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  • Thoughts on India's [epic 2015] flu season

    What are your thoughts on India? I had a twitter exchange with Gregory Hartl of WHO yesterday who said levels were higher during the pandemic. That is just demonstrably wrong. Both the rate of confirmed fatalities (250-300 per week vs 100-150 per week) and the GISRS surveillance are much higher than in 2009-10.

    I see two possibilities, or perhaps a combination of both;

    - The influenza situation is worse this year than it has ever been before and with a total lack of sequencing we don't know why.
    - Indian surveillance and testing is better than it was 5 years ago and more patients are being tested, thus more confirmed cases & fatalities. During the pandemic a confirmed death was estimated to be representative of 31-45 undocumented deaths in India, now - who knows?

    But when we get reports that 77 of the 89 fatalities in the states of Telangana and Andhra Pradesh are in the city of Hyderabad, that suggests to me that entire portions of those states are not being tested.

    To compare:

    From May 2009 to March 2011, India officially reported 46,777 total cases & 2,772 H1N1 deaths across all three waves of the pandemic. The majority of the deaths occurred over a period of 15 months from August 2009 to November 2010. The most intense period was during the third wave in August/September 2010.

    From August 2nd to Oct 3rd that year, 39,862 samples were taken; 8,941 (22.4%) were positive and 900 died (14 deaths per day, 10.0% of confirmed cases).
    https://flutrackers.com/forum/forum/...ober-17th-2010

    From Jan 1 to March 14th of this year 29,103 cases & 1,674 deaths have been confirmed (23 deaths per day, 5.75% of confirmed cases). Most of those deaths have occurred in just a six week period. Unfortunately I don't have data on the actual number of tests performed.
    https://flutrackers.com/forum/forum/...talities/page4

    What do you think?
    Twitter: @RonanKelly13
    The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

  • #2
    Maharashtra keeps some of the best records, but unfortunately they expunged their archive. We kept some of the data on FT in this thread: https://flutrackers.com/forum/forum/...alities/page12

    From August 1 - Aug 31, 2010, Maharashtra screened 389,527 people for H1N1, prescribed 107,081 with Tamiflu and admitted 6,844 to hospital. around 30-40% of the hospitalized population was positive for H1N1. 1,926 positive cases were reported Jul 30-Aug 29 on the consolidated status update http://pib.nic.in/newsite/erelease.aspx?relid=65426 and http://pib.nic.in/newsite/erelease.aspx?relid=61262 . 216 died.

    From Jan 1-Mar 10 this year, Maharashtra screened 267,664 people for H1N1, prescribed 27,953 with Tamiflu and admitted 6,546, 43% (2,847) of the hospitalized population has tested positive. 235 died. https://arogya.maharashtra.gov.in/Si...ate-Report.pdf

    So it would seem that ILI in the community is not as high, at this point, as it was in 2010.

    Comparison/ 2010 / 2015
    Screened per day: 12,565 / 3,879 - not really valid comparison, Maha has seen most cases in only the past few weeks.
    % of screened given Tamiflu: 27.5% / 10.4%
    % of screened admitted: 1.76% / 2.45%
    ratio of positive vs admitted: 28.1% / 43.5%
    ratio of deaths vs admitted: 3.16% / 3.59%




    Twitter: @RonanKelly13
    The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

    Comment


    • #3
      I think we have too few data to be able to express a judgement about the current epidemic, however there is no doubt that there has been a worsening compared to previous seasons.
      It may depend on local factors ( such as the weather, crowding, low attention to the control measures) but also on small variations of the viral genome.
      In Italy there has been a recurrent wave of H1N1 with many people in ICU and deaths, but unlike what happened in India, there has been an age shift toward older people. What strikes me is that in India there are many young people to die.

      Comment


      • #4
        I agree. We just don't have the data to say for certain, but....

        A report from Madhya Pradesh indicates that 43 % of fatal cases were aged 16-40 years old;

        Swine Flu: Death Review report was shocking, 43% of young victims
        Rohit SrivastavaMar 17, 2015, 01:56 AM IST

        Bhopal. However, the Government of the young swine flu infection is excluded from the list of high-risk patient, but the reality is the opposite. Swine flu deaths in the state, including the capital, 43 per cent are young. Their age is between 16 and 40 years. Analysis revealed that swine flu death reported to have occurred in the control room. Ripaert the youth because of swine flu infection disease at the beginning of the transition is to ignore him.

        Swine Flu: Death Review report was shocking, 43% of young victims
        ...
        https://flutrackers.com/forum/forum/...102#post727102
        Last edited by Ronan Kelly; April 3rd, 2015, 02:01 AM.
        Twitter: @RonanKelly13
        The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

        Comment


        • #5
          New data from Maharashtra released yesterday on fatality demographics. A significant number of deaths in women aged 20-40. 85% of all deaths were aged under 60 years old.
          https://flutrackers.com/forum/forum/...294#post728294

          And from Karnataka showing that the % positives this year is far higher at 37.5% than any other year including the pandemic. Also, Bangalore accounts for 38 of the 85 deaths (44.7%), but 71.9 % of the positive tests. This suggests to me that testing outside of the major urban areas may still be lacking.
          https://flutrackers.com/forum/forum/...406#post728406
          Twitter: @RonanKelly13
          The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

          Comment


          • #6
            I think we are going to find that this was a bad year in most countries with the number of flu deaths. The number of deaths in otherwise healthy people in their prime is very disturbing.
            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


            • #7
              I just read the full text of a Tetano import re. the stats for age and gender study of severe flu cases in China between H1N1 and H7N9. http://journals.plos.org/plosone/art...l.pone.0120999

              The H1N1 stats were both surprising and unsettling. They were younger and had fewer prior complications of ill health. That included such conditions as asthma, diabetes, ... Why is H1N1 hitting us so hard?
              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


              • #8
                I would guess that some of the reported H1N1 flu mortality in India could be due to better testing, but don't doubt that there could also be an unusual age group effect. We had that in 2013-2014 and the best theory I read on that was the 'original antigenic sin' theory. (Based on early exposure to that 1977 lab escape H1N1.):

                http://www.pnas.org/content/111/44/15798.full

                So perhaps India is experiencing this phenomenon this season. So far I haven't seen anyone independent of potential financial conflicts of interest promoting fear of anything more than this.

                https://in.news.yahoo.com/hello--any...104901301.html
                What about panic stations?
                Meanwhile, is it a good idea to get vaccinated? The MIT paper is an opinion piece that calls for greater surveillance, but also speaks of "widespread vaccine campaigns" as a strategy to tackle influenza.
                Sasisekharan, the corresponding author for the MIT paper, is a well-known scientist and professor of biological engineering at MIT. He’s also a biotech entrepreneur who founded the company Visterra, which is working on an influenza A vaccine (H1N1 is a subtype of influenza A) and, according to the MIT News Office, possibly laying the ground for a universal influenza vaccine. The MIT paper ends with a small acknowledgement that Sasisekharan is on Visterra's board. When an Indian newspaper asked him about the Indian government's hints that he had an agenda to push by suggesting H1N1 had mutated for the worse, he wrote, “It has no relevance to this study.” Sasisekharan did not respond to emails from this reporter seeking his comments on the subject.
                “‘i love myself.’ the quietest. simplest. most powerful. revolution ever.” ---- nayyirah waheed

                Avatar: Franz Marc, Liegender Hund im Schnee 1911 (My posts are not intended as advice or professional assessments of any kind.)

                Comment


                • #9
                  Thanks for linking that story Emily. It's a very nicely written article. What I get from it is that the MIT group has made their findings public in a peer reviewed paper and released their sequences to GISAID. The NIV has denied that the mutations are in the original sequences, but has not released those sequences.
                  Update: The CDC has now also agreed that the mutations are present, but do not automatically imply more severe disease. https://flutrackers.com/forum/forum/...514#post728514

                  The whole idea of improved surveillance in India is moot without some sort of guidance from The Indian CDC or MOHFW. We simply don't know. What is needed is an analysis of the raw figures. But that would involve a paradigm shift for Indian healthcare & politics. Because they rely on those absolute figures. India compares absolute numbers year to year regardless of the testing regime, regardless of reality some might say. Some states deliberately discourage testing to make their reportable disease numbers better. What we do know is that testing for strains of Influenza other than H1N1 rarely happens. This glaring absence argues against an improved surveillance and testing regime. And that 37.5% positive test number from Karnataka suggests a pretty significant flu season.

                  Then there's the WHO who publish the chart below each week. Surely this glaringly large influenza season needs to be investigated more thoroughly! You know that if the American CDC produced a chart like this without explanation, there would be a widespread cry of Why? What's going on? But with India, it's always just - Meh, probably nothing. Sure doesn't look like nothing.
                  Click image for larger version

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                  http://gamapserver.who.int/gareports...spx?ReportNo=7
                  Last edited by Ronan Kelly; April 3rd, 2015, 04:12 AM. Reason: See Update
                  Twitter: @RonanKelly13
                  The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

                  Comment


                  • #10
                    I agree it would be nice to have some context to those numbers. There does seem to be an increase in testing for 'swine flu' this year.

                    "These laboratories and hospitals are taking undue advantage of the situation. Last year, the trend was totally opposite as just one case of the influenza was reported from the city. But this year, more and more people are getting themselves tested for swine flu, even as a precautionary measure. With the scare looming, these private labs and the hospitals are making money," a health department official told MAIL TODAY.
                    “‘i love myself.’ the quietest. simplest. most powerful. revolution ever.” ---- nayyirah waheed

                    Avatar: Franz Marc, Liegender Hund im Schnee 1911 (My posts are not intended as advice or professional assessments of any kind.)

                    Comment


                    • #11
                      So one year later looking at figures for 2016 we do not see such huge numbers being reported. This strongly suggests that 2015 was indeed an epic year for H1N1 in India and not just a result of improved surveillance. Would be interested to see if any studies follow this up.

                      Click image for larger version

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                      http://gamapserver.who.int/gareports...spx?ReportNo=7
                      Twitter: @RonanKelly13
                      The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

                      Comment


                      • #12
                        Influenza Surveillance: 2014–2015 H1N1 “Swine”-Derived Influenza Viruses from India
                        Kannan Tharakaraman, Ram Sasisekharancorrespondenceemail
                        DOI: http://dx.doi.org/10.1016/j.chom.2015.02.019 |
                        Article has an altmetric score of 271 4
                        Summary
                        Full Text
                        Images
                        References
                        Summary
                        The 2014-2015 H1N1 outbreak in India has reportedly led to 800 fatalities. The reported influenza hemagglutinin sequences from India indicate that these viruses contain amino acid changes linked to enhanced virulence and are potentially antigenically distinct from the current vaccine containing 2009 (Cal0709) H1N1 viral hemagglutinin.
                        http://www.cell.com/cell-host-microb...128(15)00076-1

                        J Glob Infect Dis. 2015 Apr-Jun; 7(2): 56–59.
                        doi: 10.4103/0974-777X.157236
                        PMCID: PMC4448325
                        2015 Resurgence of Influenza A (H1N1) 09: Smoldering Pandemic in India?
                        Baijayantimala Mishra
                        ...
                        CONCLUSION
                        The present resurgence of pandemic virus cannot be attributed to any single factor at this stage. The prolong cold and dry weather, possibility of drift virus, absence of annual flu vaccination could have played an integrated role in resurfacing of pandemic virus. The role of sero-epidemiology should be given its due importance for vaccination policy along with the molecular surveillance of the influenza virus circulating strains which is already ongoing in India through an established influenza surveillance network. Vaccination campaign, public awareness and education measures should continue in an optimum mode, even during the inter resurgence interval period, balancing the necessity vis-a-vis public panic. Lastly, considering the ecology, epidemiology, molecular biology of the pandemic virus, a modeling system should be developed to predict such resurgence in future and building up of herd immunity against all the circulating influenza viruses along with pdm H1N1 is essential to fight the battle with the virus.
                        http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448325/

                        Dynamics of Influenza Seasonality at Sub-Regional Levels in India and Implications for Vaccination Timing
                        Mandeep S. Chadha , Varsha A. Potdar, Siddhartha Saha, Parvaiz A. Koul, Shobha Broor, Lalit Dar, Mamta Chawla-Sarkar, Dipankar Biswas, Palani Gunasekaran, Asha Mary Abraham, Sunanda Shrikhande, Amita Jain, Balakrishnan Anukumar, Renu B. Lal, Akhilesh C. Mishra

                        Published: May 4, 2015DOI: 10.1371/journal.pone.0124122
                        ...
                        Conclusions

                        Our data shows that India, though physically located in northern hemisphere, has distinct seasonality that might be related to latitude and environmental factors. While cities with temperate seasonality will benefit from vaccination in September-October, cities with peaks in the monsoon season in July-September will benefit from vaccination in April-May. Continued surveillance is critical to understand regional differences in influenza seasonality at regional and sub-regional level, especially in countries with large latitude span.
                        http://journals.plos.org/plosone/art...l.pone.0124122

                        Reemergence of Swine Flu H1N1 in India: First Outbreak
                        of 2015

                        Sharma RB and Husain M*
                        Department of Biotechnology, Jamia Millia Islamia
                        Central University, India
                        *Corresponding author: Husain M, Department of
                        Biotechnology, Jamia Millia Islamia Central University,
                        India
                        Received: June 25, 2015; Accepted: September 24,
                        2015; Published: October 03, 2015
                        ...
                        Conclusion
                        The current review focuses on the re-emergence of H1N1 virus
                        that has caused morbidity, mortality and socio-economic loss to the
                        world during its pandemic phases. Again the same virus has alarmed
                        in India from January 2015 by infecting thousands of people with
                        severe mortality. Though the country prepared in terms of diagnostic
                        and preventive measures but there is no such data available which can
                        narrate the current scenario of influenza immunization in the high
                        risk group or in general population. Although the control measures
                        for flu seems to be very unyielding as it is airborne and able to
                        transmit easily and rapidly in Indian scenario. As the influenza virus
                        is very prone to genetic shift and drift, its mutation, transmission and
                        spread is impossible to control but taking proper preventive measure
                        can reduce the disease severity and economic burden. Annual
                        influenza vaccination to all would be a good preventive measure but
                        if not possible at least high risk group (children, health care workers,
                        elders, immune-compromised etc.) should receive it. Designing viral
                        conserved region based vaccines would be more helpful to protect
                        against all influenza strains as well as against novel pandemic strains.
                        https://www.google.com/url?sa=t&rct=...16274245,d.cWw

                        H1N1 Revisited After Six Years : Then and Now
                        Shobha Itolikar1, Milind Y Nadkar2
                        1Asst. Prof., 2Professor, Dept. of Medicine, Seth GS Medical College & KEM Hospital, Mumbai, Maharashtra
                        Received: 12.03.2015; Accepted: 13.03.2015
                        ...
                        Are we Seeing Tip of the Iceberg?: There are several factors that make it difficult to determine accurately the numbers of deaths caused by flu regardless of reporting. Some of the challenges in counting influenza-associated deaths include the following: the sheer volume of deaths to be counted; not everyone that dies with an influenza-like illness is tested for influenza; and influenza-associated deaths are often a result of complications secondary to underlying medical problems, and this may be difficult to sort out.5
                        ...
                        http://www.japi.org/april_2015/08_ua...after_six.html
                        Twitter: @RonanKelly13
                        The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

                        Comment


                        • #13
                          Ronan they do not seem to reach a consensus as to the cause of the spike. On a more reassuring note none of them single out antigenic drift as a significant problem.
                          Do you know what the sequencing regime is like? I recall you did not have a high opinion of it before but one of these papers seemed to think it was working.
                          ... along with the molecular surveillance of the influenza virus circulating strains which is already ongoing in India through an established influenza surveillance network.
                          also do you know where they are submitted GISAID, Genebank or internally.

                          Comment


                          • #14
                            Agreed, no consensus and I haven't seen any more recent papers than June 2015. Doesn't mean they aren't out there. There are 681 hits for "India H1N1 2015" at GenBank, but I'm afraid I cannot interpret the results. Most seem to be partials. I presume there are others at GISAID. I'm really not sure how comprehensive the surveillance network is. There is nothing like a national "FluView". Some states publish numbers, some don't. I'm not sure how well funded it is or whether it exists in name only. Information on flu types other than H1N1 is hard to come by.
                            Twitter: @RonanKelly13
                            The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

                            Comment


                            • #15
                              Last Modified: Fri, Mar 20 2015. 11 51 AM IST
                              The curious case of the H1N1 mutation
                              India’s rejection of an MIT study on swine flu reveals a transcontinental trail of unanswered questions about the genetic data involved
                              ...
                              I reached out to Ram Sasisekharan, a professor of biological engineering at the Massachusetts Institute of Technology (MIT) in Boston, to talk about the growing dread in India about H1N1, popularly called swine flu.
                              ...
                              Had a mutation occurred in India to explains H1N1’s greater virulence? When I spoke with him last month [Feb 2015 - Ro], Sasisekharan said it was hard to tell because there was little or no “sequence information” on the Indian H1N1 strain circulating in global, genetic databases. This was frustrating, he said, because such information-sharing allowed collaborative efforts, which were key to surveillance, management and predicting the spread of the virus. Back in India, the only information made available by unnamed scientific sources in a couple of newspapers was that H1N1 genetic sequences with the National Institute of Virology (NIV) in Pune showed no mutations.
                              ...
                              On 6 March, MIT public relations alerted me—one of many heads-up that I get from scientific institutions around the world; in India, I get none—to a forthcoming paper from Sasisekharan.
                              ...
                              His paper—published in Cell Host and Microbe, a global scientific journal—essentially said that the Indian H1N1 virus, a genetic sample of which he had obtained from a global database, showed changes in a gene called heammaglutinin, known to mark virulence. In other words, the Indian virus may have mutated, which might explain the unexplained virulence and unprecedented death toll (although the infection rate, compared to 2010, is not particularly worrying for a flu outbreak). The paper also noted that India ranked a low 14th in a global list of contributors of complete H1N1 genetic sequences.
                              ...
                              the government—within 24 hours—put out a press release. It denied there were any mutations.
                              ...
                              Neither did an analysis of the virus by the US Centers for Disease Control and the World Health Organization report genetic changes or resistance to oseltamivir, the main anti-H1N1 drug, the release said.
                              ...
                              “I think you can have a look on passage level C1 & C2 also.” The GISAID database did have that entry. I asked him what he meant. He never replied, but his implication was that the genetic sequence that the MIT scientists used was not original and hence unreliable.

                              This kind of a defence--if you can call it that--only raises more questions:

                              Since NIV has samples of the H1N1 virus panicking India, why does it not release the genetic sequences? The H1N1 virus’ proclivity to mutate is now common scientific knowledge, so--instead of running down warnings--does it not make sense to share its current and evolving genetic profile? Given the dangerous global history of influenza, should not worldwide collaboration be a preferred option to bland, unconvincing denial?

                              The quicker NIV and India’s government start answering these questions, the better.

                              Samar Halarnkar is editor of IndiaSpend.org, a data-driven, public-interest journalism non-profit. He also writes the column Our Daily Bread in Mint Lounge.
                              http://www.livemint.com/Opinion/PyAP...-mutation.html

                              Twitter: @RonanKelly13
                              The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

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