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Volume 15, Number 12—December 2009


Genomic Signatures of Influenza A Pandemic (H1N1) 2009 Virus

Guang-Wu ChenComments to Author  and Shin-Ru Shih
Author affiliations: Chang Gung University, Taoyuan, Taiwan, Republic of China

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Table 3

Position-specific residue transitioning for influenza A virus among avian, recent ancestral swine, pandemic (H1N1) 2009, and human strains, for those 8 positions of pandemic (H1N1) 2009 virus showing human-characteristic signatures*

Gene Position Avian virus residue Recent swine viruses residue† Pandemic (H1N1) 2009 virus residue Human virus residue
T(2,758), I(47), A(21), M(5), Q(1)
A(17), S(1)
A(2,770), T(15), S(1)
V(3,350), I(26), A(16)
I(2,595), V(168), T(1)
PA 356 K(3,309), R(34), N(7), E(1), I(1) K(16), R(1) R(61) R(2,705), K(30)

S(3,100), N(191), G(4), I(1), R(1), K(1)
N(2,723), S(11),I (1)
NP 33 V(3,173), I(284), A(1), D(1) I(18) I(121) I(2,876), V(25)
100 R(3,422), K(34), V(23), S(1) V(17), I(1) V(68), I(46) V(2,842), I(52), R(4), A(3), L(1), M(1)
305 R(3,238), K(32), S(2) K(18) K(114) K(3,052), R(33)
357 Q(2,766), K(33), T(3), R(2) K(17), R(1) K(114) K(3,052), R(46), Q(5)

*Boldface indicates dominant amino acid residue type. PB, polymerase B; PA, polymerase A; NP, nucleoprotein.
†Eighteen recent ancestral swine viruses as listed in the Appendix Table. We consider recent ancestral strains phylogenetically neighboring to the pandemic 2009 strains, in particular for PB2 and PA genes they are clustered together with recent avian strains because the pandemic (H1N1) viruses were reported to originate from avian viruses around 1998. Note that for 1 strain, A/swine/Missouri/4296424/06(H2N3), the PA sequence was not found anywhere near the other 17 recent swine strains of interest. Two PB1 sequences, A/swine/Hong Kong/78/2003(H1N2) and A/swine/Korea/C13/2008(H5N2), were also found distantly located from the other 16 recent swine PB1 sequences. We excluded these 3 sequences from the amino acid statistics in this table because of their genetic deviation from the remaining ancestral swine viruses we have collected here.

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