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  • Re: Sequences at Genbank!

    mixin said:
    > My comments on your theory:
    >
    >> It originated in LaGloria in Jan. or Feb.
    >> One or more pigs were infected with it
    >> and then it was in pig-waste or other fomites where
    >
    > Smithfield told officials to check the many backyard pigs in the area.
    > Apparently individuals don't vax their pigs, like Smithfield does.

    how many backyard pigs as compared to Granjas Carroll-pigs ? Must be tiny.
    Backyard farmers are less likely to contact Asian pigs.

    >> it survived for months until the 50f tax-collector from Veracruz got it.
    >
    > If any of the pigs on private farms, the tax collector could have come in contact while doing her job.

    she could have got it from somone else who had got it from a pig.
    Mexico may have a list...
    Remember, when they first announced to sample Hermelina xx ? But then later said
    it were no longer necessary. They may have found the source by then.

    >> Then she infected Gutierrez.
    >
    > That's why it would be good to know the age, sex and condition of the 2 InDRE cases.
    > It won't prove anything but it could disprove our theory.
    > *If someone has this info, please share it!!*

    Yes, anything is useful.
    Gutierrez samples reportedly were sent to Canada/InDRE

    >> Others in LaGloria got it earlier (from the same fomite ?),
    >> there was an outbreak in Feb. in LaGloria.
    >> The virus mutated,..infected Edgar Hermandez and others,
    >
    > Only Edgar was infected in La Gloria, according to the 25-30 tests.
    > Of course, we hear about all the false negatives so who knows.

    I think you misunderstood. Or there were maybe other tests later.
    3955 is clearly related to Edgar=4108, where shall all these other confirmed cases
    since 11.March be from ? Where did they collect samples on 11.March ?

    >> One other virus traveled to Mexico-City and did spread there,
    >> only one introduction.
    >
    > I had thought all the sequences with just "Mexico/##" were probably from Mexico City;
    > but now I see a bunch of sequences named "Mexico City"; so my speculation appears to be wrong.

    yes, Mexico-City sequences were released yesterday

    >Did the WHO/CDC collect that first bunch of samples? and what area are they from?

    I'm not aware that CDC,WHO did collect anything in Mexico

    They have a team now to investigate LaGloria. So apparantly they think it could
    be the origin. But we hear nothing from the team. Why dont they email,tweet,... ?
    Is it (still) secret ? But time is important
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

    Comment


    • Re: Sequences at Genbank!

      segments 1 and 3 were released today. Just exactly the two segments
      out of 8 which have a mutation.
      How likely that this is just coincidence ? 8C2=28
      I'm interested in expert panflu damage estimates
      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

      Comment


      • Re: Sequences at Genbank!

        I think you misunderstood.
        # No. The numbers given were different according to different sources; but there were others taken and it was announced Edgar was the only positive.

        Or there were maybe other tests later.
        3955 is clearly related to Edgar=4108, where shall all these other confirmed cases since 11.March be from ? Where did they collect samples on 11.March ?
        # Good questions... and where did the CDC submitted squence samples come from?

        I'm not aware that CDC,WHO did collect anything in Mexico
        # I think I still have that article where Edgar's mother said the *scientists* came and took a sample from him. I assumed it was either InDRE (my first choice) or the WHO/CDC.

        They have a team now to investigate LaGloria. So apparantly they think it could be the origin. But we hear nothing from the team. Why dont they email,tweet,... ?
        Is it (still) secret ? But time is important
        # Yes, we heard nothing.
        What exactly does a WHO team do when they go to an area to "investigate"? I assume they were talking to people, taking samples of whatever. If it was just lab work, would they send a team?
        The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

        Comment


        • Re: Sequences at Genbank!

          the team is from Mexico, plus some scientists from USA (Galveston?)
          we had a thread about it
          I'm interested in expert panflu damage estimates
          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

          Comment


          • Re: Sequences at Genbank!

            El reporte "Brote de Influenza Humana A H1N1", de la Dirección General Adjunta de Epidemiología de la Secretaría de Salud


            En esas fechas, el Centro Nacional de Vigilancia Epidemiológica y Control de Enfermedades (Cenavece) había detectado brotes de "probable influenza" en Huamantla, Tlaxcala, el 10 de abril; en Pañhe, Hidalgo, el 11 de abril; y en La Gloria, Veracruz, el 11 de abril.

            Este último fue señalado por la Secretaría de Salud como el origen del primer caso confirmado, el del niño Édgar Hernández.

            El siguiente caso confirmado por las autoridades se presentó hasta el 17 de marzo y fue a partir del 12 de abril que los casos comenzaron a crecer rápidamente.


            ------------------------------------------
            I'm not sure how to translate.
            did they say the outbreak in La Gloria was until 17.March ?
            ----edit----


            Is that report available ? Brote de Influenza Humana ...
            I'm interested in expert panflu damage estimates
            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

            Comment


            • Re: Sequences at Genbank!

              Originally posted by gsgs View Post
              public sequences, that may not be published here, well.
              Why do you want me to register ? That I can no longer post my
              tables here and discuss the mutations _in public_ ?

              What sort of "public" is that ?
              Seems to be the same as with the "sequence hoarders"
              you complain about. Public to those who registered and agree
              to keep it unpublic to those who don't.

              For you it just depends on whether you are in the club
              (="public" , ="whining") or outside (="hoarders").
              The sequences are public. Anyone who registers can access them. I just find it annoying that you continue to misrepresent the availability of the sequences.

              They are NOT being hoarded. They are PUBLIC.

              The fact that you STILL don't understand the difference between hoarding, where only a couple of labs can see the sequences, and publishing them at GISAID, where anyone who registers can see the sequences, is remarkable (but not unexpected).

              Comment


              • Re: Sequences at Genbank!

                Originally posted by gsgs View Post
                not made available to public on May 1.
                By any reasonable definition of public.
                They could have been posted to FT on May 1, but weren't.
                No discussion here by you or anyone until today.
                Thanks GISAID.

                It is reasonable to assume that else we would have had threads
                about it here long ago.
                Sequences were public on May 1, as indicated MANY times.

                Comment


                • Re: Sequences at Genbank!

                  Originally posted by mixin View Post
                  My comments on your theory:

                  It originated in LaGloria in Jan. or Feb.
                  One or more pigs were infected with it
                  and then it was in pig-waste or other fomites where
                  # Smithfield told officials to check the many backyard pigs in the area. Apparently individuals don't vax their pigs, like Smithfield does.

                  it survived for months until the 50f tax-collector from Veracruz got it.
                  # If any of the pigs on private farms, the tax collector could have come in contact while doing her job.

                  Then she infected Gutierrez.
                  # That's why it would be good to know the age, sex and condition of the 2 InDRE cases. It won't prove anything but it could disprove our theory. *If someone has this info, please share it!!*

                  Others in LaGloria got it earlier (from the same fomite ?),
                  there was an outbreak in Feb. in LaGloria.
                  The virus mutated,..infected Edgar Hermandez and others,
                  # Only Edgar was infected in La Gloria, according to the 25-30 tests. Of course, we hear about all the false negatives so who knows.

                  One other virus traveled to Mexico-City and did spread there,
                  only one introduction.
                  # I had thought all the sequences with just "Mexico/##" were probably from Mexico City; but now I see a bunch of sequences named "Mexico City"; so my speculation appears to be wrong.

                  Did the WHO/CDC collect that first bunch of samples? and what area are they from?
                  I haven't been paying attention to this analysis because the number of sequences from Mexico is VERY limited. I looked at the two InDRE sequences, as well as a few others from Mexico and none have infomation on the patient. I doubt that any of the early sequences from Mexico have patient data.

                  Comment


                  • Re: Sequences at Genbank!

                    Originally posted by gsgs View Post
                    not made available to public on May 1.
                    By any reasonable definition of public.
                    They could have been posted to FT on May 1, but weren't.
                    No discussion here by you or anyone until today.
                    Thanks GISAID.

                    It is reasonable to assume that else we would have had threads
                    about it here long ago.
                    The original Mex/4115 was posted to GISAID on 4-28, but only one segment. The C1 passage of Mex/4115 was posted to GISAID on 5-01, and included all but the PA segment. It was updated on 6-23 and included PA.

                    There is nothing unusual about the sequence that I can tell. It is CDC variant "i" consensus as are 40% of the Swine Flu viruses. It is the very same virus that showed up in Texas in mid February.

                    Comment


                    • Re: Sequences at Genbank!

                      Apparantly it was secret enough that noone dared to comment here, despite my frequent demands.
                      This is closest to the origin from what is at genbank. If we want to know, where/how it went
                      from swine to humans, then we should examine where/how she(50f) got it from.

                      If it can go once from swine to humans, then it can presumably do it again (and reassort
                      with currentflu)

                      I don't know what variant "i" is and google didn't tell me either.

                      what was in Texas in mid February ? (Presumably a typo)
                      I'm interested in expert panflu damage estimates
                      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                      Comment


                      • Re: Sequences at Genbank!

                        Originally posted by gsgs View Post
                        Apparantly it was secret enough that noone dared to comment here, despite my frequent demands.
                        This is closest to the origin from what is at genbank. If we want to know, where/how it went
                        from swine to humans, then we should examine where/how she(50f) got it from.

                        If it can go once from swine to humans, then it can presumably do it again (and reassort
                        with currentflu)

                        I don't know what variant "i" is and google didn't tell me either.

                        what was in Texas in mid February ? (Presumably a typo)
                        Sorry, my mistake. The first known outbreak in Texas was 4-14 (mid April).

                        As to the variants, I gave you ther URL to the research paper supplemental material that lists them and their genetically distinct characteristics. This was a well done bit of work headed by the CDC. Once again, the URL is:



                        As to the origin of these viruses, it is going to be quite difficult to pinpoint since this stuff has likely been circulating for many, many weeks prior to the La Gloria outbreak, but hidden within the seasonal flu circulating at the same time. The mild symptoms of the Swine Flu virus allowed it to fly under the radar screen.

                        Perhpas our best hope lies in sequencing some older samples still in the freezer to see if Swine Flu pops up ealier. Seraprevalence studies may also provide some answers with time and effort. We may be very surprised at the locations and dates of where this bug has been.

                        Comment


                        • Re: Sequences at Genbank!

                          thanks for the URL. I may have seen it before, but forgot

                          CDC- variants: (from 22.May)



                          they only look at antigenic differences (amino-acids)
                          while I think that we should look at genetic differences (nucleotides)
                          to determine substrains=variants

                          my substrains
                          Code:
                          
                          name (markers) [#30.May,#12.June]   marker1(segment),...
                          ----------------------------------------------------------------
                          early Mex (0)[6,6]
                             Northern (2)[8,9]         A1741C(3),C1118T(5)
                                swine (6)[6,6]         A0588G(3),A1741C(3),C0022A(4),C1118T(5),A0283G(6),C0738A(8)
                                Jersey (6)[6,8]        G0799A(1),A1741C(3),G0687T(4),A0877G(4),G1173A(4),C1118T(5)
                                Hamburg (3)[10,12]     A1577G(1),A1741C(3),C1118T(5)
                             Texas (7)[9,9]            G1308A(1),T0450C(2),A0561C(3),G1173A(4),G1563A(4),G0522A(7),A0775G(8)
                             early US (3)[4,5]         A1218G(1),G1986T(3),A1044G(6) 
                             airplane (1)[6,7]         G0546A(1)
                               England (6)[7,9]        G0546A(1),A2030G(1),A0300G(2),A1058G(2),A0008G(3),C0145A(4),C0132T(5)
                             Korea (3)[1,2]            G0298A(5),G1143A(5),G0316A(6)
                                Japan (9)[9,9]         T1711C(1),G1945A(1),G0636A(2),T2000C(2),G0936A(3),G0298A(5),G1143A(5),G0316A(6),G0456A(8)
                                pre-Cancun (5)[11,14]  C1408T(4),G0298A(5),G1143A(5),G0316A(6),A0742G(6)
                                   Cancun (11)[73,111] G2163A(1),T0658A(4),C1408T(4),G0298A(5),G1143A(5),G1248A(5),G0316A(6),A0742G(6),G0492A(7),G0600A(7),A0367G(8)

                          their S224P in PA is my T670C(3)
                          M582L in PA is A1741C(3)
                          S91P in HA is T298C(4)
                          S206T in HA is T658A(4)
                          V323I in HA is G1012A(4)
                          V100I in NP is G298A(5)
                          T373I in NP is C1118T(5)
                          V106I in NA is G316A(6)
                          N247D in NA is A742G(6)


                          so their variant i is my "early Mex"
                          their variant ii is my "Northern"
                          their varint iii is my "pre-Cancun"
                          their variant iv is my "Cancun"
                          their variant v is my "early US" (they don't include Texas/15 here)
                          Attached Files
                          I'm interested in expert panflu damage estimates
                          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                          Comment


                          • Re: Sequences at Genbank!

                            has anyone tried to register to InDRE ?

                            It's all in Spanish...

                            I went through it but no password, no email confirmation

                            I'm interested in expert panflu damage estimates
                            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                            Comment


                            • Re: Sequences at Genbank!

                              Well, I had thought that CDC variant "v" (early US, CA/04) had completely died out, but lo and behold, a recent post to GenBank from Japan has proven me wrong.

                              A/Fukuoka-C/1/2009

                              No date given as to when collected, but certainly well after (weeks) CA/04. Interesting.

                              Comment


                              • Re: Sequences at Genbank!

                                Originally posted by Mamabird View Post
                                Well, I had thought that CDC variant "v" (early US, CA/04) had completely died out, but lo and behold, a recent post to GenBank from Japan has proven me wrong.

                                A/Fukuoka-C/1/2009

                                No date given as to when collected, but certainly well after (weeks) CA/04. Interesting.

                                I was also noticing that this morning - i think Fukuoka were initial cases from early may.

                                Comment

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