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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.
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.
Code:
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)