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July San Paolo Sequence Released

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  • #16
    Re: July San Paolo Sequence Released

    Originally posted by hawkeye View Post
    So the San Paolo Sequence is not of the same Novel H1N1 source?
    No. San Paolo is the Novel H1N1 with 3 changes in HA (as represented by the three travel logs posted).

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    • #17
      Re: July San Paolo Sequence Released

      Originally posted by Rwilmer View Post
      Dr. Niman, what does this mutation mean? More virulence? Will the vaccine still work?
      This may affect the vaccine (it seems to make a big difference in Influenza B, which I really don't follow closely).

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      • #18
        Re: July San Paolo Sequence Released

        You still haven't answered my question, what effects will this mutation have on the viruses virulence?

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        • #19
          Re: July San Paolo Sequence Released

          Originally posted by Rwilmer View Post
          So does this mean that swine has a much higher virulence as a result, Dr. Niman? What is V252M associated with, virulence, transmissability? I was reading up on this a little and found that seasonal flu also has this mutation, is that correct? http://synapse.koreamed.org/Synapse/...jbv-39-125.pdf
          Translation from Korean of abstract

          Journal of Bacteriology and Virology 2009. Journal of Bacteriology and Virology 2009. Vol. Vol. 39, No. 39, No. 2 p.125 – 136 2 p.125 - 136
          DOI 10.4167/jbv.2009.39.2.125 DOI 10.4167/jbv.2009.39.2.125

          Genetic Characteristics and Phylogenetic Analysis of Influenza Type B Viruses Isolated from Nasopharyngeal Suction Samples of Korean Patients


          Yun Hee Baek, Young Jun Song, Min-Suk Song, Philippe Noriel Q. Yun Hee Baek, Young Jun Song, Min-Suk Song, Philippe Noriel Q. Pascua, Jun Han Lee, Pascua, Jun Han Lee,
          Heon-Seok Han, Sung-Il Woo, Seok-Yong Kim and Young-Ki Choi


          College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea


          To investigate the genetic characteristics of human influenza type B viruses circulating in Chungbuk province, Korea, we tested 510 clinical samples of nasopharyngeal suction from pediatric patients diagnosed with respiratory illness between June 2007 and June 2008. Twelve out of thirty-six isolates were identified as type B influenza virus by RT-PCR

          Interestingly, genetic characterization of type B viruses isolated in this study revealed that all type B influenza viruses were the Yamagata lineages, a vaccine strains of southern hemisphere during 20072008, type B influenza viruses were the Yamagata lineages, rather than the Victoria lineage of northern hemisphere during 20072008.

          Furthermore, there were a total of twelve unique mutations (HA: H40Y, D/G230S, V252M and K272R and NA: P3H, P/T/S42Q, N59S) occurred in our type B isolates. These results suggest that relative high prevalence of type B viruses in Korea during 20072008 season might be due to the wrong vaccine strains selection.

          Taken together, the results of this study demonstrate continuous evolutions of human type B viruses by antigenic drift and also highlight the need to closely monitoring of influenza viruses to aid
          the early detection of potentially pandemic strains as well as underscore the need for new therapeutics.

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          • #20
            Re: July San Paolo Sequence Released

            This was collected almost a month ago. How far has it spread in that time?
            Wotan (pronounced Voton with the ton rhyming with on) - The German Odin, ruler of the Aesir.

            I am not a doctor, virologist, biologist, etc. I am a layman with a background in the physical sciences.

            Attempting to blog an nascent pandemic: Diary of a Flu Year

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            • #21
              Re: July San Paolo Sequence Released

              Originally posted by theforeigner View Post
              Thanks for trying to explain Niman but I still don´t understand . The thing is I have no clue concerning sequenses ect, so what I am asking for is your bid, in plain english, what the consequeses are? is this a mutation making the H1N1 more virulent?

              I belive we are MANY who wish that thise newsreports on sequenses would always be followed by a short explanation, in plain english, because we dont have knowledge about the issue.
              Here is a quick rundown. The July sequence from San Paulo is the most recent pandemic H1N1 sequence released to date. Most of the other sequences are from isolates in April, May, and early June. The characterization sheet indicates this isolate came from an 11 year old girl who was fatally infected with H1N1.
              Only the HA (codes for the H1 in H1N1) sequence was released, and it has three changes. The travel logs listed show which other sequences in the data base have that change. The search string requires sequence identity on at least one side of the change (there are too many differences between infleunza A and influenza B to pick up shared polymorphisms), so I don't know if V252M in influenza B corresponds to V252M based on influenza A H3 numbering.

              However, for the bottom line, V252M may allow the virus to escape from the vaccine being developed, because that change is important in influenza B immunologoical recognition and may be one of the reasons half of the time the influenza B vaccine is a mis-match.

              However, apart from the vaccine issue, this change was present in the 1918 pandemic strain (as represented by the three 1918 HA sequences in the database).

              The 1918 pandmeic strain combined pieces from H1N1 seasonal flu with H1N1 swine flu, and V252M is found in seasonal flu (2006 isolates from Peru) as well as early (pre-1957) seasonal H1N1. It is also in swine H1N1, so the profile for V252M is not a good one.

              The other two changes are in 2009 pandemic isolates, but in different sets of isolates signaling recombination, which is what is used to jumble up the changes to create novel sequences with new properties.

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              • #22
                Re: July San Paolo Sequence Released

                This report also discusses V252M in influenza B with respect to vaccines

                http://www.nimr.mrc.ac.uk/wic/report...t_mar_2006.pdf

                Comment


                • #23
                  Re: July San Paolo Sequence Released

                  Originally posted by wotan View Post
                  This was collected almost a month ago. How far has it spread in that time?
                  This sequence probably came from the first fatality in Brazil (hat tip Shiloh)

                  Almost a month after the death of the daughter of 11 years (the first fatal victim of swine influenza in São Paulo), Paula Nilce Laguna, 40 years, and John Laguna, of 57, spoke in this Saturday for the first time on the subject. The couple confirmed that her daughter never had hantavirus contamination - contracted by rats - who supposedly had weakened his immune system and facilitated the death by influenza virus A (H1N1).

                  - The challenge that was run by the Department of Health As you can tell that her body was weakened? And now that the examination was negative? Based on what has been said that - Nilce said, presenting the certificate issued by the Institute Adolfo Lutz, showing that the girl had no previous health problems.

                  Announcing the death of the child, the state Secretary of Health, Luiz Roberto Barradas, said that the victim was suspected hantavirus in childhood. On Friday, in response, the Department of Health said it investigated the possibility that the girl had shaken the immunity of any infection before, but that would be a possibility.

                  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.

                  - I have suffered an emotional distress, was not able to speak. It was all played in the media and I was at home taking care of my son with my husband admitted - Nilce bubble.

                  In the coming days, she, her husband and son will travel to São Paulo.

                  - The confusion took my right to come and go. Some people believe, others not. Confidentiality is a right of the family and I need privacy - Nilce said. <!-- / message -->

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                  • #24
                    Re: July San Paolo Sequence Released

                    Originally posted by Sally View Post
                    I did a quick look for V252M in influenza B and believe I found it and it would be V236M using H3 numbering (so these are NOT the same).

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                    • #25
                      Re: July San Paolo Sequence Released

                      Originally posted by niman View Post
                      I did a quick look for V252M in influenza B and believe I found it and it would be V236M using H3 numbering (so these are NOT the same).
                      So what does this mean niman, the vaccine will work?

                      Comment


                      • #26
                        Re: July San Paolo Sequence Released

                        Originally posted by niman View Post
                        The change (V252M) was present in 1918. The isolates at the bottom of the list (South Carolina, Brevig Mission, and New York) were from dead patients from 1918 (if you click on the link you will see a full description of each isolate).
                        Seasonal flu (from Peru!), swine, and 1918 are a bad combination.
                        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?

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                        • #27
                          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?
                          I was working at the nucleotide level which matches 1918 (as seen in the travel log), but the match only goes to the first position of the 252 codon, so that produces V252M in 2009 swine pandemic H1N1, but V252I in the 1918 pandemic strains (I used H3 numbering - it is position 266 in the H1 sequence).

                          Thus, positions 249-252 (using H3 numbering) are:

                          GNLV = wild type H1N1
                          GNLM = 2009 pandemic H1N1
                          GNLI = 1918 pandemic H1N1

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                          • #28
                            Re: July San Paolo Sequence Released

                            Thanks Dr. Niman for answering all these questions. I have one additional

                            With these three changes is the virus obtaining more "human" genes? (re: 1918 being 50/50 pig/human).

                            Comment


                            • #29
                              Re: July San Paolo Sequence Released

                              Originally posted by hawkeye View Post
                              Thanks Dr. Niman for answering all these questions. I have one additional

                              With these three changes is the virus obtaining more "human" genes? (re: 1918 being 50/50 pig/human).
                              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.

                              Comment


                              • #30
                                Re: July San Paolo Sequence Released

                                Initial description of case:

                                Girl, 11 years is the first fatal victim of swine influenza in São Paulo
                                Rosanne D'Agostino
                                From UOL News
                                In Sao Paulo

                                A girl of 11 years who died at the end of June is the first fatal victim of avian A (H1N1) in São Paulo State, informed the Secretariat of Health of the State this Friday. This is the second death related to the disease in Brazil - the first was a truck driver in Rio Grande do Sul

                                The girl was hospitalized in a private hospital in Osasco and died on June 30. Two days before the girl felt abdominal pain and vomiting, with symptoms of the disease and was referred to the health unit.

                                Eventually released and returned with signs of septic shock the day he died because of a cardiorespiratory arrest. The swine flu was confirmed only after death.


                                The parents of the girl, her brother and a person close also showed signs of disease, but are good. The family is middle class and the children are enrolled in public schools, informed the Secretary of Health, Luiz Roberto Barradas Barata. He said the way the girl is contaminated is under investigation.

                                "We believe this was not the cause of death, but the flu helped it reduce the immune system, which was already compromised," the secretary said in press conference. He said the child suffered from other problems, including pneumonia, and has had low immunity.

                                The Secretary said that nothing will change on the policy to combat the disease in São Paulo. "The case shows that the state is on alert," he said.

                                According to relatives, the child does not go abroad nor had contact with patients with symptoms of influenza. On July 1, a brother of the child of 7 years, showed symptoms of flu and was taken to the Emilio Ribas Institute to be hospitalized in isolation. He was discharged with recommendation for home insulation.

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