Table 3. Adaptive mutations observed in the 5'UTR and P1 regions of EV71:TLLm and EV71:TLLmv viral genomes.

	EV71:BS vs EV71:TLLm				EV71:BS vs EV71:TLLmv
		Amino acid changes				Amino acid changes
Genome region	Nucleotide changes	Polyprotein1	Mature protein2	Genome region	Nucleotide changes	Polyprotein6	Mature protein7
Cloverleaf				Cloverleaf	C 140 G
IRES 3	A 141 G			IRES	A 141 C
	G 195 C				T 209 C
	T 209 C				G 258 A
	G 258 A				C 370 T
	C 370 T	Not applicable			G 448 A	Not applicable
	G 448 A				A 502 C
	T 502 C				G 675 T
	C 709 T				T 677 C
	A 671 T				C 687 T
	G 675 T				C 709 T
	T 678 INS4				678-681 INS
					726-745 DEL5
VP4	A 809 G	E 21 G	E 21 G	VP4	A 809 G	E 21 G	E 21 G
VP2	G 1359 A	V 204 I	V 135 I	VP2	G 1359 A	V 204 I	V 135 I
	G 1385 C	S 213 T	S 144 T		G 1385 C	S 213 T	S 144 T
	A 1400 T	K 218 I	K 149 I		A 1400 T	K 218 I	K 149 I
					T 1428 C	E 228 P	E 159 P
					G 1429 C	E 228 P	E 159 P
VP3					G 1900 C	A 385 P	A 62 P
					A 2287 G	T 514 A	T 191 A
					A 2421 G	I 558 M	I 235 M
VP1	T 2462 C	V 572 A	V 7 A	VP1	T 2462 C	V 572 A	V 7 A
	C 2725 T	L 660 F	L 95 F		C 2530 A	Q 595 K	Q 30 K
	A 2734 G	K 663 E	K 98 E		A 2719 G	I 658 V	I 93 V
	A 2752 G	N 669 D	N 104 D		T 2724 A	D 659 E	D 94 E
	A 2876 C	E 710 A	E 145 A		C 2725 T	L 660 F	L 95 F
	A 2943 T	E 732 D	E 167 D		A 2734 G	K 663 E	K 98 E
	C 2947 T	L 734 F	L 169 F		A 2752 G
	C 3165 T	S 806 L	S 241 L		A 2753 G	N 669 G	N 104 G
					A 2876 C	E 710 A	E 145 A
					A 2943 T	E 732 D	E 167 D
					C 2947 T	L 734 F	L 169 F
					C 3165 T	S 806 L	S 241 L
					T 3175 C	Y 810 H	Y 245 H
					G 3184 A	V 813 I	V 248 I
					G 3319 T	A 858 S	A 293 S

¹Numbering of amino acids in the uncleaved polyprotein prior to maturation.

²Numbering of amino acids in the mature protein.

³IRES - Internal Ribosome Entry Site.

⁴INS – Insertion.

⁵DEL – Deletion.