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recombinations in HA and NA of Chinese H9N2

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  • recombinations in HA and NA of Chinese H9N2

    2 in HA and 2 in NA = 4 in total ?
    Arch Virol. 2010 Mar 19. [Epub ahead of print]
    Codon usage bias and recombination events for neuraminidase and hemagglutinin genes
    in Chinese isolates of influenza A virus subtype H9N2.
    Liu X, Wu C, Chen AY.
    The representative complete neuraminidase sequences (NA) of 138 Chinese isolates and
    hemagglutinin sequences (HA) of 128 Chinese isolates of influenza A virus subtype H9N2
    were analyzed to reveal codon usage bias and recombination events. A plot of the effective
    number of codons (ENC) against G + C context at the third position of the codons (ENC-plot)
    and correlation analysis demonstrated that mutational pressure is the main factor determining
    the codon usage bias in the H9N2 subtype. The high ENC values (51.31 for NA and 48.83 for HA)
    indicated that the codon usage bias in Chinese H9N2 isolates was very low. Plots of correspondence
    analysis and an ENC plot indicated that the HA and NA genes had different codon usage bias.
    Recombination analysis revealed two possible recombination events for HA and NA gene sequences
    in the Chinese isolates. Subsequent phylogenetic analysis further supported the validity of these
    recombination events. In addition, one false-positive recombinant for HA gene was found, which
    may have been derived from contamination during PCR amplification.

    recombination in N2-NA , se7a62, 3687 sequences 
    p=0.0000000000000000000  2269/Moscow/346/03(H3N2)                       1/parakeet/Chiba/1/97(H9N2) 
    p=0.0000000000000000000  3112/Moscow/343/03(H3N2)                       2/Japan/305/57(H2N2) 
    p=0.0000000000000000000  3526/Moscow/346/03(H3N2)                       3/Sw/Miyagi/5/03(H1N2) 
    p=0.0000000000000000000  3527/Moscow/343/03(H3N2)                       4/Nagasaki/N01/05(H3N2) 
    p=0.0000000000000000000  2756/Ck/NY/14677-13/98(H6N2)                2753/Ck/CA/S0403106/04(H6N2) 
    p=0.0000000000000000023   239/Dk/HK/86/76(H9N2)                      2459/Qa/Shantou/1912/01(H9N2) 
    p=0.0000000000000034670  3557/Sw/Chachoengsao/NIAH586/05(H3N2)       2796/Sw/Nakhon pathom/NIAH586-1/05(H3N2) 
    p=0.0000000000000979039  2404/Dk/Xuzhou/05/01(H9N2)                  2403/Dk/Xuzhou/07/03(H9N2) 
    recombination in H9-HA, se7a49.nam, 902 sequences 
    p=0.0000000000000000014   435/chicken/Shantou/9909/2005(H9N2)         439/chicken/Shantou/20817/2005(H9N2) 
    p=0.0000000000000039272   109/Chicken/Gansu/1/99(H9N2)                117/Chicken/Shandong/1/98(H9N2) 
    p=0.0000000000012278532   797/quail/Shantou/365/2002(H9N2)            507/partridge/Shantou/4525/2002(H9N2) 
    p=0.0000000000028797782   123/Chicken/Tianjing/1/96(H9N2)             115/Chicken/Liaoning/1/00(H9N2) 
    p=0.0000000000129866722   298/chicken/Shandong/1/02(H9N2)             177/Chicken/Henan/98(H9N2) 
    p=0.0000000000226611338   739/swine/Shandong/fLS/2003(H9N2)           601/chicken/Guangdong/56/01(H9N2) 
    p=0.0000000031786447575   693/Ck/HK/NT142/2003(H9N2)                  313/chicken/HongKong/NT142/03(H9N2)
    I'm interested in expert panflu damage estimates
    my current links: ILI-charts: