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Volume 12, Number 9—September 2006

Genomic Signatures of Human versus Avian Influenza A Viruses

Guang-Wu Chen*1, Shih-Cheng Chang*1, Chee-Keng Mok*, Yu-Luan Lo*, Yu-Nong Kung*, Ji-Hung Huang*, Yun-Han Shih*, Ji-Yi Wang*, Chiayn Chiang*, Chi-Jene Chen*, and Shin-Ru Shih*Comments to Author 
Author affiliations: *Chang Gung University, Taoyuan, Taiwan, Republic of China

Main Article

Table 1

Validated amino acid signatures separating avian influenza viruses from human influenza viruses*

Gene Position Avian residues Human residues Associated functional domains
PB2 44 A(208),S(7) S(831),A(10),L(2) PB1–1, NP-1 (9), MLS (10)
199 A(210),S(5) S(842),A(3) NP-1 (9)
271 T(210),A(3),I(1),M(1) A(836),T(6),S(1) Cap-N (11)
475 L(214),M(1) M(839),L(3) NLS (12)
588 A(203),T(6),V(6) I(835),V(3),A(2) PB1–2, NP-2 (9)
613 V(212),A(3) T(816),I(16),A(8),V(1) PB1–2, NP-2 (9)
627 E(196),K(19) K(838),R(2),E(1) PB1–2, NP-2 (9)
674 A(204),S(6),T(2),G(2),E(1) T(836),A(2),I(2),P(1) PB1–2, NP-2 (9)
PB1 327 R(147),K(3) K(766),R(66) cRNA (13)
336 V(142),I(8) I(773),V(59) cRNA (13)
PB1-F2 73 K(397),R(6),I(1) R(594),K(87),S(1) ANT3, VDAC1 (14), mitochondrial localization (15), predicted amphipathic helix (16)
76 V(401),A(3) A(625),V(57) ANT3, VADC1 (14), predicted amphipathic helix (16)
79 R(369),Q(34),L(1) Q(607),R(75) ANT3, VADC1 (14), predicted amphipathic helix (16)
82 L(382),S(22) S(596),L(86) ANT3, VADC1 (14), predicted amphipathic helix (16)
87 E(389),G(14),K(1) G(637),E(45) ANT3, VADC1 (14)
PA 28 P(213),S(1) L(831),P(9),R(2) Proteolysis (17)
55 D(214) N(836),D(5) Proteolysis (17)
57 R(210),Q(4) Q(829),R(6),L(4),K(2) Proteolysis (17)
225 S(213),C(1) C(829),S(10) Proteolysis (17), NLSII (18)
268 L(214) I(827),L(11), P(1)
356 K(212),X(1),R(1) R(827),K(11)
382 E(208),D(5),V(1) D(824),E(11),V(2),N(1)
404 A(214) S(828),A(9),P(1)
409 S(189),N(24),I(1) N(830),S(7),I(1)
552 T(213),N(1) S(835),T(1),I(1)
HA 237 N(582),R(49),D(2),H(1),S(1) R(1209),N(12),S(2),D(1),K(1)
389 D(659),N(20),G(1),Y(1) N(819),D(121)
NP 16 G(356),S(9),D(6),T(2) D(646),G(7) RNA binding (19), BAT1/UAP56 (20), MxA (21), PB2–1 (22)
33 V(355),I(18) I(638),V(15) RNA binding (19), MxA (21), PB2–1 (22)
61 I(366),M(6),V(1) L(642),I(8) RNA binding (19), MxA (21), PB2–1 (22)
100 R(360),K(11),V(2) V(619),I(32),A(1),M(1) RNA binding (19), MxA (21), PB2–1 (22)
109 I(359),V(10),M(2),T(2) V(614),I(34),T(3),A(2) RNA binding (19), MxA (21), PB2–1 (22)
214 R(352),K(20),L(1) K(640),R(10) NLS (23), CRM1 (24), NP-1 (25)
283 L(372),P(1) P(643),L(7) NP-1 (25), PB2–2 (22)
293 R(371),K(2) K(622),R(28) NP-1 (25), PB2–2 (22)
305 R(369),K(4) K(636),R(14) NP-1 (25), PB2–2 (22)
313 F(371),I(1),L(1) Y(642),F(8) NP-1 (25), PB2–2 (22)
357 Q(368),K(4),T(1) K(644),R(8),Q(1) NAS (26), NP-1 (25), PB2–3 (22)
372 E(357),D(15),K(1) D(630),E(23) NAS (26), NP-2 (25), PB2–3 (22)
422 R(373) K(630),R(23) CTL epitope (27), NP-2 (25), PB2–3 (22)
442 T(372),A(1) A(629),T(23),R(1) NP-2 (25), PB2–3 (22)
455 D(373) E(630),D(22),T(1) NP-2 (25), PB2–3 (22)
M1 115 V(856),I(2),L(1),G(1) I(981),V(9)
121 T(840),A(19),P(1) A(988),T(2)
137 T(859),A(1),P(1) A(974),T(12)
M2 11 T(434),I(11),S(2) I(911),T(44) Host restriction specificities (28), ectodomain (29)
20 S(471),N(13) N(926),S(29) Host restriction specificities (28). ectodomain (29)
57 Y(481),C(1),H(1) H(913),Y(33),R(2),Q(1) CRAC (30), endodomain (29)
86 V(378) A(924),V(10),T(4),D(1) Endodomain (29)
NS1 227 E(692),G(9),K(1),S(1) R(897),G(5),K(1),E(1)
NS2 70 S(453),G(21),D(1) G(903),S(2) M1, NEP dimerization domain (31)
107 L(468),S(2),F(1) F(777),L(16),S(1) M1, NEP dimerization domain (31)

*Numbers in parentheses in residue columns are the number of sequences yielding the specific amino acid residue; bold indicates dominant amino acid residue type.

Main Article

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Main Article

1These authors contributed equally to this article.

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