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  • New 2013 Human Strain Designation for Egypt

    Background reports: 36-year old female from Delengat District
    Animal Production and Health Commision for Asia and the Pacific, APHCA ECTAD-HPAI Situation Update 07-Feb-2013 - Issue no. 565
    AFRICAN REGION
    Egypt
    OFFICIAL
    05/02/13 Confirmed H5 HPAI outbreaks in poultry, Behera, Giza, Menofia (FAO Field Officer)
    Between 22 January and 29 February 2013, four H5 HPAI outbreaks were detected in poultry in Behera (1), Giza (2) and Menofia (1) Governorates. Two were detected in live-bird markets in Menofia and Giza Governorates, one outbreak was detected in household chickens and ducks in Giza, and one outbreak was detected in vaccinated chickens in the commercial farm sector in Behera. The infected poultry found in the live-bird markets and at the household were not vaccinated. The infected poultry in live-bird markets were detected through active surveillance, and other outbreaks were detected through passive surveillance.
    30/01/13 Confirmed H5 HPAI outbreaks in poultry, Behera, Dakahlia and Menofia (FAO Field Officer)
    Between 23 and 30 January 2013, four H5 HPAI outbreaks were detected in poultry in the Behera (1), Dakahlia (2) and Menofia (1) Governorates. In Menofia, H5 HPAI was detected in a turkey, in a live-bird market of which the vaccination status was unknown, and the other three outbreaks were detected in households with unvaccinated poultry in Behera
    1) and Dakahlia (2) Governorates. The outbreaks were detected through targeted surveillance in Menofia (1), active surveillance in Behera (1) and through community-based animal health outreach (CAHO) in Dakahlia (2).
    28/01/13 Confirmed H5N1 infection in a human, Behera (FAO Field Officer)
    H5N1 infection was reported in a 36-year old female from Delengat District, Behera Governorate. She developed symptoms on 16 January 2013 and died on 26 January 2013. Initial RT-PCR testing was positive at the sub-national virology laboratory in the Alexandria Governorate; confirmed by RT-PCR at the Central Public Health Laboratory [WHO National Influenza Center (NIC)] on 27 January 2013. Investigations into the source of infection indicated that the case had exposure to sick and dead backyard poultry (chickens and ducks) through raising and slaughtering the poultry.

    http://www.aphca.org/Avian%20Infuenz...50-NAMRU3/2013

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

    GENERAL INFO
    Disease Event ID: 174499
    Reporting date: 28/01/2013
    Observation date: 16/01/2013
    LOCATION
    Region: Africa
    Admin 1 (Country): Al Buhayrah (Behera) (Egypt)
    Locality: Delengat
    Lat/Long: 30.84262/30.559778
    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: RT-PCR (reverse transcription - PCR)
    Result: Positive
    Result Date: 27-01-2013
    Reference Laboratory:

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

    http://empres-i.fao.org/empres-i/2/o...k=174449&rss=t

    -----
    Influenza at the human-animal interface
    Summary and assessment as of 15 February 2013
    Snip
    Egypt has reported one new human case with influenza A(H5N1) virus infection in Behera Governorate. The A(H5N1) virus is also endemic in poultry in some areas of Egypt, and additional sporadic human cases are possible.
    http://www.who.int/influenza/human_a...ce_15Feb13.pdf


    ---------------------------------------------------------
    Influenza Virus Traceability Mechanism (WHO IVTM)
    https://extranet.who.int/ivtm/Tree.aspx?matid=752

    Influenza type A (H5N1): 2 of 2 materials

    Source IVTM-SRC378, Human, Egypt
    Source Type Human
    Country/Area Egypt
    Notes Case #170
    Provided to GISRS from:
    Laboratory CDC Atlanta, USA

    Original Specimen IVTM-ORG751, Human, Egypt
    Date of collection 20-Jan-2013
    IVTM Parent IVTM-SRC378
    Notes Case #170
    CDC ID# 2013758448
    Influenza type A (H5N1)
    Specimen Type throat swab
    Place of collection Egypt
    Provided to GISRS from:
    Laboratory CDC Atlanta, USA

    Virus IVTM-VIR752, A/Egypt/01050-NAMRU3/2013
    Current Designation A/Egypt/01050-NAMRU3/2013
    Creation Date 28-Feb-2013
    IVTM Parent IVTM-ORG751
    Notes CDC ID# 2013758448
    Influenza type A (H5N1)
    Isolation System Virus isolate egg
    Is Reference Virus? No
    Is Candidate Vaccine Virus? No

    -------------------------------------------------------------
    This is the 5th human strain designation of 2013

    A/Cambodia/X0123311/2013 (WHO)
    A/Cambodia/X0123312/2013 (WHO)
    A/Guizhou/1/2013 (GISAID)
    A/Guizhou/2/2013 (GISAID)
    and now
    A/Egypt/01050-NAMRU3/2013 (WHO IVTM)

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

    Antigenic and genetic characteristics of A(H5N1), A(H7N3), A(H9N2) and variant influenza viruses and candidate vaccine viruses developed for potential use in human vaccines
    20 February 2013

    A/Cambodia/X0123311/2013 (WHO) HA Clade 1.1
    A/Cambodia/X0123312/2013 (WHO) HA Clade 1.1
    A/Guizhou/1/2013 (WHO) HA Clade 2.3.4.2
    A/Guizhou/2/2013 (WHO) HA Clade 2.3.4.2

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


    --------------------------------------------------------------
    2013 Guizhou H5N1 Sequences Match 2012 Fatal Case
    Recombinomics Commentary
    February 25, 2013

    Snip
    The WHO Chinese National Influenza Center has released H5N1 sequences (at GISAID) from two recent cases in Guizhou Province. The agency is to be commended for the rapid release of these important sequences (full sequences for all gene segments except PB2).

    One set was from a fatal case (21 years old), A/Guizhou/1/2013, with a collection date of February 8, which would match the recently described fatal case (21F). The second sequence (A/Guizhou/2/2013) was from a February 9 collection from a 31 year old, which would match the case (31M) who recently died. Initial reports cited an absence of contact with poultry.

    Both of the 2013 sequences are closely related to each other as well as the 2012 fatal case (39M) from Guizhou, A/Guizhou/1/2012. The H5 sequence from the 2012 has been described. It had a number of receptor binding domain changes flanking position 190 (A188E, A189T, T199I, I202V), as well as a cluster of changes around S133L. All of these features, which were noted in the 2012 sequence, are also present in the two 2013 sequences. All three sequences also gained a glycosylation site due to T219N.

    Although these features are found in the three human sequences from 2012 and 2013, these combinations of changes are not found in any recent poultry sequences. A BLAST analysis of the H5 sequence, as well as the other 6 segments, yields closest relationships with H5N1 sequences from isolates collected 5-7 years ago.

    2013 Guizhou H5N1 Sequences Match 2012 Fatal Case
    http://www.recombinomics.com/News/02...zhou_2013.html

    If anybody has further background of Cambodian Strain designations in relation to 2013 cases please reply or message me!


  • #2
    Re: New 2013 Human Strain Designation for Egypt

    ECTAD-HPAI Hyperlink updated!
    Animal Production and Health Commision for Asia and the Pacific, APHCA ECTAD-HPAI Situation Update 07-Feb-2013 - Issue no. 565
    http://www.aphca.org/Avian%20Infuenz...ate_130207.pdf

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