Table 2.

Shared non-synonymous mutations identified in ≥2.0 per cent of West Nile virus isolates from New York State, 2000 − 15.

NT	AA	Gene	Frequency	Years	Variant	Selection
G301A	S36N	C	0.02	02-12	G	a
A408G	K104R	C	0.02	06-14	E
T459C	V121A	C	0.02	08-13	–
T915C	M273T	M	0.02	04-14	–
C1443T	V449A	E	0.90	02-15	–
T1501A	L468Q	E	0.02	01-03	–
G2893T	K932N	NS1	0.02	07-10	R
C3681T	T1195I	NS2A	0.04	07-15	–
A3794G	M1233V	NS2A	0.05	01, 05-07, 09-10	A/L/T
C3809T	L1238F	NS2A	0.04	03, 06-15	–
C3881T	H1262Y	NS2A	0.03	02-04, 06-08, 11, 15	–	a
G4089A	R1331K	NS2A	0.11	06, 09-15	–	a
G4196A	A1367T	NS2B	0.04	00-04, 08	V/T	a
T4515C	M1473T	NS2B	0.02	05-08	–
G4540T	I1481M	NS2B	0.02	03-05, 08-09	V
G4574A	V1493I	NS2B	0.02	01-08	–
G4577A	V1494I	NS2B	0.02	06-14	–
A5152T	E1685D	NS3	0.04	03-04, 11-13	–
T5612A	S1839T	NS3	0.05	07, 09-15	F
G6722A	A2209T	NS4A	0.10	02-12	S, V	b
G6872A	V2259M	NS4A	0.02	03-05, 07, 09-10	–	a
G6957T	S2287I	NS4B	0.05	07, 09-15	–
A6987G	K2297R	NS4B	0.03	03-06	–	a
G7003A	M2302I	NS4B	0.02	05-06, 09, 13	–
A7058G	T2321A	NS4B	0.02	02-08	–
G7227A	G2377E	NS4B	0.06	01-07, 09-15	–	b
A7736G	I2513M	NS4B	0.12	05-15	–	a
A8300G	V2735I	NS5	0.02	10, 12, 14	–
A8622G	K2842R	NS5	0.05	02-08	–	a
G8946A	R2950K	NS5	0.02	06-09, 15	–	a
A9319T	R3074S	NS5	0.04	02-07	–	a

^aPositive selection detected in the US dataset.

^bPositive selection detected in NYS dataset only.