TABLE 4.

Nucleotide variants in challenge stocks relative to the GenBank reference sequence. Only variants found in >5% of sequences are shown

Isolate	Mutation	Nucleotide position	Frequency (%)	Amino acid change	Protein	Codon position
Challenge stock: Zika virus/H.sapiens-tc/PUR/2015/PRVABC59-3329. Reference: KU501215.1	G → T	1964	92.06	V → L	E	330
	T → G	2780	5.36	W → G	NS1	98
	T → C	3147	12.27	M → T	NS1	220
	C → T	5679	54.31	S → F	NS3	356
	C → T	7915	10.56	None (G)	NS5	83
Challenge stock: Zika virus/H.sapiens/PAN/2015/PA 259249. Reference: KX156775	→ A	67/68	6.34	Frameshift	C	4
	→ A	275/276	7.56	Frameshift	C	73
	C → T	440	7.87	None (R)	prM	6
	T → C	2611	7.42	F → S	NS1	58
Challenge stock: Zika virus/H.sapiens/MEX/2016/R116265. Reference: KX766029	→ A	321/322	5.06	Frameshift	C	73
	C → T	3138	12.47	None (I)	NS1	218
	T → C	8118	5.67	None (S)	NS5	152
	C → R	8348	12.8	T → I	NS5	229
	A → T	9753	13.82	K → N	NS5	697
	G → T	10681	6.67		3′ UTR
	G → T	10687	10		3′ UTR
Challenge stock: Zika virus/H.sapiens/Brazil/2015/Paraiba_01. Reference: KX280026.1	A → G	693	18.75	T → A	prM	74
	T → C	798	18.82	S → P	M	16
	C → T	970	40.91	A → V	M	73
	C → T	4184	43.32	None (N)	NS2A	212
	G → T	4994	9.57	None (A)	NS3	127
	C → T	5680	54.21	S → F	NS3	356
	T → C	5693	48	None (V)	NS3	360
	A → G	6373	18.76	K → R	NS3	587
	C → A	7943	45.68	None (A)	NS5	92
	G → T	8281	6.99	G → V	NS5	205
Challenge stock: Zika virus/H.sapiens-tc/CAM/2010/FSS13025-7376. Reference: JN860885	No changes