to post #49 adding detail to the Cytokinic Dysregulation comments.

          Comment


          • #65
            Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

            it is assumed that 225G doesn't transmit but rather happens
            in the host each time independently, just like Tamiflu-resistance
            usually happens independently.
            This could be encouraged by some cells in some area which can
            only be infected by 225G viruses.

            The Ukraine virus in the Ukraine population may be more suitable
            to infect those cells in connection with 225G, while -despite
            225G- there are still problems in other regions of the world
            to infect them.
            This could be due to host genetics or nutrition or to other
            mutations in the virus which interact.

            If that virus spreads , it may still often develope 225G and severe
            disease, even if it enters the host with 225D

            ---------------------edit---------------

            pjie2 formulates it better in the comments-section:
            But 2009 H1N1 virus without this amino acid change can already replicate deep in the respiratory tract of ferrets

            How labile are flu viruses within an individual patient? Is the D225G polymorphism transmitting between patients, or is the same mutation recurring in many different patients? One could hypothesise a scenario where only virus particles with a D at position 225 are able to transmit, but the subsequent course of the infection depends on whether the the virus happens to pick up a G at position 225 within each given patient. Whether you detect a D or a G when you come to sequence a sample would depend on how long-established the infection was, how deep you were sampling within the respiratory tree, etc.

            On a related note, how certain are we about what was going on in the ferrets? If I remember rightly, the study infected ferrets with H1N1 flu (i.e. with D at 225) and observed deep lung pathology. Did they then re-isolate the virus from the deep lung lesions and check whether it still had a D at position 225?

            Perhaps the pathogenic factor is not whether a given strain has G at 225, but the ease (or otherwise) with which it can acquire a G as it replicates within the host.

            Same goes for any other polymorphism that increases lethality but decreases transmission. If you need half a dozen nucleotide changes to get from the transmissible sequence to a lethal sequence, you're safer than if it's only a single hop away.


            h1n1_watcher 6 hours ago in reply to pjie2

            Good questions pjie2.

            However, the question remains which selective advantages such sporadic "in-patient-mutated" virus could have over its non-mutated competitors during the course of the infection within the patient ?

            As long as the "front of the infection wave" has not reached the deep lung tissue, the reproduction rate of the non-mutated version would be superior... and will thus stop before the deep lung tissue is reached.

            Maybe it is only those rare cases where the "jump" happen to occur in a virus particle just at the peripheric border of the infection wave far enough down the respiratory tree to reach the first susceptible "2,3"-type cells. from which point on a "second wavefront" of the infection would be started running down the lower part of the respiratory tract.

            just a thought ...


            pjie2 5 hours ago in reply to h1n1_watcher

            Eh, that implies spread of flu in the respiratory tree is like some kind of slow-moving fluid, rather like the adverts for cough syrup. Does flu actually work like that? I mean, an air molecule can get from the outside world down to the deepest parts of the respiratory tree within a single breath - it's how breathing works. Virus particles won't be quite that mobile, but even so...

            The picture I had in mind was a lot simpler - you have an active upper respiratory infection with D at 225. Periodically, random mutations happen which create a G at 225 - along with a host of other mutations, of course, since the sheer number of viral RNAs synthesised pretty much guarantees that any given mutation will arise at least once. These mutant particles get released and go wherever the air flow takes them, be that up or down.

            If they get coughed out and land on someone else, there's no effect as they don't transmit well. If they get inhaled deeper into the lungs, then they may set up shop there. They won't get outcompeted by the parent virus because the parent virus isn't infecting the same cells.

            I wonder if new deep sequencing technology will help answer these questions. Would it let you look at the whole population of viral sequences within an infection, and/or at different locations within the lung, rather than getting a consensus sequence?
            I'm interested in expert panflu damage estimates
            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

            Comment


            • #66
              Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

              it was said, that there are 10 sequences from Ukraine at GISAID,
              4 from fatal cases and exactly those 4 have 225G.

              Is this confirmed ?
              Why does WHO,CDC,ECDC,... not comment on that ?
              Why aren't those sequences made public ?
              And why are journalists complacent with that situation
              and apparantly don't even ask ?
              I'm interested in expert panflu damage estimates
              my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

              Comment


              • #67
                Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

                update via email -

                2009-11-24

                Norway: 1 Mixture of 225D/225G, 5 of 25 have 225E; Spain: 7 of 19 have 225E

                225E is becoming fixed.

                GenBank Deposits 2009-11-23

                Norway: 5 of 25 have 225E
                Spain : 7 of 19 have 225E

                A/Norway/2924, sampled on 2009-08-10 from a 40F, is a mixture of wt 225D and 225G after canine cell passage. The sample also carries the prevalent 206T.

                The data collection must begin in earnest after this development. The first data quality improvement might be to release the sample site and the patient outcome please.

                We have no evidence that the cases discussed here are related to the three previously reported instances in Norway of 1 serious illness and 2 fatalities. Sweden is also today reporting 2 cases of 225G that were serious and treated via ECMO during the summer. No outcomes noted as yet on Sweden. Finland reports at midday 1 case of 225G in July. The list of recent reports extends with the counts actively growing:

                Ukraine
                Norway
                Sweden
                Finland

                Our team expects widespread reporting of 225G in the next few days as the revision is most certainly seeded throughout the world and is probable in any European country with a suitable sample size that is investigating.

                The most noticable empty slot should be posted as soon as the pizza finishes on the west side of the Adriatic oven.

                Islands like Cyprus, Mauritius, Brac (Croatia), Sicily (Italy), Sardinia (Italy), Majorca (Spain), Ibiza (Spain), Corsica (France), Crete (Greece) and Rhodes (Greece) are attractive examination sites in descending order of potential. Our team would be amazed if reasonable sampling had occurred on these islands and more than 3 of the 10 failed to demonstrate 225G. A 50% probability exists in our framework (with a reasonable sample population) that all 10 islands should display at least one case of 225G.

                Slovakia, Germany, Iceland, Latvia, Lithuania, Moldova and Bosnia from Europe are candidate areas in order of descending potential.

                Africa displays somewhat equal potential at South Africa, Cameroon and Ghana.

                The matter of 225G range and transmissibility may best be settled with full sequence publication.

                This post will be updated as corroborationg data is made available.

                Comment


                • #68
                  Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

                  2009-11-25

                  Norway Sequence with 225G Mixture also Carries syn413K Silent Marker found on the 4 fatal flashfire cases

                  A/Norway/2924, sampled on 2009-08-10 from a 40F, and reported yesterday to carry a mixture of wt 225D and 225G with the 206T pairing also demonstrates syn413K, an Avian H1N1 SNP found in the most recent 225G sequences from the widely reported fatal cases in the ongoing flashfire that is now nearing 1.7 million cases with 397 deaths and 99,661 hospitalisations.

                  Norway2924 HA
                  • 225G *
                  • syn413K encoded from A1281G, AAa->AAg *
                  • syn464G encoded from A1435G, GGa->GGg

                  * SNP Matches the 4 fatal flashfire cases

                  The silent 413K and 464G are both found on a very special bird from Argentina.

                  ReAssortment is downrated as a 225G transfer mechanism from Norway to the flashfire due to Norway2924 having an additional unmatched silent SNP, A1435G, GGa->GGg, coding for a synonymous Glycine at 464 (syn464G). This SNP is novel to ΣPF11 and is found widely on Swine H1N1 and H1N2, including most recently on A/swine/Hong Kong/294/2009 (H1N2), and Avian H1N1 in the red-winged tinamou/Argentina/MP1/2008 (HA 225G, 277N, 286H, 298V / NA 106I, 248N, 286G).

                  225G on 5 sequences (Norway2924 and 4 flashfire specimens) all sharing a rare syn413K on 5 distinctly different backgrounds closes the door on spontaneous and / or random mutation in this dataset.

                  With the two pillars of genetic acquisition impeached, deduction leads us to Dr. Niman's Recombination theory if we seek an explanation based on data.

                  Comment


                  • #69
                    Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

                    2009-11-26

                    The Ukraine, Norway and Spain Share Paired HA and NA Changes

                    A/Norway/3364-2, sampled 2009-09-08 on a tracheal swab from an adult female, is a very special individual in the team of 9 Norwegian sequences that each demonstrate HA syn413K, an Avian H1N1 SNP found in the most recent 225G sequences from the widely reported fatal cases in the ongoing flashfire that has now over 1.7 million cases with 404 deaths and more than 100,000 hospitalisations. The synonymous 413K is traveling worldwide, potentially laying landing strips for 225G.

                    What would you think if I told you that syn413K was traveling with another silent companion . . . who lives on a different gene segment? Norway3364 is the only recent sequence from that country with a published Neuraminidase segment. And this time, they gave us a very useful one. Cross segment linking is occurring regularly in ΣPF11 and this sequence provides an opportunity to examine one pair.

                    Norway3364 carries HA syn413K and NA syn407V. This particular version of 407V is widespread in H5N1 and the cross-segment pair is also noted under the virulent serotype.

                    Cross-Linked HA and NA from Norway to the Ukraine
                    • HA:syn413K encoded from A1281G, AAa->AAg *
                    • NA:syn407V encoded from T1221C, GTt->GTc *

                    * SNP Matches the 4 fatal flashfire cases

                    A limited inspection demonstrates a wide range for this paired set of travelers. The following list is not comprehensive, but is a representative geographic sample of other sequences that carry the pair. Any attempt at a comprehensive study will only result in disappointment as you'll find that many sequences with syn413K have no NA to evaluate and many sequences with syn407V have no related HA. Patterns do not precisely define themselves without data, but the range is impressive even with the limited dataset.

                    Norway, the Ukraine, Sweden, Spain, Russia, the United States and Singapore are identified in this sequence range.

                    • LvivN2
                    • LvivN6
                    • TernopilN10
                    • TernopilN11
                    • Norway3364
                    • CatS1096
                    • CatS1162
                    • CatS1181
                    • CatS1268
                    • CatS1402
                    • CatS1501
                    • CatS1687
                    • CatS1748
                    • CatS1751
                    • CatS1761
                    • SingaporeON1156
                    • Stockholm31
                    • Omsk02
                    • NY3702
                    • NY3715
                    • NY3828
                    • RhodeIsland08

                    Very few of these sequences share 100&#37; homology, meaning that most of the backgrounds are diverse on which these paired, cross-segment changes, HA syn413K and NA syn407V, are overlaid. Those overlays onto differing genetic templates each require a precise sub-segment data acquisition at the Hemagglutinin paired with a second precise sub-segment acquisition at the Neuraminidase.

                    We have provided 22 examples so that random mutation and / or spontaneous mutation proponents may think before answering the probabilities of these outcomes under those outdated frameworks.
                    Last edited by sharon sanders; November 28, 2009, 07:03 AM. Reason: edit via email from NS1

                    Comment


                    • #70
                      Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

                      there could have been reassortment in the Zhejiang/DTID viruses.

                      Their NA looks like Netherlands/602 - and no other.

                      But that Netherlands/602 virus was used in the ferrets experiments
                      and maybe other trials.

                      coincidence ?

                      it may be generally available to labs for experiments
                      I'm interested in expert panflu damage estimates
                      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                      Comment


                      • #71
                        Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

                        Originally posted by Florida1 View Post
                        2009-11-25

                        Norway Sequence with 225G Mixture also Carries syn413K Silent Marker found on the 4 fatal flashfire cases

                        A/Norway/2924, sampled on 2009-08-10 from a 40F, and reported yesterday to carry a mixture of wt 225D and 225G with the 206T pairing also demonstrates syn413K, an Avian H1N1 SNP found in the most recent 225G sequences from the widely reported fatal cases in the ongoing flashfire that is now nearing 1.7 million cases with 397 deaths and 99,661 hospitalisations.

                        Norway2924 HA
                        • 225G *
                        • syn413K encoded from A1281G, AAa->AAg *
                        • syn464G encoded from A1435G, GGa->GGg

                        * SNP Matches the 4 fatal flashfire cases

                        The silent 413K and 464G are both found on a very special bird from Argentina.

                        ReAssortment is downrated as a 225G transfer mechanism from Norway to the flashfire due to Norway2924 having an additional unmatched silent SNP, A1435G, GGa->GGg, coding for a synonymous Glycine at 464 (syn464G). This SNP is novel to ΣPF11 and is found widely on Swine H1N1 and H1N2, including most recently on A/swine/Hong Kong/294/2009 (H1N2), and Avian H1N1 in the red-winged tinamou/Argentina/MP1/2008 (HA 225G, 277N, 286H, 298V / NA 106I, 248N, 286G).

                        225G on 5 sequences (Norway2924 and 4 flashfire specimens) all sharing a rare syn413K on 5 distinctly different backgrounds closes the door on spontaneous and / or random mutation in this dataset.

                        With the two pillars of genetic acquisition impeached, deduction leads us to Dr. Niman's Recombination theory if we seek an explanation based on data.
                        The red-winged tinamou (Argentina) is a mostly ground dwelling bird, with a threatened (ie low) population. How likely is it that this bird is a donor? within the time span given 2008-2009.

                        Comment


                        • #72
                          Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

                          Originally posted by Sally View Post
                          The red-winged tinamou (Argentina) is a mostly ground dwelling bird, with a threatened (ie low) population. How likely is it that this bird is a donor? within the time span given 2008-2009.
                          Attempts are made to domesticate it

                          Due to its broad geographic dispersion, omnivorous feeding habit, and the taste of its meat, the domestication of the Red-winged Tinamous (Rhynchotus rufescens), also called South American partridge, has become attractive for economic purposes. The pressure to domesticate this and other tinamous species also stems from the limited supply of birds in nature (Homma, 1993). Studies carried out using this bird in an environment similar to that used to raise broilers have shown good performance in terms of growth rate (Queiroz et al., 2004; Tholon et al., 2004), excellent carcass and breast yields (Moro et al., 2006), and perfect adaptation to meal (Moro, 1996) and pelleted (Hoshiba et al., 2003) feeds. However, the reproductive performance of this species in captivity is still a problem that needs to be solved. http://www.scielo.br/scielo.php?pid=...pt=sci_arttext

                          Comment


                          • #73
                            Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

                            > how likely is it

                            very unlikely. There are ~400 mutations, no big surprise that
                            those two are among them.
                            Flu rarely goes from birds to human.
                            Flu rarely reassorts.
                            More rarely recombines.
                            Even more rarely recombines at short chunks to change single positions


                            very distant, unrelated virus
                            392,320,291,431,252,307,77,246
                            differences to ****** in the 8 segments
                            I'm interested in expert panflu damage estimates
                            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

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                            • #74
                              Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

                              #75:...

                              Yes.

                              But we can also said: highly likely, if that piece was an lab workout ...

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                              • #75
                                Re: 225G Preliminary Worldwide Tracking &amp; Evaluation

                                how would a lab "generate" such a virus, distant from all normal strains ?

                                better export some suitable birds with different flus to a remote island
                                and wait hundred years.
                                (in proximity to poultry and swine)


                                the first flu-threat to America was the existing other continents
                                who "discovered" it
                                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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