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ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

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  • ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

    The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh
    Published: September 2013
    Size: 202.61 kB
    Published By: icddr,b
    Health and Science Bulletin, VOLUME 11 • NUMBER 3 • SEPTEMBER 2013 ISSN 1729-343X

    Clip:
    Previously six human cases of avian influenza A (H5N1) were identified in Bangladesh between 2008 and 2012; all cases experienced mild respiratory illness.
    On 12 February 2013, a 23-month old boy from Comilla was hospitalized for febrile convulsions and enrolled in a respiratory virus research study. Laboratory tests conducted on 12 March suggested that the boy had influenza A (H5) infection. This was the 7th case of A (H5N1) identified in Bangladesh. A joint IEDCR-icddr,b outbreak response team investigated to explore the child’s exposure history and clinical outcome and to look for additional cases in the community. Several chickens raised in the family’s backyard became sick a few days before he became ill; they were slaughtered and the boy played with the carcasses. The child died on February 18 with evidence of severe pneumonia, meningitis and disseminated intravascular coagulation; no other human cases were identified. Viral sequences from the child and slaughtered chicken confirmed that both were infected with influenza A (H5N1), clade 2.3.2.1. This first identified death from avian influenza infection in Bangladesh presented primarily with neurologic rather than respiratory symptoms and was apparently infected through contact with sick chickens. Clinicians should consider avian influenza infection in the differential diagnosis for any patient with severe respiratory or neurologic infection with a history of contact with sick poultry. All such patients should be treated with oseltamivir.

    see full report:
    The first fatal human infection with highly | Vol. 11 No. 3 (English) (2013) | Health and Science Bulletin (Bangla and English) | icddr,b Periodicals - icddr,b
    http://www.icddrb.org/what-we-do/pub...-in-bangladesh

  • #2
    Re: ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

    I'll post individually for cases 1-6 information resources for a possible FT's line list!

    First confirmed human infection with avian influenza A (H5N1) virus in Bangladesh

    http://www.icddrb.org/media-centre/n...ngladeshladesh icddr,b Periodicals, Health and Science Bulletin, Vol. 6 No. 2 June 2008
    Clip:
    15-month old male Kamalapur resident developed cough and runny nose on 22 January 2008. By 27 January his breathing was labored. On 29 January his mother brought him to the ICDDR,B clinic in Kamalapur. On examination the child had a temperature of 38.1 °C, a respiratory rate of 40 breaths per minute, pulse of 124, weight for age was the 78th percentile and no abnormal sounds were heard on chest auscultation. Because the child was part of the active surveillance system, a chest radiograph was obtained. The child was also selected for nasopharyngeal wash and influenza viral culture, based on the one in five sampling method. The initial clinical impression was that the child had enteric fever. The child was treated with amoxicillin. The chest radiograph was initially read by the radiologist as normal, but later interpreted by the clinicians as showing an alveolar infiltrate. Because the child was in the surveillance system, a field worker visited him daily at his home. He was also seen in the clinic for follow-up on 31 January, 5 February, 10 February and 13 February. Although the mother reported the child had fever at home as late as 7 February, an elevated temperature was not identified on exam after the initial clinic visit. The child completed a 13 day course of amoxicillin. On his last clinic visit on 13 February the child was clinically well. The final clinical diagnosis was upper respiratory tract infection. The child was not diagnosed as pneumonia because chest auscultation was consistently normal. The child was re-evaluated on 22 May and remained clinically well.

    See full report:
    http://www.icddrb.org/media-centre/n...-in-bangladesh

    ----
    Avian Influenza in Bangladesh and India Report of the High-level Consultation 27-28 August 2008, Dhaka, Bangladesh
    Section
    5.6 Avian Influenza country situation-Bangladesh:
    Health perspectives
    Professor Mahmudur Rahman, Director, Institute of Epidemiology,
    Disease Control and Research (IEDCR) & National Influenza Centre
    (NIC), Bangladesh Bangladesh reported the first case of H5N1 on May 22, 2008. A 16 month old boy from Dhaka reported to one of the surveillance centres with fever, running nose, mild cough, loose stool, sore on the tongue and sweating. Samples were collected as routine surveillance for seasonal influenza. Diagnosed at ICDDRB as Influenza A and samples sent to CDC Atlanta, which confirmed the case as H5N1 on May 21. The virus belonged to Clade 2.2, corresponding with the viruses in poultry in Bangladesh as well as with the viruses in Kuwait/Afghanistan/West Bengal/Pakistan.
    http://209.61.208.233/LinkFiles/Publ...SEA-CD-181.pdf

    ---

    Brooks et al. 2009 , Avian Influenza Virus A (H5N1), Detected through Routine Surveillance, in Child, Bangladesh - Vol. 15 No. 8 - August 2009 - Emerging Infectious Disease journal - CDC
    http://wwwnc.cdc.gov/eid/article/15/...83_article.htm

    Avian influenza - situation in Bangladesh
    28 May 2008 - The Ministry of Health, Bangladesh has confirmed its first case of human infection with H5N1 avian influenza. The case was identified retrospectively as part of seasonal surveillance activities run by the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDRB).

    -------
    The case is a 16-month-old male from Komalapur, Dhaka. He developed symptoms on 27th January 2008 and subsequently recovered. The case was confirmed as being infected with A(H5N1) by the WHO H5 Reference Laboratory, US Centers for Disease Control and Prevention (CDC). The case was exposed to live and slaughtered chickens at his home. Specimens have been collected from his family members and neighbours. All remain healthy to date.

    http://www.who.int/csr/don/2008_05_28/en/index.html

    A/Bangladesh/207095/2008 - Nucleotide - NCBI
    http://www.ncbi.nlm.nih.gov/nuccore?...F207095%2F2008

    FJ573465,FJ573466,FJ573467,FJ573468,FJ573469,FJ573 470,FJ573471,FJ573472
    • 2.2 (2.2.2)
    • PB2-E627K


    Influenza Research Database - Details for Strain A/Bangladesh/207095/2008(H5N1)
    http://www.fludb.org/brc/fluStrainDe...ator=influenza

    IDCDC-RG11
    http://www.who.int/influenza/resourc...irusupdate.pdf

    ----
    Highly Pathogenic Avian Influenza A(H5N1), , Human

    GENERAL INFO
    Disease Event ID: 159003
    Reporting date: 27/05/2008
    Observation date: 26/01/2008

    LOCATION
    Region: Asia
    Admin 1 (Country): Dhaka (Bangladesh)
    Locality: Kamalapur
    Lat/Long: 23.7956488409 / 90.2599965798
    Quality of Coordinates: Centroid Admin2

    DISEASE
    Status: Confirmed
    DISEASE: Highly Pathogenic Avian Influenza
    Serotype: H5N1
    Source: WHO
    LABORATORIES

    Disease Tested: Highly Pathogenic Avian Influenza
    Species: …
    Test: ...
    Result: Positive
    Result Date: ....

    Reference Laboratory: No data

    EMPRES-i - Global Animal Disease Information System#h=1
    http://empres-i.fao.org/eipws3g/#h=1

    Comment


    • #3
      Re: ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

      Government of Bangladesh and ICDDR,B researchers identify Avian influenza A(H5N1) in humans - icddr,b

      Clip:
      On 16 March 2011, the Ministry of Health and Family Welfare in Bangladesh reported a confirmed human case of avian influenza A(H5N1). The case was detected through an influenza surveillance centre run by the Institute of Epidemiology Disease Control and Research (IEDCR) and ICDDR,B.

      The case was a 16-month old baby girl, living in Kamalapur, in the heart of Dhaka city. The baby’s parents brought her to an influenza sentinel surveillance centre on March 8 with a history of fever. Two days later, a two-year-old boy also living in the area was diagnosed with the same virus. The boy also displayed signs of a fever and cough.

      To confirm infection, both children were tested through nasal pharyngeal washes as well as blood samples. The children are not related nor do they live in the same household. However, both have since made a full recovery without requiring any hospitalisation or anti-viral treatments.

      A team of epidemiologists from IEDCR, ICDDRB and WHO Bangladesh have begun a detailed epidemiological investigation and contact follow up to determine the source of the recent


      http://www.icddrb.org/media-centre/n...h5n1-in-humans

      -----
      Outbreak of mild respiratory disease caused by H5N1 and H9N2 infections
      among young children in Dhaka, Bangladesh, 2011
      ICDDR,B • Health and Science Bulletin • Vol. 9 No. 2 • June 2011
      http://www.icddrb.org/media-centre/n...-in-bangladesh


      On March 13, 2011, the Kamalapur urban surveillance site reported a human
      case of avian influenza A (H5N1). The same surveillance site reported two
      more human cases, one with avian influenza A (H5N1) and another with
      avian influenza A (H9N2) in the following 10 days.
      Immediately after the first case was reported, the Institute of Epidemiology,
      Disease Control and Research (IEDCR) and International Centre for Diarrhoeal
      Diseases Research, Bangladesh (ICDDR,B) jointly formed a collaborative
      team of epidemiologists, veterinarians and anthropologists to conduct an
      outbreak investigation. The objective of this investigation was to understand
      the pathway of transmission and to explore the factors that contributed to
      the occurrence of these three human cases of avian influenza. In this report we present the epidemiological, clinical and virological findings of these
      cases.

      Clip case A
      Case A was a 13 month old girl who developed a cough on March 5 followed
      by fever on March 7. She visited the ICDDR,B Kamalapur Field Clinic on
      March 9. On examination she had fever (39°C) with otherwise normal
      findings (Table 1). Physician on duty classified her as a case of influenza like
      illness (ILI) and collected a NPW specimen from her as part of the ongoing
      influenza surveillance. The NPW specimen tested positive by real-time RTPCR
      for influenza A (H5) on March 13, and IEDCR immediately reported
      the case to the World Health Organization as per the International Health
      Regulations. On March 14, when we interviewed the case, she reported no
      fever since March 11 but she still had cough and had one episode of loose
      motion on that day (Figure 2).

      Table 1: Clinical features of human cases of avian influenza H5N1 and H9N2
      infection in Bangladesh, February-March 2011

      Seven days before her onset of illness, seven chickens were slaughtered,
      defeathered and skinned inside Case A’s home while she was at home. Case
      A visited her grandparents house in Munshiganj district for three days, five
      days before her symptoms began. While in Munshiganj, she was in the
      company of her great grandmother, who was diagnosed with bronchial
      asthma and was suffering from respiratory distress during that period.

      There were reports of crow die-offs in the village in recent weeks and the
      investigative team observed one sick crow and five dead crows, as well as
      freely roaming chickens raised by neighbours.

      Viruses were isolated from NPW specimens of all three cases and full genome
      sequencing of the cultured isolates was performed. Phylogenetic analysis of
      the two isolated H5N1 viruses indicates that they belong to the clade 2.2
      lineage and that they are closely related to H5N1 virus isolates of avian origin

      -----
      WHO
      Avian influenza - situation in Bangladesh

      16 March 2011 - The Ministry of Health and Family Welfare, Government of the People's Republic of Bangladesh has confirmed a case of human infection with avian influenza A (H5N1) virus. The case was detected through the influenza sentinel surveillance centre run by the Institute of Epidemiology Disease Control and Research (IEDCR) and the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B).

      The case is a 16 month old female from Kamalapur, Dhaka. She presented at a influenza sentinel surveillance on 8 March with a history of cough and fever and subsequently recovered.

      A detailed epidemiological investigation and contact follow up is being conducted by a team of epidemiologists from IEDCR, ICDDRB and WHO Bangladesh.

      The case was confirmed as being infected with A(H5N1) by the Institute of Epidemiology Disease Control and Research (IEDCR).

      http://www.who.int/csr/don/2011_03_16/en/index.html

      ------

      A/Bangladesh/3233/2011
      A/Bangladesh/3233/2011 - Protein - NCBI
      http://www.ncbi.nlm.nih.gov/protein?...%2F3233%2F2011

      CY088766,CY088767,CY088768,CY088769,CY088770,CY088 771,CY088772,CY088773,
      PB2 E627K
      2.2.2

      Influenza Research Database - Details for Strain A/Bangladesh/3233/2011(H5N1)
      http://www.fludb.org/brc/fluStrainDe...ator=influenza

      ------

      Highly Pathogenic Avian Influenza A(H5N1), , Human

      GENERAL INFO
      Disease Event ID: 160490
      Reporting date: 15/03/2011
      Observation date: 28/02/2011

      LOCATION
      Region: Asia
      Admin 1 (Country): Dhaka (Bangladesh)
      Locality: Kamalapur
      Lat/Long: 23.737409 / 90.425484
      Quality of Coordinates: Centroid Admin1

      DISEASE
      Status: Confirmed
      DISEASE: Highly Pathogenic Avian Influenza
      Serotype: H5N1
      Source: WHO

      LABORATORIES
      Disease Tested: Highly Pathogenic Avian Influenza
      Species: …
      Test: ...
      Result: Positive
      Result Date: 16/03/2011

      Reference Laboratory: No data

      EMPRES-i - Global Animal Disease Information System#h=1
      http://empres-i.fao.org/eipws3g/#h=1

      Comment


      • #4
        Re: ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

        Outbreak of mild respiratory disease caused by H5N1 and H9N2 infections
        among young children in Dhaka, Bangladesh, 2011
        ICDDR,B • Health and Science Bulletin Vol. 9 No. 2 June 2011
        http://www.icddrb.org/media-centre/n...-in-bangladesh
        or
        icddr,b. Outbreak of mild respiratory disease caused by H5N1 and H9N2
        infections among young children in Dhaka, Bangladesh. Health Sci Bul
        2011;9:5-12.

        Clip case B
        Case B, a 31 month old boy, developed cough and runny nose on March 1,
        and conjunctivitis on March 2. On March 5 the child developed fever and
        on March 6 he had one episode of vomiting and loose motion (Table 1).
        On March 7, the physician at the Kamalapur Field Clinic found his tonsils
        inflamed and as the case fulfilled the recruitment criteria of ILI collected his
        NPW specimen. The physician treated him with amoxicillin with clavulanic
        acid syrup. The child’s NPW tested positive for influenza A (H5) on March
        15 (Figure 2).
        Ten or twelve days before his illness Case B touched live poultry while his
        mother purchased a live chicken from a roaming vendor. The child was
        present when the chicken was eviscerated. His mother also mentioned that
        the child had cut his hand with a knife while she was preparing the chicken
        and she pressed her hand on his wound to stop the bleeding while her hand
        was still contaminated with raw chicken. Many of their neighbours in the
        slum where they live raised ducks, chicken and quail in the yard where the
        child played. The mother took the child along with her inside the wet market
        where poultry are sold during the week prior to his illness.

        A pool of chicken fecal samples from two live bird markets located close to
        the houses of these three cases in Kamalapur tested positive for influenza A
        (H5) by RT-PCR.

        ----
        2nd Human case of Influenza H5N1 in 2011
        A case of Influenza H5N1 has been identified from one of our surveillance sites in Dhaka on 15th of March 2011. This was confirmed by Real-time RT-PCR.
        This is 31 month old male child who has presented with a history of cough and fever.
        Nasal and throat swab and blood were collected and found positive for H5N1.
        He has no symptom of illness now and completely recovered.
        This is the 2nd case of H5N1 infections in human this year.
        It may be mention here that the first human case of H5N1 was reported in Bangladesh in May 2008.

        http://www.iedcr.org/images/Healthme...0of%20H5N1.pdf

        ----
        Avian influenza - situation in Bangladesh - update
        11 April 2011 - The Ministry of Health and Family Welfare, Government of the People's Republic of Bangladesh has confirmed a new case of human infection with avian influenza A(H5N1) virus.

        The case is a 2 years old male from Kamalapur, Dhaka. He developed symptoms on 1 March. He visited the influenza sentinel surveillance site on 9 March where he was sampled. He completely recovered.

        Detailed epidemiological investigation and contact follow up was conducted by a team from the Institute of Epidemiology Disease Control and Research (IEDCR), the International Centre for Diarrhoeal Disease Research, Bangladesh ( ICDDRB) and WHO Bangladesh, and no further cases were identified.

        The investigation into the source of infection indicate that the case had exposure to sick poultry. Although the case is from the same locality as the previous case they had no direct contact with each other.

        The case was confirmed as being infected with A(H5N1) by the Institute of Epidemiology Disease Control and Research (IEDCR).

        http://www.who.int/csr/don/2011_04_11a/en/index.html

        ----
        Highly Pathogenic Avian Influenza A(H5N1), , Human

        GENERAL INFO
        Disease Event ID: 160439
        Reporting date: 13/03/2011
        Observation date: 07/03/2011

        LOCATION
        Region: Asia
        Admin 1 (Country): Dhaka (Bangladesh)
        Locality: Kamalapur
        Lat/Long: 23.737409 / 90.425484
        Quality of Coordinates: Centroid Admin1

        DISEASE
        Status: Confirmed
        DISEASE: Highly Pathogenic Avian Influenza
        Serotype: H5N1
        Source:WHO

        LABORATORIES
        Disease Tested: Highly Pathogenic Avian Influenza
        Species: …
        Test: ...
        Result: Positive
        Result Date: 14/03/2011

        Reference Laboratory: No data

        EMPRES-i - Global Animal Disease Information System#h=1
        http://empres-i.fao.org/eipws3g/#h=1

        Comment


        • #5
          Re: ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

          Fourth H5N1 human case in Bangladesh
          A 40 year old male has been diagnosed as fourth case of Human Avian Influenza (H5N1) in Bangladesh. This case has been reported from live bird market surveillance system in Dhaka City on 26 February 2012. This was confirmed by rRT-PCR. The patient is a live bird market worker.
          The case presented with cough. Throat and nasal swabs were collected and found positive for H5N1. Presently he is free from symptom. IEDCR & ICDDR,B jointly investigating the case and monitoring the situation.
          In Bangladesh the first case was detected in 2008, second and third cases were found in 2011, fourth case was found on 26 February 2012.
          Published on 27.02.2012

          http://www.iedcr.org/pdf/files/influ...Bangladesh.pdf


          ----
          WHO
          Avian influenza – situation in Bangladesh
          2 March 2012 - The Ministry of Health and Family Welfare, Bangladesh has confirmed the fourth case of human infection with H5N1 avian influenza in the country.

          The case is a 40 year-old male from Dhaka City, who was identified as part of the live bird market surveillance system on 26 February 2012. The case presented with cough and currently has recovered.

          The case was confirmed by the Institute of Epidemiology, Disease Control and Research (IEDCR) and the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B).

          An epidemiological investigation and monitoring of the situation is currently being conducted jointly by IEDCR and ICDDR,B.

          The first case of human infection with H5N1 was reported in the country in 2008, and two cases were reported in 2011.

          http://www.who.int/csr/don/2012_03_02/en/index.html

          --
          Highly Pathogenic Avian Influenza A(H5N1), Bangladesh, Human

          GENERAL INFO
          Disease Event ID: 168208
          Reporting date: 01/03/2012
          Observation date: 25/02/2012

          LOCATION
          Region: Asia
          Admin 1 (Country): Dhaka (Bangladesh)
          Locality: Dhaka
          Lat/Long: 23.7956488409 / 90.259969..

          DISEASE
          Status: Confirmed
          DISEASE: Highly Pathogenic Avian Influenza
          Serotype: H5N1
          Source: National Authorities

          LABORATORIES
          Disease Tested: Highly Pathogenic Avian Influenza
          Species: …
          Test: …
          Result: Positive
          Result Date: ....
          Reference Laboratory: …

          http://empres-i.fao.org/empres-i/2/o...k=169290&rss=t


          -----
          Retrospective report:

          Backyard poultry raising practices in Bangladesh: implications for risk of
          avian influenza infection in humans
          Health and Science Bulletin VOLUME 10 • NUMBER 3 • SEPTEMBER 2012 ISSN 1729-343X

          Since 2007, highly pathogenic avian influenza A virus subtype H5N1 has been confirmed in
          poultry in 52 of 64 districts of Bangladesh and 57 outbreaks in backyard
          poultry have been officially reported (Figure 1).

          In 2008, a child from the icddr,b Kamalapur urban surveillance site in Dhaka tested positive for H5N1, along with another two children in 2011 (6,7).

          Three adult poultry workers from live bird markets of Dhaka tested positive for H5N1 in 2012 (8,9).

          All six had a history of close contact with poultry. Although all confirmed human cases of H5N1 infection identified in Bangladesh only developed mild illness, 358 deaths have occurred among 607 confirmed H5N1-infected cases reported worldwide since 2003 (10)

          Comment


          • #6
            Re: ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

            Fifth and Sixth H5N1 human case in Bangladesh

            Two cases of Influenza H5N1 has been reported from the same surveillance site, as of fourth case, at live bird market in Dhaka City (South) on 04 March 2012.
            This was confirmed by Real time RT-PCR. It may be mentioned that they are the fifth and sixth cases of laboratory confirmed Influenza H5N1 cases of Bangladesh since the first case detected in 2008.

            The fifth case is 26 year old male and sixth case is 18 year old male who had presented with history of fever, sore throat, cough. Now they are free from symptoms. Nasal and throat swab were collected and found positive for H5N1. They are also live bird market workers, like the fourth case.
            They are being treated and followed up by National Rapid Response Team members from IEDCR and ICDDR,B.

            Published on 05.03.2012 Updated on 07.03.2012

            http://www.iedcr.org/pdf/files/influ...Sixth_H5N1.pdf

            ----

            Backyard poultry raising practices in Bangladesh: implications for risk of
            avian influenza infection in humans
            Health and Science Bulletin VOLUME 10 • NUMBER 3 • SEPTEMBER 2012 ISSN 1729-343X

            Since 2007, highly pathogenic avian influenza A virus subtype H5N1 has been confirmed in
            poultry in 52 of 64 districts of Bangladesh and 57 outbreaks in backyard
            poultry have been officially reported (Figure 1).

            In 2008, a child from the icddr,b Kamalapur urban surveillance site in Dhaka tested positive for H5N1, along with another two children in 2011 (6,7).

            Three adult poultry workers from live bird markets of Dhaka tested positive for H5N1 in 2012 (8,9).
            All six had a history of close contact with poultry. Although all confirmed human cases of H5N1 infection identified in Bangladesh only developed mild illness, 358 deaths have occurred among 607 confirmed H5N1-infected cases reported worldwide since 2003 (10)

            ---
            WHO

            Avian influenza – situation in Bangladesh – update
            7 March 2012 - The Ministry of Health and Family Welfare, Bangladesh has confirmed two new cases of human infection with highly pathogenic avian influenza A(H5N1) virus in the country. These are the 5th and 6th cases reported in the country since 2008.‬‪

            These two cases, 26 year-old and 18 year-old males, presented with history of cough, and both have recovered. They were identified in the same live bird market surveillance site in Dhaka City as the fourth case recently reported, and were confirmed by the National Influenza Centre (NIC) of the WHO Global Influenza Surveillance and Response System (GISRS) in Bangladesh.‬‪

            Epidemiological investigation and follow-up is being conducted by National Rapid Response teams of the Institute of Epidemiology, Disease Control and Research (IEDCR) and the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B).‬‪

            http://www.who.int/csr/don/2012_03_07/en/index.html

            ---
            5th
            Highly Pathogenic Avian Influenza A(H5N1), Bangladesh, Human

            GENERAL INFO
            Disease Event ID: 168243
            Reporting date: 06/03/2012
            Observation date: ...
            LOCATION
            Region: Asia
            Admin 1 (Country): Dhaka (Bangladesh)
            Locality: Dhaka
            Lat/Long: 23.7956488409 / 90.259969..
            DISEASE
            Status: Confirmed
            DISEASE: Highly Pathogenic Avian Influenza
            Serotype: H5N1
            Source: National Authorities
            LABORATORIES
            Disease Tested: Highly Pathogenic Avian Influenza
            Species: …
            Test: …
            Result: Positive
            Result Date: ....
            Reference Laboratory: …

            http://empres-i.fao.org/empres-i/2/o...k=169290&rss=t

            ---
            6th
            GENERAL INFO
            Disease Event ID: 168243
            Reporting date: 06/03/2012
            Observation date: ...

            LOCATION
            Region: Asia
            Admin 1 (Country): Dhaka (Bangladesh)
            Locality: Dhaka
            Lat/Long: 23.7956488409 / 90.259969..

            DISEASE
            Status: Confirmed
            DISEASE: Highly Pathogenic Avian Influenza
            Serotype: H5N1
            Source: National Authorities

            LABORATORIES
            Disease Tested: Highly Pathogenic Avian Influenza
            Species: …
            Test: …
            Result: Positive/Positive
            Result Date: ....
            Reference Laboratory: …

            http://empres-i.fao.org/empres-i/2/o...k=169290&rss=t

            finished! LOL

            Comment


            • #7
              Re: ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

              Note: Flu trackers posts:

              Bangladesh: first human case of H5N1 bird flu - 2008 - FluTrackers
              http://www.flutrackers.com/forum/showthread.php?t=69091

              Bangladesh - Kamalapur, Dhaka, female, 16 months, H5N1 positive (second human case in Bangladesh) - FluTrackers
              http://www.flutrackers.com/forum/sho...d.php?t=164209

              Bangladesh - Male, 3, H5N1 confirmed (third case in Bangladesh, second case in 2011) - FluTrackers
              http://www.flutrackers.com/forum/sho...d.php?t=164386

              Bangladesh - Man, 40, confirmed 4th H5N1 case - FluTrackers
              http://www.flutrackers.com/forum/sho...d.php?t=183418

              Bangladesh - 2 additional market workers infected with bird flu - 3 total for 2012 - FluTrackers
              http://www.flutrackers.com/forum/sho...d.php?t=183700

              Bangladesh, First bird flu death in 5 years (BDNews24, April 7 2013) - FluTrackers
              http://www.flutrackers.com/forum/sho...d.php?t=203162

              Comment


              • #8
                Re: ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

                7th case IVTM post:

                Original Specimen IVTM-ORG772, Human, Bangladesh
                An Original specimen of type A (H5N1) collected (nasopharyngeal swab) from a human in Bangladesh on/in 2013-02-02.

                Summary of Diagnostic Results (auto-generated)
                Influenza type A (H5N1): 1 of 1 materials

                Source IVTM-SRC388, Human, Bangladesh
                Source Type Human
                Country/Area Bangladesh
                Notes CDC ID# 2013759680
                Laboratory CDC Atlanta, USA

                Original Specimen IVTM-ORG772, Human, Bangladesh

                Date of collection 02-Feb-2013
                IVTM Parent IVTM-SRC388
                Notes CDC ID# 2013759680
                Influenza type A (H5N1)
                Specimen Type nasopharyngeal swab
                Place of collection Bangladesh

                Notes CDC ID# 2013759680
                Laboratory CDC Atlanta, USA

                Influenza Virus Traceability Mechanism
                https://extranet.who.int/ivtm/Tree.aspx?matid=772

                Created on 12-Apr-2013 20:19:39 | Last modified on 12-Apr-2013 20:19:39


                "Note: the derivation tree is still a work in progress and therefore diagnostic results might change until a final diagnostic result gets published"

                I'm not sure if the human sequence is available at GISAID considering it is 2.3.2.1 or even the Frozen chicken sample???

                Comment


                • #9
                  Re: ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

                  WHO Full Text - February 2012
                  Clip:
                  Clade 2.3.2.1 viruses were detected in wild birds in Bangladesh and China Hong Kong Special Administrative Region (China Hong Kong SAR), in poultry in Bangladesh, China, China Hong Kong SAR, the Islamic Republic of Iran, Nepal and Viet Nam, and in a human in China. Those clade 2.3.2.1 viruses belonging to the A/barn swallow/Hong Kong/D10-1161/2010-like genetic group, which included the human virus from China, reacted well with post-infection ferret antiserum to the candidate vaccine virus A/barn swallow/Hong Kong/D10-1161/2010 (Table 4a) and were genetically similar to each other (Figure 4).

                  Some recent clade 2.3.2.1 avian viruses from Bangladesh and Viet Nam belonging to the A/Hubei/1/2010-like genetic group showed reduced reactivity with postinfection ferret antiserum against A/Hubei/1/2010, a virus from which a candidate vaccine virus has been developed. They retained good reactivity with post-infection ferret antiserum against A/common magpie/Hong Kong/5052/2007, a virus from which a candidate vaccine virus has been developed (Table 4b). Increased genetic heterogeneity in HA gene sequence was observed within the A/Hubei/1/2010-like group (Figure 4).

                  http://www.who.int/influenza/vaccine...irusupdate.pdf

                  Note: (personal summary notes on clade expansion with reference to WHO)
                  2.2.2 = 2007-2011 Bangladesh, India (avian, human), candidate vaccine A/chicken/India/NIV33487/2006 and A/bar-headed goose/Qinghai Lake/1A/2005 reacted well with the recent clade 2.2.2 viruses

                  2.3.4.2 = 2011-2013 Bangladesh, Myanmar, Vietnam; expanding region to China (mixed avian, few human- i.e. A/Guizhou/1/2012,A/Guizhou/1/2013,A/Guizhou/2/2013)
                  candidate vaccine viruses A/chicken/Hong Kong/AP156/2008, A/duck/Laos/3295/2006, and A/Japanese white eye/Hong Kong/1038/2006 did not react well with post-infection ferret antisera against the clade 2.3.4

                  Clade 2.3.4.2 viruses were isolated from humans in Guizhou province China. These viruses were genetically similar to A/Guizhou/1/2012 and showed reduced HI titres with post-infection ferret antisera raised against the candidate vaccine viruses A/Anhui/1/2005 and A/chicken/Hong Kong/AP156/2008- A/Guizhou/1/2013-like clade 2.3.4.2 candidate vaccine virus is proposed (few avian, few Human)

                  http://www.who.int/influenza/gisrs_l...h5fulltree.pdf
                  http://www.who.int/influenza/gisrs_l...5smalltree.pdf
                  http://www.who.int/influenza/resourc...irusupdate.pdf
                  http://www.who.int/influenza/gisrs_l...ualdiagram.pdf

                  ---
                  Clade designation criteria

                  1) Maintain previously designated clade numbers when possible (i.e., Clade 2.2 remains 2.2 and Clade 1 remains 1)

                  2) New clade designations based on phylogenetic tree topology derived from the large tree
                  - H5N1 progenitors (closest to gs/Guangdong/1/96) designated as Clade 0
                  - Subsequent clades numbered starting from Clade 3 (i.e., Clades 3-9)
                  - Clades designated by the presence of a distinct common node shared by at least 4 isolates
                  - Subclades/sub-subclades designated as a single clade evolves into more than
                  one distinct lineage (based on sharing of a common node)

                  3) Average percentage pairwise distances between and within clades (using the Kimura 2-parameter):
                  - Distinct clades should have ≥ 1.5% average distances between other clades
                  - Distinct clades should have ≤ 1.5% average distances within the clade (may be slightly higher in clades that have highly evolved outliers (i.e., ck/Shanxi/2/06 in Clade 7)

                  4) Bootstrap support for clade defining node (based on 1000 replicates)
                  - >60 at clade defining node

                  5) Antigenic properties as measured by the hemagglutination inhibition assay should be used as a correlate of clade designation when the data is available

                  http://www.who.int/influenza/gisrs_l.../en/index.html

                  Comment


                  • #10
                    Re: ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

                    Antigenic and genetic characteristics of zoonotic influenza viruses and development of candidate vaccine viruses for pandemic preparedness
                    September 2013

                    Clip:

                    Clade 2.3.2.1 viruses fall into three HA genetic groups as follows.

                    A/barn swallow/Hong Kong/D10-1161/2010-like viruses were detected in birds in China and Viet Nam but in reduced numbers compared to recent reporting periods. These viruses were genetically similar to viruses detected previously.

                    A/Hubei/1/2010-like viruses were detected in birds and/or environmental samples from Bangladesh, China, India, Nepal, and Viet Nam (Figure 2). While some viruses reacted well with post-infection ferret antisera raised against the available candidate vaccine virus produced from A/Hubei/1/2010, others did not (Table 3). Due to these observations and the widespread distribution of these viruses, a new A/duck/Bangladesh/19097/2013-like candidate vaccine virus is proposed.

                    A/Hong Kong/6841/2010-like viruses were detected in China, Democratic People’s Republic of Korea, Indonesia (detected in birds illegally imported into Europe), and Viet Nam. Antigenically (Table 4) and genetically (Figure 3) some of these viruses have diverged from available candidate vaccine viruses, hence a new A/duck/Viet Nam/1584/2012-like candidate vaccine virus is proposed.

                    Clip:
                    Table 3. Haemagglutination inhibition reactions of influenza A(H5N1) Clade 2.3.2.1 Hubei-like viruses


                    Table 4. Haemagglutination inhibition reactions of influenza A(H5N1) Clade 2.3.2.1 Hong Kong 6841-like viruses

                    Influenza A(H5N1) candidate vaccine viruses
                    Based on the available antigenic, genetic and epidemiologic data, A/duck/Bangladesh/19097/2013-like (clade 2.3.2.1),
                    A/duck/Viet Nam/NCVD-1584/2012-like (clade 2.3.2.1) and A/Cambodia/W0526301/2012-like (clade 1.1) candidate vaccine viruses are proposed.

                    See Table 5. Status of influenza A(H5N1) candidate vaccine virus development
                    A/chicken/Bangladesh/11RS1984-30/2011-like (2.3.4.2, CDC, Pending)
                    A/duck/Bangladesh/19097/2013-like (2.3.2.1 SJCRH Pending)

                    http://www.who.int/influenza/vaccine...irusupdate.pdf

                    Comment


                    • #11
                      Re: ICDDR,B-Health and Science Bulletin: The first fatal human infection with highly pathogenic avian influenza A (H5N1) virus detected in Bangladesh

                      Fourth H5N1 human case in Bangladesh in 2012:
                      40(M) No publically available information (A/Bangledesh/? /2012?)

                      Most likely strain designations:
                      Fifth and Sixth H5N1 human case in Bangladesh in 2012

                      5th case
                      26(M) A/Bangledesh/2/2012
                      Figure 2. Phylogenetic relationships of influenza A(H5N1) clade 2.3.2.1 A/Hubei/1/2010-like virus HA genes. The available candidate vaccine virus is in red. Human viruses are indicated (#). The scale bar represents the number of substitutions per site.
                      http://www.who.int/influenza/vaccine...irusupdate.pdf

                      IVTM connection:
                      Summary of Diagnostic Results
                      Influenza type A (H5N1): 1 of 1 materials

                      Source IVTM-SRC357, Human, Bangladesh
                      Source Type Human
                      Country/Area Bangladesh
                      Notes CDC ID# 2012783889
                      Created on 29-Aug-2012 15:24:34 | Last modified on 29-Aug-2012 15:24:34
                      Laboratory CDC Atlanta, USA

                      Original Specimen IVTM-ORG697, Human, Bangladesh
                      Date of collection 20-Mar-2012
                      IVTM Parent IVTM-SRC357
                      Notes CDC ID# 2012783889
                      Influenza type A (H5N1)
                      Specimen Type nose swab
                      Place of collection Bangladesh
                      Laboratory CDC Atlanta, USA

                      Influenza Virus Traceability Mechanism
                      https://extranet.who.int/ivtm/Tree.aspx?matid=697

                      ------
                      6th case
                      18(M) A/Bangledesh/3/2012
                      Figure 2. Phylogenetic relationships of influenza A(H5N1) clade 2.3.2.1 A/Hubei/1/2010-like virus HA genes. The available candidate vaccine virus is in red. Human viruses are indicated (#). The scale bar represents the number of substitutions per site.
                      http://www.who.int/influenza/vaccine...irusupdate.pdf


                      IVTM connection:
                      Influenza Virus Traceability Mechanism:WHO
                      Influenza type A (H5N1): 1 of 1 materials

                      Source IVTM-SRC358, Human, Bangladesh
                      Source Type Human
                      Country/Area Bangladesh
                      Notes CDC ID# 2012783891

                      Original Specimen IVTM-ORG698, Human, Bangladesh
                      Date of collection : 2012
                      IVTM Parent IVTM-SRC358
                      Notes CDC ID# 2012783891
                      Influenza type A (H5N1)
                      Specimen Type nose swab
                      Place of collection Bangladesh

                      Influenza Virus Traceability Mechanism
                      https://extranet.who.int/ivtm/Tree.aspx?matid=698

                      2013:
                      7th case
                      2(M) (23 months) - A/Bangladesh/8002/2013

                      http://www.who.int/influenza/vaccine...irusupdate.pdf

                      ----- in 2013
                      The frozen chicken connection most likely [but use with caution] is A/Chicken/Bangladesh/1-B/2013 as seen in Figure 2. Phylogenetic relationships of influenza A(H5N1) clade 2.3.2.1 A/Hubei/1/2010-like virus HA genes. The available candidate vaccine virus is in red and the HI reference viruses are in blue. The proposed vaccine canidate are indicted by circle. Human viruses are indicated (#). The scale bar represents the number of substitutions per site.

                      http://www.who.int/influenza/vaccine...irusupdate.pdf

                      Comment

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