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July San Paolo Sequence Released

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  • #31
    Re: July San Paolo Sequence Released

    Originally posted by niman View Post
    Only the first change is human, but that is the only one that is "new". The other two are also in earlier 2009 pandemic sequences (but different combinations).

    It is V252M that is not found in other pandemic swine sequences, but a single change can have a big effect.

    From the quote I posted, it sounds like many family members died.
    I don't see where many family members died, I only see the little 11 year old girl died in that family, in brazil.

    Comment


    • #32
      Re: July San Paolo Sequence Released

      Originally posted by Rwilmer View Post
      I don't see where many family members died, I only see the little 11 year old girl died in that family, in brazil.
      I may have skimmed the reports too quickly. Many family members were infected, but I haven't found confirmation that they died (I saw tragedy and thought it refered to deaths of multiple family members).

      "The family Laguna had eight other cases of swine flu confirmed: mother, father, younger brother, three cousins, grandmother and an aunt of the girl. The tragedy led the silence of their parents.

      Comment


      • #33
        Re: July San Paolo Sequence Released

        Originally posted by Rwilmer View Post
        I don't see where many family members died, I only see the little 11 year old girl died in that family, in brazil.
        There were two additional deaths in Osasco, but no detail

        http://flutracker.rhiza.com/flu/gmap...2578125&zoom=9

        Comment


        • #34
          Re: July San Paolo Sequence Released

          Originally posted by Mamabird View Post
          I'm totally confused. How does V252M in Swine Flu have anything to do with 1918 H1N1? I see no comparison whatsoever with SC, BM, NY, etc. Are we looking at the same sequences?
          The 2001 swine sequence from Hong Kong has V252M, but most or all others in the travel log (including the Peru seasonal sequences and the 1918 sequences have V252I).
          The recombination happens at the nucleotide level, and the travel log represent nucleotide identity for the non-synonymous change, as well as the upstream region.

          Comment


          • #35
            Re: July San Paolo Sequence Released

            do we have data from the other Brasil cases ?
            Some sequences are Mexico-City , pre-Cancun and
            some Cancun (with S220T in HA)

            It could be that the Mexico-City strain is more virulent in average,
            I think we should try to figure that out so other countries
            can avoid it.
            I'm interested in expert panflu damage estimates
            my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

            Comment


            • #36
              Re: July San Paolo Sequence Released

              Originally posted by gsgs View Post
              do we have data from the other Brasil cases ?
              Some sequences are Mexico-City , pre-Cancun and
              some Cancun (with S220T in HA)

              It could be that the Mexico-City strain is more virulent in average,
              I think we should try to figure that out so other countries
              can avoid it.
              There is only one recent sequence from Brazil. The earlier seqeunces did not have V252M, but I suspect it is in Argentina. Almost all fatalities in Brazil are in the south

              http://flutracker.rhiza.com/flu/gmap...6171875&zoom=6

              Comment


              • #37
                Re: July San Paolo Sequence Released

                Originally posted by gsgs View Post
                do we have data from the other Brasil cases ?
                Some sequences are Mexico-City , pre-Cancun and
                some Cancun (with S220T in HA)

                It could be that the Mexico-City strain is more virulent in average,
                I think we should try to figure that out so other countries
                can avoid it.
                The travel log for the other non-synonymous change was posted earlier

                gb|GQ402203.1| Influenza A virus (A/Canada-MB/RV1982/2009(H1N... 35.6 0.008
                gb|GQ392029.1| Influenza A virus (A/Italy/127/2009(H1N1)) seg... 35.6 0.008
                gb|GQ368664.1| Influenza A virus (A/Sao Paulo/2233/2009(H1N1)... 35.6 0.008
                gb|GQ330653.1| Influenza A virus (A/Italy/56/2009(H1N1)) segm... 35.6 0.008
                gb|GQ329076.1| Influenza A virus (A/Paris/2722/2009(H1N1)) se... 35.6 0.008
                gb|CY041830.1| Influenza A virus (A/New York/3348/2009(H1N1))... 35.6 0.008
                gb|CY041822.1| Influenza A virus (A/New York/3352/2009(H1N1))... 35.6 0.008
                gb|CY041782.1| Influenza A virus (A/New York/3337/2009(H1N1))... 35.6 0.008
                gb|GQ323551.1| Influenza A virus (A/Massachusetts/08/2009(H1N... 35.6 0.008
                gb|GQ323451.1| Influenza A virus (A/Rhode Island/03/2009(H1N1... 35.6 0.008
                gb|GQ323446.1| Influenza A virus (A/Maine/03/2009(H1N1)) segm... 35.6 0.008
                gb|GQ287625.1| Influenza A virus (A/Tokushima/1/2009(H1N1)) s... 35.6 0.008
                gb|GQ283493.1| Influenza A virus (A/Finland/555/2009(H1N1)) s... 35.6 0.008
                gb|GQ232044.1| Influenza A virus (A/Rhode Island/02/2009(H1N1... 35.6 0.008
                gb|GQ232007.1| Influenza A virus (A/Vermont/03/2009(H1N1)) se... 35.6 0.008
                gb|GQ200287.1| Influenza A virus (A/Shandong/1/2009(H1N1)) se... 35.6 0.008
                gb|GQ166222.1| Influenza A virus (A/Italy/07/2009(H1N1)) segm... 35.6 0.008

                Comment


                • #38
                  Re: July San Paolo Sequence Released

                  Updated travel log

                  gb|GQ414768.1| Influenza A virus (A/Sao Paulo/43812/2009(H1N1... 32.2 11
                  gb|GQ229293.1| Influenza A virus (A/swine/Hong Kong/NS1659/20... 32.2 11
                  gb|EU521831.1| Influenza A Virus (A/Yurimaguas/FLU4785/2006(H... 32.2 11
                  gb|EU521815.1| Influenza A Virus (A/Chanchamayo/FLU4292/2006(... 32.2 11
                  gb|EU521813.1| Influenza A Virus (A/Chanchamayo/FLU4036/2006(... 32.2 11
                  gb|EU521812.1| Influenza A Virus (A/Chanchamayo/FLU4032/2006(... 32.2 11
                  gb|EU521807.1| Influenza A virus (A/Chanchamayo/FLU3954/2006(... 32.2 11
                  gb|DQ431990.1| Influenza A virus (A/swine/Taiwan/CO935/2004(H... 32.2 11
                  gb|DQ447187.1| Influenza A virus (A/swine/Taiwan/CO935/2004(H... 32.2 11
                  gb|AY060041.1| Influenza A virus (A/SW/NE/21147/01(H1N2)) hem... 32.2 11
                  gb|CY009332.1| Influenza A virus (A/Fort Worth/50(H1N1)) segm... 32.2 11
                  gb|CY008988.1| Influenza A virus (A/Denver/57(H1N1)) segment ... 32.2 11
                  gb|AY377929.1| Influenza A virus (A/swine/Taichung/200-8/2002... 32.2 11
                  gb|AF117241.1|AF117241 Influenza A virus (A/South Carolina/1/... 32.2 11
                  dbj|D00837.1|FLA39HA Influenza A virus (A/swine/Cambridge/193... 32.2 11
                  dbj|AB043486.1| Influenza A virus (A/Saga/2/1957(H1N1)) HA ge... 32.2 11
                  dbj|AB043485.1| Influenza A virus (A/Meguro/1/1956(H1N1)) HA ... 32.2 11
                  dbj|AB043484.1| Influenza A virus (A/Yamagishi/55(H1N1)) HA g... 32.2 11
                  dbj|AB043483.1| Influenza A virus (A/Taiwan/13/1954(H1N1)) HA... 32.2 11
                  dbj|AB043482.1| Influenza A virus (A/Kojiya/1/1952(H1N1)) HA ... 32.2 11
                  gb|AF116576.1|AF116576 Influenza A virus (A/New_York/1/18(H1N... 32.2 11
                  gb|AF116575.1|AF116575 Influenza A virus (A/Brevig_Mission/1/... 32.2 11
                  gb|U04859.1|IAU04859 Influenza A virus (H1N1) A/swine/Cambrid... 32.2 11

                  Comment


                  • #39
                    Re: July San Paolo Sequence Released

                    Updated travel log 2

                    gb|GQ414768.1| Influenza A virus (A/Sao Paulo/43812/2009(H1N1... 38.2 0.19
                    gb|GQ411907.1| Influenza A virus (A/Shanghai/143T/2009(H1N1))... 38.2 0.19
                    gb|GQ402203.1| Influenza A virus (A/Canada-MB/RV1982/2009(H1N... 38.2 0.19
                    gb|GQ392029.1| Influenza A virus (A/Italy/127/2009(H1N1)) seg... 38.2 0.19
                    gb|GQ368664.1| Influenza A virus (A/Sao Paulo/2233/2009(H1N1)... 38.2 0.19
                    gb|GQ330653.1| Influenza A virus (A/Italy/56/2009(H1N1)) segm... 38.2 0.19
                    gb|GQ329076.1| Influenza A virus (A/Paris/2722/2009(H1N1)) se... 38.2 0.19
                    gb|CY041830.1| Influenza A virus (A/New York/3348/2009(H1N1))... 38.2 0.19
                    gb|CY041822.1| Influenza A virus (A/New York/3352/2009(H1N1))... 38.2 0.19
                    gb|CY041782.1| Influenza A virus (A/New York/3337/2009(H1N1))... 38.2 0.19
                    gb|GQ323551.1| Influenza A virus (A/Massachusetts/08/2009(H1N... 38.2 0.19
                    gb|GQ323451.1| Influenza A virus (A/Rhode Island/03/2009(H1N1... 38.2 0.19
                    gb|GQ323446.1| Influenza A virus (A/Maine/03/2009(H1N1)) segm... 38.2 0.19
                    gb|GQ287625.1| Influenza A virus (A/Tokushima/1/2009(H1N1)) s... 38.2 0.19
                    gb|GQ283493.1| Influenza A virus (A/Finland/555/2009(H1N1)) s... 38.2 0.19
                    gb|GQ232044.1| Influenza A virus (A/Rhode Island/02/2009(H1N1... 38.2 0.19
                    gb|GQ232007.1| Influenza A virus (A/Vermont/03/2009(H1N1)) se... 38.2 0.19
                    gb|GQ200287.1| Influenza A virus (A/Shandong/1/2009(H1N1)) se... 38.2 0.19
                    gb|GQ166222.1| Influenza A virus (A/Italy/07/2009(H1N1)) segm... 38.2 0.19

                    Comment


                    • #40
                      Re: July San Paolo Sequence Released

                      Updated travel log 3

                      gb|GQ414768.1| Influenza A virus (A/Sao Paulo/43812/2009(H1N1... 34.2 2.9
                      gb|GQ377095.1| Influenza A virus (A/California/24/2009(H1N1))... 34.2 2.9
                      gb|GQ359765.1| Influenza A virus (A/Stockholm/31/2009(H1N1)) ... 34.2 2.9
                      gb|GQ292961.1| Influenza A virus (A/Mexico City/22/2009(H1N1)... 34.2 2.9
                      gb|GQ229293.1| Influenza A virus (A/swine/Hong Kong/NS1659/20... 34.2 2.9
                      gb|GQ232085.1| Influenza A virus (A/Guangdong/02/2009(H1N1)) ... 34.2 2.9
                      gb|GQ223435.1| Influenza A virus (A/Guangdong/05/2009(H1N1)) ... 34.2 2.9
                      gb|GQ132144.1| Influenza A virus (A/Canada-ON/RV1529/2009(H1N... 34.2 2.9

                      Comment


                      • #41
                        Re: July San Paolo Sequence Released

                        Note that the 2001 Hong Kong swine has 2 of the 3 polymorphisms (no random mutations required).

                        Comment


                        • #42
                          Re: July San Paolo Sequence Released

                          Originally posted by niman View Post
                          Updated travel log 2

                          gb|GQ414768.1| Influenza A virus (A/Sao Paulo/43812/2009(H1N1... 38.2 0.19
                          gb|GQ411907.1| Influenza A virus (A/Shanghai/143T/2009(H1N1))... 38.2 0.19
                          gb|GQ402203.1| Influenza A virus (A/Canada-MB/RV1982/2009(H1N... 38.2 0.19
                          gb|GQ392029.1| Influenza A virus (A/Italy/127/2009(H1N1)) seg... 38.2 0.19
                          gb|GQ368664.1| Influenza A virus (A/Sao Paulo/2233/2009(H1N1)... 38.2 0.19
                          gb|GQ330653.1| Influenza A virus (A/Italy/56/2009(H1N1)) segm... 38.2 0.19
                          gb|GQ329076.1| Influenza A virus (A/Paris/2722/2009(H1N1)) se... 38.2 0.19
                          gb|CY041830.1| Influenza A virus (A/New York/3348/2009(H1N1))... 38.2 0.19
                          gb|CY041822.1| Influenza A virus (A/New York/3352/2009(H1N1))... 38.2 0.19
                          gb|CY041782.1| Influenza A virus (A/New York/3337/2009(H1N1))... 38.2 0.19
                          gb|GQ323551.1| Influenza A virus (A/Massachusetts/08/2009(H1N... 38.2 0.19
                          gb|GQ323451.1| Influenza A virus (A/Rhode Island/03/2009(H1N1... 38.2 0.19
                          gb|GQ323446.1| Influenza A virus (A/Maine/03/2009(H1N1)) segm... 38.2 0.19
                          gb|GQ287625.1| Influenza A virus (A/Tokushima/1/2009(H1N1)) s... 38.2 0.19
                          gb|GQ283493.1| Influenza A virus (A/Finland/555/2009(H1N1)) s... 38.2 0.19
                          gb|GQ232044.1| Influenza A virus (A/Rhode Island/02/2009(H1N1... 38.2 0.19
                          gb|GQ232007.1| Influenza A virus (A/Vermont/03/2009(H1N1)) se... 38.2 0.19
                          gb|GQ200287.1| Influenza A virus (A/Shandong/1/2009(H1N1)) se... 38.2 0.19
                          gb|GQ166222.1| Influenza A virus (A/Italy/07/2009(H1N1)) segm... 38.2 0.19
                          Sequences with mixtures at this position include

                          A/Canada-MB/RV2020/2009
                          A/Canada-MB/RV2013/2009
                          A/Canada-MB/RV1977/2009
                          A/Canada-MB/RV2023/2009
                          A/Canada-MB/RV1964/2009

                          Comment


                          • #43
                            Re: July San Paolo Sequence Released

                            So this mutation found was V252M, and not V252I, found in 1918?

                            Comment


                            • #44
                              Re: July San Paolo Sequence Released

                              Originally posted by Rwilmer View Post
                              So this mutation found was V252M, and not V252I, found in 1918?
                              The nucleotide change responsible for V252M is as indicated in the travel log (and is in the 1918 isolates).

                              Comment


                              • #45
                                Re: July San Paolo Sequence Released

                                The problem is that is was bad a biology in high school so I really don't understand any of this. Especially deoxyribonucleic acid.

                                Comment

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