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H7N9 discussion thread: January 24, 2014 to Feb 5 2014 (closed)

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  • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

    WOW that was fast. Very impressive.

    In a display of intellectual and logistical expertise, the Public Health Laboratory Services Branch, Centre for Health Protection in Kowloon, Hong Kong sampled material from a man on January 28, 2014, sequenced, annotated and published early on January 30, 2014, much less than 48 hours after the sample, autopsy to full genetic report in 2 days.
    Please do not ask me for medical advice, I am not a medical doctor.

    Avatar is a painting by Alan Pollack, titled, "Plague". I'm sure it was an accident that the plague girl happened to look almost like my twin.
    Thank you,
    Shannon Bennett

    Comment


    • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

      Originally posted by NS1 View Post
      Rapid Release
      Emergent H7N9
      Centre for Health Protection
      Hong Kong

      The sequences from Hong Kong in January demonstrate a virus on the move.

      In a display of intellectual and logistical expertise, the Public Health Laboratory Services Branch, Centre for Health Protection in Kowloon, Hong Kong sampled material from a man on January 28, 2014, sequenced, annotated and published early on January 30, 2014, much less than 48 hours after the sample, autopsy to full genetic report in 2 days.

      We are grateful for their demonstration of intellectual prowess because for this one, timeliness is extremely important.

      Early January Hong Kong has homology at the HA to the circulating human strains with the gain of material from pH1N1. More recent Hong Kong data shows a variance at key aminos from the circulating human Emergent H7N9 Hemagglutinin segments. The reservoir in China is under revision and is quite potentially now attractant to pH1N1 sub-segment input.

      We'd like to see the clinicals on the latest case and additional passage strategies when available.

      If a dominant input reservoir switch is at work from sH3N2 to pH1N1 for new genetic material, potential risk increases due to the established "give / take" relationship of H7 to pH1N1.
      From the press release today:

      30 January 2014

      Epidemiological investigation and follow-up actions by CHP on confirmed human case of avian influenza A(H7N9)

      snip

      "Upon genetic analysis by the PHLSB, genes of the virus from the patient's specimen were determined to be of avian origin. There were no significant differences from H7N9 viruses detected so far in the Mainland and Hong Kong, nor was there evidence of genetic reassortment with genes of human influenza origin or resistance to the antiviral Tamiflu," the spokesman remarked."

      http://www.chp.gov.hk/en/view_content/33300.html

      Comment


      • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

        My thanks to HK CHP for being good at filling out the sequence meta-data as well.

        Comment


        • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

          Originally posted by Shannon View Post
          I know I stand on the outside of accepted thought here but, I too am doubtful that chickens are the vector. If they are, I don't think they are the only vector. When seeing a doctor for their allotted 6 minutes, one of the questions asked is if they have been in contact with chickens. If they don't answer in the affirmative they don't have H7N9. Therefore, they have H1N1. I cannot help but wonder how many cases are missed? My guess is a lot are slipping through the cracks. Roughly 30% say they have not been in contact with live chickens. If they say they haven't been in contact and either die or sicken, to the point they cannot answer questions, the doctors later try to reconstruct their lives through family. The assumption is if the family says they don't know of any contact with chickens then they must be ignorant or mistaken. The person really must have come into contact because that is how you get H7N9. Entrenched thinking.
          I agree Shannon. Research suggest that mice, in particular, are a very possible vector. I posted a number of studies last year and just found the following:

          ABSTRACT A novel avian-origin influenza A/H7N9 virus infecting humans was first identified in March 2013 and, as of 30 May
          2013, has caused 132 human infections leading to 33 deaths. Phylogenetic studies suggest that this virus is a reassortant, with the
          surface hemagglutinin (HA) and neuraminidase (NA) genes being derived from duck and wild-bird viruses, respectively, while
          the six “internal gene segments” were derived from poultry H9N2 viruses. Here we determine the pathogenicity of a human
          A/Shanghai/2/2013 (Sh2/H7N9) virus in healthy adult mice in comparison with that of A/chicken/Hong Kong/HH8/2010 (ck/
          H9N2) virus, highly pathogenic avian influenza (HPAI) A/Hong Kong/483/1997 (483/H5N1) virus, and a duck influenza A H7N9
          virus of different genetic derivation, A/duck/Jiangxi/3286/2009 (dk/H7N9). Intranasal infection of mice with Sh2/H7N9 virus
          doses of 103, 104, and 105 PFU led to significant weight loss without fatality.
          This virus was more pathogenic than dk/H7N9 and
          ck/H9N2 virus, which has six internal gene segments that are genetically similar to Sh2/H7N9. Sh2/H7N9 replicated well in the
          nasal cavity and lung, but there was no evidence of virus dissemination beyond the respiratory tract. Mice infected with Sh2/
          H7N9 produced higher levels of proinflammatory cytokines in the lung and serum than did ck/H9N2 and dk/H7N9 but lower
          levels than 483/H5N1. Cytokine induction was positively correlated with virus load in the lung at early stages of infection. Our
          results suggest that Sh2/H7N9 virus is able to replicate and cause disease in mice without prior adaptation but is less pathogenic
          than 483/H5N1 virus.

          http://mbio.asm.org/content/4/4/e00362-13.full.pdf
          "I know God will not give me anything I can't handle. I just wish that He didn't trust me so much." - Mother Teresa of Calcutta

          Comment


          • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

            Originally posted by sharon sanders View Post
            From the press release today:

            30 January 2014

            Epidemiological investigation and follow-up actions by CHP on confirmed human case of avian influenza A(H7N9)

            snip

            "Upon genetic analysis by the PHLSB, genes of the virus from the patient's specimen were determined to be of avian origin. There were no significant differences from H7N9 viruses detected so far in the Mainland and Hong Kong, nor was there evidence of genetic reassortment with genes of human influenza origin or resistance to the antiviral Tamiflu," the spokesman remarked."

            http://www.chp.gov.hk/en/view_content/33300.html
            The recent polymorphic additions to the human Emergent H7N9 reservoir that have been dropped from this latest sequence are quite significant, although the underlying framework of the HA is without ReAssortment (as expected).

            Those significant drops on the current sequence considered next to the multiple pH1N1 adoptions on the HK sequence from earlier this month increase the HK reservoir risk potential due to present tense high plasticity on well-studied and on under-studied regions of the Emergent H7N9 H7 Hemagglutinin.

            As previously noted, we'd appreciate seeing multiple passage strategies, especially LLC against Avian-inductive pathways, on all available Hong Kong human sequences.

            We make this request understanding the cost and re-allocation of resources required. Defining the revision mechanism at this point in time in this particular disease pool is essential to mediating pandemic risk and, more importantly, in preventing a black swan event.

            Comment


            • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

              snip

              Editor’s note: Dr. Tom Frieden is the director for the Center for Disease Control. The views expressed are his own.
              Today marks the Lunar New Year – and the world’s largest annual migration. There will be more than 3.6 billion transit trips within China, in addition to countless international trips. Yet this celebration comes at a time of growing concern about the H7N9 avian influenza virus. And this concern is not unfounded – should this virus change into a form that easily spreads between people, the world’s next pandemic could occur in the next three weeks.


              http://www.flutrackers.com/forum/sho...d.php?t=217856

              Comment


              • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

                temperature up in Shanghai
                Attached Files
                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


                • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

                  Originally posted by sharon sanders View Post
                  snip

                  Editor’s note: Dr. Tom Frieden is the director for the Center for Disease Control. The views expressed are his own.
                  Today marks the Lunar New Year – and the world’s largest annual migration. There will be more than 3.6 billion transit trips within China, in addition to countless international trips. Yet this celebration comes at a time of growing concern about the H7N9 avian influenza virus. And this concern is not unfounded – should this virus change into a form that easily spreads between people, the world’s next pandemic could occur in the next three weeks.


                  http://www.flutrackers.com/forum/sho...d.php?t=217856
                  A change of strategy? A sincere warning? A probe? Now they are attempting to measure how the public will take the news, not the actual biological impact of the pathogenic event.

                  Predictions like that should be rather foregone for an organisation that is holding hundreds of relevant sequences from publication. The H7N9 reservoir has been actively influencing US pH1N1 for over a year, whether via avian transfer or human sub-clinical co-infection. The CDC has the information to provide a more adept guidance, but this Lunar proclamation is no more a sensible warning than it is a probe to determine net twitter traffic.

                  Comment


                  • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

                    Originally posted by NS1 View Post
                    ..... The CDC has the information to provide a more adept guidance, but this Lunar proclamation is no more a sensible warning than it is a probe to determine net twitter traffic.
                    Not a word of this huge epidemic situation on any TV screens..but I did see it on a crwly one time..8 days ago..
                    CSI:WORLD http://swineflumagazine.blogspot.com/

                    treyfish2004@yahoo.com

                    Comment


                    • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

                      I think it does not matter if no one else has the opinion that genetic bits of H1N1pdm09 are potentially influencing H7N9. The fact is that the world is a huge mixing bowl of genetic material, of all sorts, that interact with no rules. We don't even know what we don't know.

                      H7N9 is an active avian flu outbreak in Eastern China with an approximate case fatality rate of 9% in the 2nd wave. H7N9 has the capability to develop into a more easily transmissible virus at any time.

                      Comment


                      • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

                        Originally posted by sharon sanders View Post
                        I think it does not matter if no one else has the opinion that genetic bits of H1N1pdm09 are potentially influencing H7N9. The fact is that the world is a huge mixing bowl of genetic material, of all sorts, that interact with no rules. We don't even know what we don't know.

                        H7N9 is an active avian flu outbreak in Eastern China with an approximate case fatality rate of 9% in the 2nd wave. H7N9 has the capability to develop into a more easily transmissible virus at any time.
                        No rules? Wrong!

                        The rules exist and are playing everytime everywhere: it is called evolution.

                        The apparent cfr of H7N9 is not well known but should be for hospitalized patient around 33%. Taking into account the tip-of-iceberg phenomenon, it is possible that a number of mild and undiagnosed cases may reduce the actual cfr below the 10% or less.

                        A pandemic species descending from H7N9 will have an unknown cfr.

                        The interference between subtypes is another unknown but the co-circulation of H1pdm09 and H7N9 should be investigated better.

                        H1pdm09 is a dominant strain in youngsters and this hardly would not play a role in current H7N9 epidemiology.

                        Other mechanism, for example the antigen dependent enhancement (A.D.E.) may also play a role.

                        Today Clinical Infectious Diseases journal published an open access report on the first wave H7N9 outbreak cases' characteristics. I recommend strongly a read.

                        Perhaps the most important thing in the paper is the conclusion that host factors may contribute to the epidemiology and pathology observed so far.

                        Host factors are overlooked regularly both by health agencies and flublogia and this is for me a mistake.

                        We could help people to reduce risk of fall ill and developing an adverse outcome disease if we attempt to search and disseminate information about the correlations between hosts factors and illness...

                        Or - as Sharon said - there is not further space for babbling and it is time to seek for a refuge.

                        Comment


                        • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

                          See Sci Library for Reference:

                          Comparison of patients hospitalized with influenza A H7N9, H5N1, and 2009 pandemic H1N1


                          (...)


                          Table 1. Characteristics of subjects hospitalized with H7N9, H5N1, and pH1N1.

                          [H7N9 (ref group) - H5N1 - P_value - pH1N1 - P-value]
                          • Median age (range) - 63 (4, 91) - 26 (1, 75) - <0.001 - 25 (0, 100) - <0.001
                          • Interval from onset – admission days (IQR) - 4 (3,6) - 5 (3,6) - 0.155 - 4 (3,6) - 0.244
                          • Male gender - 87/123 (71%) - 67/119 (56%) - 0.019 - 1937/3486 (56%) - 0.001
                          • Any Co-existing chronic medical conditions - 42/105 (40%) - 11/104 (11%) - <0.001 - 748/3485 (21%) - <0.001
                          • Chronic heart disease - 12/105 (11%) - 1/102 (1%) - 0.001 - 147/3457 (4%) - 0.003
                          • Chronic lung disease - 10/105 (10%) - 6/100 (6%) - 0.344 - 305/3397 (9%) - 0.849
                          • Chronic renal disease - 1/105 (1%) - 1/102 (1%) - 0.984 - 91/3450 (3%) - 0.221
                          • Chronic liver disease - 5/105 (5%) - 1/101 (1%) - 0.092 - 27/3478 (1%) - 0.002
                          • Chronic neurological disease - 3/105 (3%) - 0/39 (0%) - 0.166 - 55/3472 (2%) - 0.356
                          • Diabetes - 18/105 (17%) - 1/100 (1%) - <0.001 - 185/3470 (5%) - <0.001
                          • Asthma - 0/105 (0%) - 0/0 - NA - 102/3442 (3%) - 0.013
                          • Immune compromise - 2/105 (2%) - 1/100 (1%) - 0.586 - 86/3433 (3%) - 0.685
                          • Hypertension - 51/105 (49%) - 2/41 (5%) - <0.001 - 366/3479 (11%) - <0.001
                          • Malignancy - 6/105 (6%) - 1/41 (2%) - 0.375 - 92/3468 (3%) - 0.096
                          • Pregnancy - 2/105 (2%) - 5/106 (5%) - 0.246 - 400/3436 (12%) - <0.001
                          • Smoking history - 26/105 (25%) - 10/88 (11%) - 0.015 - 541/3431 (16%) - 0.02
                          • Obesity (BMI ≥30) - 3/45 (7%) - 0/10 (0%) - 0.265 - 175/2018 (9%) - 0.623

                          _________

                          Any Co-existing chronic medical conditions is any of the following: Asthma, Diabetes, Chronic respiratory disease, Chronic heart disease, Chronic renal
                          disease, Chronic hepatic (liver) disease, Chronic neurological disease, Immune compromise (see Supplementary materials for definitions).

                          (...)


                          -
                          -----

                          Comment


                          • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

                            (...)

                            Table 5. Laboratory results on admission*

                            [Median (inter-quartile range) - H7N9 (ref group) - H5N1 - P-value - pH1N1 - P-value]
                            • White cell count - 4.5 (2.9,6.2) - 3.9 (2.5,7.1) - 0.805 - 6 (4.2,8.8) - <0.001
                            • Lymphocyte count - 0.5 (0.3,0.7) - 0.9 (0.6,1.4) - <0.001 - 1 (0.6,1.5) - <0.001
                            • Neutrophil count - 3.3 (2.2,5.4) - 3 (1.5,5.4) - 0.203 - 4.3 (2.6,6.9) - 0.004
                            • Platelet count - 114 (82,147.5) - 126 (86,196) - 0.203 - 173 (132,229.8) - 0.004
                            • Aspartate aminotransferase - 53 (38,96.5) - 100 (47,233) - 0.076 - 40 (26.4,68.5) - <0.001
                            • Alanine aminotransferase - 35.5 (24,64.5) - 48.5 (29.5,99.5) - <0.001 - 24 (15.6,44) - <0.001
                            • Serum creatinine - 70.7 (58.3,85) - 83 (54,100) - 0.028 - 62 (45.4,81) - <0.001
                            • CK - 195 (96,562) - 552 (126.5,939.8) - 0.255 - 120 (62,304) - <0.001
                            • CRP - 65 (25,113) - 51 (14.2,118.3) - 0.191 - 25.4 (7.9,75.5) - <0.001
                            • LDH - 498 (388,661) - 1025 (334.8,1832.5) - 0.525 - 307 (217,491) - <0.001
                            [n/N (&#37]
                            • Leukopenia - 48/105 (46%) - 54/107 (50%) - 0.489 - 736/3305 (22%) - <0.001
                            • Lymphopenia - 88/99 (89%) - 54/98 (55%) - <0.001 - 1601/2891 (55%) - <0.001
                            • Neutropenia - 13/103 (13%) - 24/97 (25%) - 0.027 - 221/2891 (8%) - 0.086
                            • Neutrophilia - 5/103 (5%) - 15/97 (15%) - 0.011 - 477/2891 (16%) - <0.001
                            • Thrombocytopenia - 80/104 (77%) - 69/105 (66%) - 0.073 - 1106/3066 (36%) - <0.001
                            • Elevated aspartate aminotransferase - 54/103 (52%) - 41/54 (76%) - 0.004 - 1165/3197 (36%) - 0.001
                            • Elevated alanine aminotransferase - 34/100 (34%) - 25/52 (48%) - 0.093 - 668/3167 (21%) - 0.003
                            • Elevated serum creatinine - 11/103 (11%) - 9/62 (15%) - 0.469 - 201/3054 (7%) - 0.129
                            • Elevated CK - 48/98 (49%) - 13/20 (65%) - 0.188 - 1018/2951 (34%) - 0.004
                            • Elevated CRP - 83/92 (90%) - 9/12 (75%) - 0.162 - 1193/1708 (70%) - <0.001
                            • Elevated LDH - 89/98 (91%) - 17/21 (81%) - 0.218 - 1617/2922 (55%) - <0.001
                            * Or earliest available time point after admission. NC = collected.

                            (...)

                            [AST / ALT = Liver enzymes
                            Creatinine = Kidney function
                            CK (creatin - kinase) = heart & Muscle pathology
                            CRP (Protein C reactive) = systemic infection / inflammation
                            LDH (lattico dehydrogenase) = ards / acute lung injury / systemic illness . gm]

                            -
                            -----

                            Comment


                            • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

                              Likely our contributor is referring to the mechanism of recombination, an event not fully undestood and debated in the mainstream flu research establishment.

                              But it is out of any reasonable doubt that H1 IS interfering with avian flu viruses since it is dominant in Young people.

                              How can a virus isolated in thousands of samples not influence the H7N9 epidemiology:

                              Please click on attached image
                              Attached Files
                              Last edited by sharon sanders; February 1st, 2014, 11:29 PM. Reason: deleted image for causing side scroll in internet explorer browser

                              Comment


                              • Re: H7N9 discussion thread: recent increase in cases, January 24, 2014+

                                while things are "unknown", they are not completely unknown, so to speak.
                                We have some hints. We have (subjective) probability estimates.

                                ----------------------------------------------------------------

                                H7N9 is different from H5 and pH1 in:
                                Median age - 63
                                Male gender - 87/123 (71%)
                                Diabetes - 18/105 (17%)
                                Hypertension - 51/105 (49%)
                                Smoking history - 26/105 (25%)
                                CK - 195 (96,562)
                                CRP - 65 (25,113)
                                Lymphopenia - 88/99 (89%)
                                Neutrophilia - 5/103 (5%)
                                Thrombocytopenia - 80/104 (77%)
                                Elevated LDH - 89/98 (91%)
                                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

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