TABLE 5.

Unique significant variants (>1%) common for set a and b for secondary infection cases taking as a reference the first isolate obtained during the Cuban epidemic, 2001 to 2002^a

Sample no.	Feature	Position (nt)b	Reference allele	Set a variant				Set b variant
				Allele	Amino acid no.	Change	Frequency (%)	Allele	Amino acid no.	Change	Frequency (%)
2	3′ UTR	10404	G	A	*c	*	11.859	A	*	*	12.027
3	NS4B	6853	G	C	18	E → D	64.984	C	18	E → D	62.998
	NS5	8212	C	T	223	Synonymous → G	53.212	T	223	Synonymous → G	0.905
	2K peptided	6751	C	T	7	Synonymous → L	26.347	T	7	Synonymous → L	26.578
	NS3	5956	C	T	488	Synonymous → H	24.414	T	488	Synonymous → H	24.625
6	PrM	519	C	T	35	T → I	5.444	T	35	T → I	4.605
	NS5	8080	T	C	179	Synonymous → I	3.055	C	179	Synonymous → I	1.961
	NS5	9743	C	T	734	Synonymous → L	2.825	T	734	Synonymous → L	1.11
7	NS5	10000	G	A	819	Synonymous → E	52.534	A	819	Synonymous → E	52.01
	3UTR	10481	C	T	*	*	27.601	T	*	*	27.616
	NS3	5098	G	A	202	Synonymous → R	6.53	A	202	Synonymous → R	7.952
	NS2A	3531	G	T	28	G → V	1.883	T	28	G → V	2.237
	3UTR	10359	C	T	*	*	1.881	T	*	*	1.805
	NS5	9265	C	T	574	Synonymous → N	1.339	T	574	Synonymous → N	1.423
	NS4B	7366	C	A	189	Synonymous → A	1.093	A	189	Synonymous → A	1.417
8	NS2B	4294	G	A	64	Synonymous → E	7.278	A	64	Synonymous → E	7.562
11	E	1834	G	A	307	Synonymous → K	99.597	A	307	Synonymous → K	99.93
	E	991	G	A	26	Synonymous → E	99.584	A	26	Synonymous → E	99.862
	NS5	10049	G	A	836	V → I	7.903	A	836	V → I	7.418
	NS5	10223	G	C	894	E → Q	6.094	C	894	E → Q	6.061
13	NS5	9142	C	T	533	Synonymous → D	99.288	T	533	Synonymous → D	98.715
	NS3	5371	C	T	293	Synonymous → A	96.832	T	293	Synonymous → A	99.878
	NS5	9985	C	T	814	Synonymous → N	3.203	T	814	Synonymous → N	3.15
	NS4B	7012	G	A	71	Synonymous → Q	1.723	A	71	Synonymous → Q	1.678
	NS5	7975	G	A	144	Synonymous → L	1.511	A	144	Synonymous → L	1.686
	NS5	7744	G	A	67	Synonymous → E	1.472	A	67	Synonymous → E	1.484
	NS3	5326	C	T	278	Synonymous → N	1.386	T	278	Synonymous → N	1.003
	NS4B	7366	C	T	189	Synonymous → A	1.259	T	189	Synonymous → A	0.921
	NS2A	3500	C	T	18	L → F	0.983	T	18	L → F	1.474
15	NS5	9142	C	T	533	Synonymous → D	98.963	T	533	Synonymous → D	97.096
	NS3	5371	C	T	293	Synonymous → A	97.515	T	293	Synonymous → A	99.666
	NS2B	4315	C	T	71	Synonymous → S	3.495	T	71	Synonymous → S	5.037
	E	1510	G	A	199	M → I	2.366	A	199	M → I	2.212
	NS5	9092	A	G	517	I → V	1.579	G	517	I → V	1.941
	PrM	442	G	T	9	E → D	1.114	T	9	E → D	1.283
	NS1	3373	C	T	327	Synonymous → D	1.096	T	327	Synonymous → D	1.032
	E	2235	C	T	441	A → V	0.914	T	441	A → V	0.902
16	NS5	8655	G	A	371	R → K	99.491	A	371	R → K	98.923
	NS3	6184	C	T	564	Synonymous → C	6.696	T	564	Synonymous → C	6.419
	NS4B	7444	C	A	215	Synonymous → T	1.848	A	215	Synonymous → T	2.41
17	NS1	3310	G	A	306	Synonymous → K	99.055	A	306	Synonymous → K	99.847
	NS5	8428	C	T	295	Synonymous → D	13.026	T	295	Synonymous → D	96.876
	NS5	8875	C	T	444	Synonymous → G	2.936	T	444	Synonymous → G	0.075
	NS5	9127	C	T	528	Synonymous → A	1.875	T	528	Synonymous → A	0.102
	3UTR	10283	C	T	*	*	1.817	T	*	*	0.067
	NS5	8659	C	T	372	Synonymous → V	1.143	T	372	Synonymous → V	0.086
	NS5	8743	G	A	400	Synonymous → K	0.894	A	400	Synonymous → K	0.09
	NS5	7594	A	G	17	Synonymous → L	0.856	G	17	Synonymous → L	1.16
19	NS4A	6574	T	C	75	Synonymous → G	1.48	C	75	Synonymous → G	1.116
	3UTR	10661	A	G			0.6	G			0.838
20	NS3	5791	G	A	433	Synonymous → V	96.402	A	433	Synonymous → V	99.509
	PrM	652	G	T	79	Synonymous → T	4.65	A	79	Synonymous → T	0.073
	3UTR	10514	G	C	*	*	3.956	C	*	*	4.416
	NS3	4685	C	T	65	Synonymous → L	3.66	T	65	Synonymous → L	0.286
	3UTR	10577	A	C	*	*	2.459	C	*	*	2.533
	2K peptide	6769	C	A	13	Synonymous → G	2.048	A	13	Synonymous → G	2.463
21	NS5	8212	C	T	223	Synonymous → G	39.457	T	223	Synonymous → G	97.343
	NS4A	6700	G	T	117	Synonymous → V	8.487	T	117	Synonymous → V	8.528
	NS4B	6853	G	C	18	E → D	1.086	C	18	E → D	0.797

^aBoldface indicate that these variants became predominant in the particular patient.

^bnt, nucleotide.

^cIndicates positions in noncoding region of the 3′ untranslated region (UTR).

^d2K peptide, the DENV 2K-signal sequence is a 17-amino-acid peptide linking NS4A with NS4B.