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  • #61
    Re: July San Paolo Sequence Released

    Originally posted by Rwilmer View Post
    So this mutation found was V252M, and not V252I, found in 1918?

    You understand very well. The V252M mutation that started this whole thread was stated clearly by Dr. Niman to be found in the 1918 virus. That is simply not true. V252I is found in all of the 1918 H1N1 pandemic viruses as is typically the case for modern human H1N1 Seasonal Flu.

    Most of the rest of this discussion is noncredible nonsense and pure, unscientific speculation that escalates the current situaltion to unreasonalbly high levels of concern.

    Having said that, please be aware that the Swine Flu virus could change in a fundamental way and become a serious health problem for many people around the world, but that is not currently the case.

    Comment


    • #62
      Re: July San Paolo Sequence Released

      Originally posted by Mamabird View Post
      You understand very well. The V252M mutation that started this whole thread was stated clearly by Dr. Niman to be found in the 1918 virus. That is simply not true. V252I is found in all of the 1918 H1N1 pandemic viruses as is typically the case for modern human H1N1 Seasonal Flu.

      Most of the rest of this discussion is noncredible nonsense and pure, unscientific speculation that escalates the current situaltion to unreasonalbly high levels of concern.

      Having said that, please be aware that the Swine Flu virus could change in a fundamental way and become a serious health problem for many people around the world, but that is not currently the case.
      Please. The genetic change in the San Paulo IS found in all three 1918 sequences (as well as every isolate listed in the travel log). Thus, the GENETIC change is IDENTICAL (same nucleotide at same position). Most of the human sequences have a SECOND change, which creates V252I. instead of V252M. Thus, although the protein at position 252 is either M or V, depending on changes at the second position in the codon, the first position, which is CHANGED in the Sao Paulo sequence MATCHES 1918, handwaving about protein differences notwithstanding.

      Comment


      • #63
        Re: July San Paolo Sequence Released

        Originally posted by Mamabird View Post
        You understand very well. The V252M mutation that started this whole thread was stated clearly by Dr. Niman to be found in the 1918 virus. That is simply not true. V252I is found in all of the 1918 H1N1 pandemic viruses as is typically the case for modern human H1N1 Seasonal Flu.

        Most of the rest of this discussion is noncredible nonsense and pure, unscientific speculation that escalates the current situaltion to unreasonalbly high levels of concern.

        Having said that, please be aware that the Swine Flu virus could change in a fundamental way and become a serious health problem for many people around the world, but that is not currently the case.
        WRONG. This thread started with a travel log in post #3

        http://www.flutrackers.com/forum/sho...37&postcount=3

        Travel logs are based on polymorphisms at the NUCEOTIDE level and identify sequences in the database with are IDENTICAL. The search string used for the travel log includes the new POLYMORPHISM represented in lower case in the search string
        GCAACTGGAAATCTAa
        This sequence is found in ALL sequences below (and these are the ONLY influenza sequence at Genbank which have this sequence) and as seen below, sequences which EXACTLY match include the three 1918 HA sequences (in BOLD)

        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


        • #64
          Re: July San Paolo Sequence Released

          Hi folks,

          Couple of days out of the board and them you're talking about my place
          So far I'm not observing no alarming signals on life around here. Many schools are delaying the start of classes after winter which is very wise. People are taking care in public transportation (keeping the windows open and distance etc) as much as they can... I hope this very little animal keeps calm around here, it's a too big city. Sao Paulo has people all over the world going in and out... (it can mix with anything here, Peru, Colombia, China, Korea etc - we are full of recent immigrants from those countries)

          The girl who died lived at Osasco (very poor family) was the victim who confirmed the sustained spread of the virus in Brazil. (Osasco is in the big region of Sao Paulo)

          I will try to do a track of these cases to post later today.

          Keep on the good work.

          Comment


          • #65
            Re: July San Paolo Sequence Released

            Originally posted by tropicalgirl View Post
            Hi folks,

            Couple of days out of the board and them you're talking about my place
            So far I'm not observing no alarming signals on life around here. Many schools are delaying the start of classes after winter which is very wise. People are taking care in public transportation (keeping the windows open and distance etc) as much as they can... I hope this very little animal keeps calm around here, it's a too big city. Sao Paulo has people all over the world going in and out... (it can mix with anything here, Peru, Colombia, China, Korea etc - we are full of recent immigrants from those countries)

            The girl who died lived at Osasco (very poor family) was the victim who confirmed the sustained spread of the virus in Brazil. (Osasco is in the big region of Sao Paulo)

            I will try to do a track of these cases to post later today.

            Keep on the good work.
            It would be interesting to know if the other two deaths in Osasco had any contact with the index case or any of her relatives.

            Comment


            • #66
              Re: July San Paolo Sequence Released

              The second victim at Osasco where treated at the same hospital. No link with the first one besides that...

              keep in mind that Osasco is not a small city, it's linked to São Paulo (think great NY if you wish) it's the biggest urban area in Brazil, with transportation (trains and buses) getting in and out all time in a vast area.

              Victim 2 at Osasco - 6 victim in Brazil

              died on 07/11
              man 21yo , lived at Osasco and studied at Sao Paulo, he was treated for a normal flu Went to hospital with symptoms twice (4 days before 06/28) and was sent back home 07/01 – got in at hospital - 07/11 – died pneumonia. Diagnosed only after death. - Same hospital of the 1st victim

              not related with each other, after his death the flu was declared sustained inside Brazil

              Brazil is with 60 deaths now.
              Trying to collect all the information, but still a bit messy - some doubts.
              Attached Files

              Comment


              • #67
                Re: July San Paolo Sequence Released

                Originally posted by niman View Post
                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
                Also in recently released NY sequences:

                A/New York/3449/2009
                A/New York/3324/2009
                A/New York/3499/2009
                A/New York/3498/2009
                A/New York/3389/2009
                A/New York/3338/2009
                A/New York/3514/2009

                Comment


                • #68
                  Re: July San Paolo Sequence Released

                  Mamabird said:

                  Most of the rest of this discussion is noncredible nonsense and pure, unscientific speculation that escalates the current situaltion to unreasonalbly high levels of concern.
                  Agreed...very mushy discussion!

                  But, I do have another question. Whether it's V252M or V252I, do we know how that affects the biology, the clinical picture for a patient? Or, is it just a curious coincidence that 'it', whatever 'it' is, was present in 1918, or in human H1N1?

                  Snick

                  Comment


                  • #69
                    Re: July San Paolo Sequence Released

                    Originally posted by Mamabird View Post
                    You understand very well. The V252M mutation that started this whole thread was stated clearly by Dr. Niman to be found in the 1918 virus. That is simply not true. V252I is found in all of the 1918 H1N1 pandemic viruses as is typically the case for modern human H1N1 Seasonal Flu.

                    Most of the rest of this discussion is noncredible nonsense and pure, unscientific speculation that escalates the current situaltion to unreasonalbly high levels of concern.

                    Having said that, please be aware that the Swine Flu virus could change in a fundamental way and become a serious health problem for many people around the world, but that is not currently the case.
                    Thanks mamabird. Dr. Niman is an alarmist in my opionion. Is this a 1918 re-run or is niman wrong?

                    Comment


                    • #70
                      Re: July San Paolo Sequence Released

                      Originally posted by Snicklefritz View Post
                      Mamabird said:



                      Agreed...very mushy discussion!

                      But, I do have another question. Whether it's V252M or V252I, do we know how that affects the biology, the clinical picture for a patient? Or, is it just a curious coincidence that 'it', whatever 'it' is, was present in 1918, or in human H1N1?

                      Snick
                      Please. The Sao Pualo isolate has V252M and the polymorphism causing the change is in all three 1918 HA sequences (out of three 1918 HA sequences at Genbank). This polymorphisms and the upstream region is VERY rare as shown by the travel log, which searches the entire flu database at Genbank. V252M is in the 2001 swine isolate from Hong Kong, which also has the third newly acquired polymorphism in the Sao Paulo sequences. This is NOT a coincidence. Swine have polymorphisms from 1918, which how they reappear in humans now that swine H1N1 has entered the human population. This is a rather SIMPLE concept.

                      It's the real deal. It's in the first San Paulo fatality and in 1918, hand waving about downstream sequences not withstanding. It will be in more 2009 pandemic sequences for Brazil / Argentina.

                      Comment


                      • #71
                        Re: July San Paolo Sequence Released

                        Originally posted by Rwilmer View Post
                        Thanks mamabird. Dr. Niman is an alarmist in my opionion. Is this a 1918 re-run or is niman wrong?
                        Dream on. This isn't Kansas and influenza evolution, like ALL replicating organisms is at NUCLEOTIDE (as in GENE) level, handwaving about downstream sequences notwithstanding.

                        Comment


                        • #72
                          Re: July San Paolo Sequence Released

                          Dr Niman has been tracking the evolution of Influenza for a very long time and he has more knowledge on the genetics that probably anyone here.
                          Last edited by Laidback Al; July 30, 2009, 11:51 PM. Reason: edited

                          Comment


                          • #73
                            Re: July San Paolo Sequence Released

                            Originally posted by Jeremy
                            Dr Niman has been tracking the evolution of Influenza for a very long time and he has more knowledge on the genetics that probably anyone here.
                            Thank you. I think this polymorphism is of considerable concern. An independent analysis of this changed reached the same conclusion.

                            As a quick review. The Sao Paulo isolate had three new polymorphisms, all tracing to different sources. Two were in prior 2009 pandemic sequences. One is widespread and has been seen in a prior Sao Paulo isolate. However, the third change is in other 2009 pandemic sequences, none of which have the second polymorphism (STRONG signal of recombination). However, this third polymorphism is in the 2001 Hong Kong swine sequences which also has V252M.

                            Once again, the fact that two of the three new acquisitions in the fatal infection (11F) are in the same swine sequence from Hong Kong is NOT a coincidence.

                            Swine act as a reservoir for earlier polymorphisms that were circulating in 1918, and the nucleotide creating V252M in the pandemic and swine H1N1's is also in the 1918 sequneces (but they have an additional nucleotide change, so they have V252I, as do the earlier human seasonal flu sequences).

                            The H1N1 is constantly evolving, and the latest changes are just starting to be released, which is why the Sao Paulo sequence is from the FIRST reported fatality in Sao Paulo (which is a VERY large metropolitan region).

                            I expect to see more sequences with V252M. MANY family members were also H1N1 positive and I suspect those sequences also have V252M, which was reported for the FIRST time in 2009 pandemic H1N1 when this sequences was made public yesterday.
                            Last edited by AlaskaDenise; July 31, 2009, 01:18 AM. Reason: edited

                            Comment


                            • #74
                              Re: July San Paolo Sequence Released

                              Lets keep the posts that are ON topic ON the thread, and take the OFF topic posts OFF the thread.
                              I think the moderators (aka censors) are a bit confused.

                              Comment


                              • #75
                                Re: July San Paolo Sequence Released

                                Originally posted by Snicklefritz View Post
                                Mamabird said:



                                Agreed...very mushy discussion!

                                But, I do have another question. Whether it's V252M or V252I, do we know how that affects the biology, the clinical picture for a patient? Or, is it just a curious coincidence that 'it', whatever 'it' is, was present in 1918, or in human H1N1?

                                Snick
                                Here is the genetics 101 description, which I think is a bit off topic, but many of the post on the thread have been off topic.

                                In the pandemic 2009 sequence, codon 252 is GTG, which codes for valine (V). In the Sao Paulo sequence the GTG codon is changes to ATG (the G at the first position of the codon changes to A). The A at the first position of codon 252 is also in the 1918 pandemic sequences (so it MATCHES San Paulo at this position as well as the upstream region, which is why it was in the travel log). However isoleucine (I) is present in the 1918 sequence because isoleucine can be coded by ATA, ATC, or ATT (AT anything but G). Thus, the A at the first position of codon 252 is present in the Sao Paulo sequence, as well EVERY sequence in the posted travel log, including the 1918 sequences.

                                However, sequences that change the third position to anything but G, will code for I instead of the M found in the 2009 pandemic sequence, as well as the 2001 Hong Kog swine sequence. The bottom line is the polymorphism in Sao Paulo, as well as the upstream region in the Sao Paulo sequence EXACTLY matches the 1918 sequences and every sequence in the travel log below (downstream changes notwithstand)

                                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

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