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re: China - H7N9 Human Isolates on Deposit at GISAID

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  • gsgs
    Re: China - H7N9 Human Isolates on Deposit at GISAID

    but those 2ndary things won't change the sequences, the flu-evolution.
    Or could they

    Leave a comment:

  • gsgs
    Re: China - H7N9 Human Isolates on Deposit at GISAID

    · Shanghai2_E1_27M_2013_03_03_10_f onset 2013-02-19
    · Shanghai1_E1_87M_2013_03_04_f onset 2013-02-19

    so, S1 = A/Shanghai/1/2013(H7N9) is from the 87m, onset Feb.19, "case patient 3"
    sampled Feb.26 (throat swab), died Mar.04, and that sequences are from Mar.04 ?

    A throat swab collected on
    Feb 26th tested positive for H7N9 virus

    Isolate ID: EPI_ISL_138737
    passage details/history: E1
    Gender: Male

    so, we don't really know whom S1 is from and when the swab was taken (?)

    S1 is from the m87 :
    and throat swab, so maybe the sample from Feb.26, 7 days after onset

    Throat-swab specimens obtained from three adult Chinese patients (two from Shanghai City and
    one from Anhui Province) who were hospitalized with severe bilateral pneumonia, leukopenia, and
    lymphocytopenia were sent to Shanghai Public Health Clinical Center, the Shanghai Centers for
    Disease Control and Prevention (CDC), and the Anhui CDC, respectively. After preliminary detection
    of respiratory pathogens, the samples were sent to the Chinese National Influenza Center (CNIC)
    on March 25, 2013.

    Throat-swab specimens obtained from all three patients were maintained in a viral-transport medium.
    The specimens were propagated in the allantoic sac and amniotic cavity of 9-to-11-day-old specific
    pathogen-free embryonated chicken eggs for 48 to 72 hours at 35°C.

    RNA was extracted from throat-swab samples with the use of the QIAamp Viral RNA Mini Kit (Qiagen),
    according to the manufacturer's instructions. Specific real-time reverse-transcriptase–polymerase-chain
    -reaction (RT-PCR) assays for seasonal influenza viruses (H1, H3, or B), H5N1, severe acute respiratory
    syndrome coronavirus (SARS-CoV), and novel coronavirus were used. Real-time RT-PCR assays with
    self-designed specific primer and probe sets for detecting H1 to H16 and N1 to N9 subtypes were then
    performed to verify the viral subtypes.

    A total of 198 primer sets were used to amplify the full genome for sequencing, with the
    use of Qiagen OneStep RT-PCR Kit. PCR products were purified from agarose gel with the
    use of the QIAquick Gel Extraction Kit (Qiagen). We performed the sequencing using an
    ABI 3730xl automatic DNA analyzer (Life Technologies) and the ABI BigDye Terminator v3.1
    cycle sequencing kit (Life Technologies), according to the manufacturer's recommendations.
    Full genome sequences of the viruses from these patients were deposited in the Global
    Initiative on Sharing Avian Influenza Data (GISAID) database on March 29, 2013 (accession
    numbers are provided in Table S1 in the Supplementary Appendix, available with the full text
    of this article at

    Patient 1 was an 87-year-old man with chronic obstructive pulmonary disease (COPD)
    and hypertension who reported a cough and sputum production at the onset of illness.
    High fever and dyspnea developed 1 week after the onset of illness. He had no known
    history of exposure to live birds during the 2 weeks before the onset of symptoms.

    Influenza viruses A/Shanghai/1/2013 (H7N9), A/Shanghai/2/2013 (H7N9), and A/Anhui/1/2013 (H7N9)
    were isolated from Patients 1, 2, and 3, respectively.

    Attached Files

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  • gsgs
    started a topic re: China - H7N9 Human Isolates on Deposit at GISAID

    re: China - H7N9 Human Isolates on Deposit at GISAID

    I assume one version is usually dominant, the one virus that first
    replicates should have an advantage.
    And when you exhale,sneeze you won't have a statistical sample
    of all your viruses. These come from close, related locations.

    I remember the Tamiflu-resistance mutations, they often developed
    in the humans after some days, and were not detected at
    the beginning.
    I'm not sure with E627K, but I think it was similar ?!
    e.g. the Dutch vet in 2003