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Vaccine analysis - What do wort the current experimental vaccines ?

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  • Vaccine analysis - What do wort the current experimental vaccines ?

    Hello to all,

    We are in a strange situation where a pandemic is announced by a large part of the scientific community while no substancial large scale efforts are made to produce right away a vaccine for this announced disaster.

    Many cause haved been claimed to be the reason for this situation.

    - Nobody really are sure of which strain will trigger the pandemic,
    - Lack of appropriate industrial infrastructure and poor investment in vaccinal industry.
    - Poor immunity driven by the current avian H5 strain vaccine.
    - The fear for industrials to loose money if they produce massively a wrong vaccine.
    - Stringent regulation coupled with this low profit sector.
    - And more again, the debate in scientific community is just still not over.

    Despite this, more and more voice start to picture a whole new dominant point of view.

    Just one or two year ago, the dominant point of view in the community and for WHO was to wait for the "Reassortment event" and that many other strain such as H7N7, H2N2 , or H6 virus could as well sparks the next pandemic.

    Slowly but constantly, driven by the constant exchange in the community and also by the different media such as peer reviewd journals, pedagogic journals, main stream media and also by blog and forum like ours, the widespread idea are changing.

    The possibility that the H5N1 step directly in our species without any reasortment event like the 1918 virus could have done too is more and more accepted.
    The constat that H5N1 is the most advanced virus in the way to a pandemic is also more and more accepted.

    The epidemiologic data do not show any sign of reduction in case/mortality rate but the current data is just too much incredible for everyone and every agency or gov or organisation to prep based on this data.

    Recently the idea to count on cross-immunity and count on currently availables vaccinal strain haved raised.

    Even, Dr.Webster which was from the "we wait for the reassortment" clan has begun to puch this idea for wich I am in agreement.

    So...

    What do wort the currently availables vaccinals strains against this nasty virus ?

    I propose here a little analysis of theses strains based on the most common way to analyse vaccinal strain used in laboratories.

    This analysis will be based on the percentage homology between current vaccinal strain and the most recent data for human H5N1 sequences.

    We will also try a analysis for the projected antigenic sites based on a previous scientific paper.

    This is just the introduction

    Please if you want to try the whole process, go in the molecular biology link section in the Mingus's Lab and download the BIOEDIT freeware sequence editor as you can.

    As a database containing human H5N1 sequence + vaccinal strain will be kept , every new data could be add and we will asess every new human strain the same way.

    I'll try a pedagogic effort to explain all step of my work.

    All comments are welcome,

    It may be slow... forgive me and be patient... I fight everiday with time
    Last edited by Mingus; July 4, 2006, 08:02 PM.

  • #2
    Re: Vaccine analysis - What wort current experimental vaccine ?

    Ok,

    So if you are interested in the process, just dowload the sequence editor there

    BioEdit

    or there if it is not available

    BioEdit Alternative

    As soon as you make youself at ease with is
    Try to download the current vaccinal strain selected as presented by the LosAlamos Flu database.

    By clicking on the blue HA you will find the raw sequence data in long serie of ATCG.

    In the BioEdit software, just find the "New aligment" in the menu function and "New sequence".

    Copy the raw (copy/paste) data in this, then the name of the strain "A/species/country/number/year" then the "Close and apply" button.

    Add all the five H5 vaccinal strain HA (we will only analyse haemeglutinnin gene for now).

    Comment


    • #3
      Re: Vaccine analysis - What wort current experimental vaccine ?

      After you haved select new alignement,
      select new sequence.
      Click image for larger version

Name:	new sequence.bmp
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      Here is the New Sequence window
      Click image for larger version

Name:	New Sequence menu.bmp
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      You put the raw base pair ATCG data in the bigger window, put the name and select DNA as the sequence type.
      Push apply and close to finish.
      To enter the next one, start this again.
      There is other way i'll explain another time.

      Comment


      • #4
        Re: Vaccine analysis - What wort current experimental vaccine ?

        Now, you should haved this on on your alignement window
        Click image for larger version

Name:	raw sequence.bmp
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        Imagine there was a time wen researchers was doing aligment manually

        Now you can align as much sequence as you want.

        Select all the sequence you want to align then go click there
        Click image for larger version

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        The more sequences you get the longer it take, depending on your computer accuracy...

        Comment


        • #5
          Re: Vaccine analysis - What wort current experimental vaccine ?

          Now a new window should appear with the new alignment inside

          Click image for larger version

Name:	alignement polymorphims.bmp
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          What you see is the raw nucleic acid alignement composed of the 4 nucleic acid bases:

          A : Adenine

          T: Thymine ( in RNA there is U : Uracyl that replace this one )

          C : Cytosine

          G : Guanine


          When the polymerases translate a RNA into a protean, there is a three basepair code that code for the right amino acid.
          See
          http://www.flutrackers.com/forum/sho...4817#post14817
          for more about this

          This three letter alphabet of life is called codon.

          It is easy to see like that;

          Each dot represent the same base than the sequence above, the differents bases are written, they are the polymorphism.
          Play with the quick function in the window above the alignement, there is several graphic way to see.
          Choose the one you prefer...

          Comment


          • #6
            Re: Vaccine analysis - What wort current experimental vaccine ?

            There is the Codon Table



            Left is the first base of the codon in the right reading frame;
            Up is the second base pair of the codon;
            Right is the third base pair of the codon.

            As you see, a mutation that occur at the third base have less chance to made the aminoacid to change...
            That's why a third base change is often a silent mutation.

            Inside the table is the corresponding aminoacid that is linked to the last one when the ribosome built the protean.

            You have not to do it yourself, BioEdit is well built.

            Just select all the sequences then just do CTRL-G

            you should see this now...
            Click image for larger version

Name:	alignement prot.bmp
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            Do it again to return to the nucleic acid sequence
            re-do it and you see the protein sequence.

            There is three possible reading frame so if you see several * in the protein sequence you are not in the good one.
            Delete the first base of each sequence in the edit sequence mode and try it again.
            If you see again several * then the right reading frame is in the next.
            Delete the first base of each sequence again then Ctrl-G.

            Comment


            • #7
              Re: Vaccine analysis - What wort current experimental vaccine ?

              Ok, I forgot something.

              I add A/HK/213/03 as potential vaccine strain for one good reason.
              The St-jude hospital team have asess different aminoacid change in vaccine to see which one have the ability to enhance the immunogenicity of the strain and they found the S227N polymorphism to greatly enhance the efficacity of a vaccine af any strain.

              Why?

              S227N is in the Receptor binding site...

              It could be comprenhensible to think that a polymorphism that enhance specificity to a-2,6 receptor for the upper-respiratory track have also the ability to trigger a better immunity in human and mammals.

              In fact, this should be a evolutionnary advantage for human to react more to an airborn virus than to virus with avian specificity. Evolutionnary, It makes sense.

              So ,A/HK/213/03 have S227N polymorphism as do two of the Turkish human isolates like Dr.Niman has predicted it could emerge as soon as last october.

              Should they be a good vaccinal strain ?
              Should this polymorphism be include in every new vaccine trial ?
              I think so

              http://www.h5n1experts.org/forum/showthread.php?t=429
              MICROBIOLOGY
              Role of specific hemagglutinin amino acids in the immunogenicity and protection of H5N1 influenza virus vaccines Erich Hoffmann *, Aleksandr S. Lipatov *, Richard J. Webby, Elena A. Govorkova, and Robert G. Webster

              Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105-2794

              Contributed by Robert G. Webster, July 27, 2005

              Comment


              • #8
                Re: Vaccine analysis - What wort current experimental vaccine ?

                Ok now,

                Is theses strain are far from each other ?

                How could we asess the cross-immunity each one could trigger for others ?

                __________________________________________________ _


                We could start with a simple analysys.

                We will do a "percentage homology table based on protein sequences".

                I we would try to asess the genetic distance we sould use pair base data.

                We want to asess the immunity so we will use the protein sequences which do not take the silent mutation in account.

                select all the vaccinal sequences and do a
                "sequence identity matrix"
                Click image for larger version

Name:	sequence id matrix.bmp
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                Comment


                • #9
                  Re: Vaccine analysis - What wort current experimental vaccine ?

                  Give it a name that you will remember

                  This file will be open with Excel in *.*

                  This is a raw data file that need to be trickle a little bit.

                  Change all the 0.9555 data in percentage...
                  give this table a better look then you will have something like this

                  Ok it seem that the Excel format cannot being download in this forum, it's sad but it do something like that ( I did just screen capture my table )

                  Comment


                  • #10
                    Re: Vaccine analysis - What wort current experimental vaccine ?

                    I'll come later with more data on which percentage could give a good cross-reaction immunity and on how to use this database canva to compare and check every new human cases for wich vaccine could be the best in this case.

                    Which one could be the better vax to use from the current known data ?

                    This is just a percentage analysys, we will also try also a "antigenic site" check-up.

                    A lot of works to do folks!

                    - Mingus

                    Comment


                    • #11
                      Re: Vaccine analysis - What wort current experimental vaccine ?

                      Excellent as always Mingus - thanks!

                      Try saving your *.xls as *.csv, then rename the extension as *.txt and this should work as an attachment. Once downloaded the user can rename it to *.csv and it will load OK (minus some formating).

                      Comment


                      • #12
                        Re: Vaccine analysis - What wort current experimental vaccine ?

                        I know you Jjackson haved download BioEdit some time ago.

                        Sonny did it too.

                        Don't be shy to ask if one step in my explanation is "not clear".

                        At least with you two, I don't feel talking only with myself

                        Comment


                        • #13
                          Re: Vaccine analysis - What wort current experimental vaccine ?

                          For those following this thread.

                          This link is to A/HK/213/03
                          http://www.ncbi.nlm.nih.gov/entrez/v...e&val=47834861

                          You may not be able to use your mouse 'Right click' to paste in sequences but should use 'Ctrl V' .

                          Mingus I have tried to follow your steps but the A/HK/213/03 sequence above is shorter and so I get lower % but proprtionally the same as yours.

                          You put the raw base pair ATCG data in the bigger window, put the name and select DNA as the sequence type.
                          I have selected RNA but I assume that will not matter.
                          I use have

                          Comment


                          • #14
                            Re: Vaccine analysis - What wort current experimental vaccine ?

                            From the homology table we get from the potential vaccinal strains, we saw thet no strain is less homologous the 93.9% from each other.

                            Is that the sign of a very distant strain ?

                            Let me put that in perspective.

                            We do this kind of analysys very often for PRRSv, veterinary ask us to do that to know wich vaccine to choose.
                            With that virus which is different from influenza, a strain is considered almost identical when homology is higher than 98%.
                            The virus is considered very similar for homology higher than 96%.
                            Cross-immunity considered valuable for homology higher than 94%.
                            Condidered very different strain below 92%.
                            The most different are around 86% homologous.
                            A total sub-strain(european is about 60% homologous).

                            Last summer, during the canadian swine H3N2 epidemic, we did similar analysis for the new H3N2 strain to compare it with the then-available vaccinal strain and known reference strain.

                            We get that...

                            Click image for larger version

Name:	H3 homology table.bmp
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                            the strain at the top was the new epidemic strain...
                            The strain at left where the known reference and vaccinal strains.

                            As you can see, the homology are mostly lower than the average homology H5 vaccinal strain have between each other.

                            In a serological study with result I just can't put in that board, we test our new IHA test made of than new strain and the older one made with the A/Swine/texas/98 strain which is just 91.2% homologeous to the new H3N2 strain.
                            Every time a serum was positive with the Canadian strain we get lower but still present cross-reaction with the texas strain.
                            However serum with lower titter did no show that cross-reaction.

                            But 92.3% is really lesser than the data we see now from the current vaccinal H5 strain.

                            So, there is some hope

                            We will do that analysys with the available human H5 strain later

                            Comment


                            • #15
                              Re: Vaccine analysis - What wort current experimental vaccine ?

                              Originally posted by JJackson
                              Mingus I have tried to follow your steps but the A/HK/213/03 sequence above is shorter and so I get lower % but proprtionally the same as yours.

                              Yes, I forgot,

                              I cut the sequence for make them the same lenght, it is important.

                              When you see the protein sequence you see a * at the end this is the stop codon.

                              In the begining of the sequence, I just cut for the smaller...

                              Comment

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