TABLE 6.

Unique significant variants (>1%) common for set a and b present in two samples corresponding to the same patient at days 2 and 4 after fever onset, taking as a reference the first isolate obtained during the Cuban epidemic, 2001 to 2002^a

Sample and feature	Position (nt)b	Read coveraged	Reference allele	Set a variant				Set b variant
				Allele	Amino acid no.	Change	Frequency (%)	Allele	Amino acid no.	Change	Frequency (%)
Cuba_553_2001
NS5	9142	30,246	C	T	533	Synonymous → D	99.288	T	533	Synonymous → D	98.715
NS3	5371	8,024	C	T	293	Synonymous → A	96.832	T	293	Synonymous → A	99.878
NS5	9985	30,249	C	T	814	Synonymous → N	3.203	T	814	Synonymous → N	3.15
NS4B	7012	16,819	G	A	71	Synonymous → Q	1.723	A	71	Synonymous → Q	1.678
NS5	7975	19,551	G	A	144	Synonymous → L	1.511	A	144	Synonymous → L	1.686
NS5	7744	18,047	G	A	67	Synonymous → E	1.472	A	67	Synonymous → E	1.484
NS3	5326	8,654	C	T	278	Synonymous → N	1.386	T	278	Synonymous → N	1.003
NS4B	7366	15,691	C	T	189	Synonymous → A	1.259	T	189	Synonymous → A	0.921
NS2A	3500	12,713	C	T	18	L → F	0.983	T	18	L → F	1.474
Cuba_558_2001
NS5	9142	13,986	C	T	533	Synonymous → D	98.963	T	533	Synonymous → D	97.096
NS3	5371	18,626	C	T	293	Synonymous → A	97.515	T	293	Synonymous → A	99.666
NS2B	4315	27,529	C	T	71	Synonymous → S	3.495	T	71	Synonymous → S	5.037
E	1510	24,416	G	A	199	M → I	2.366	A	199	M → I	2.212
NS5	9092	12,493	A	G	517	I → V	1.579	G	517	I → V	1.941
PrM	442c	19,513	G	T	9	E → D	1.114	T	9	E → D	1.283
NS1	3373	18,492	C	T	327	synonymous>D	1.096	T	327	Synonymous → D	1.032
E	2235	30,874	C	T	441	A → V	0.914	T	441	A → V	0.902

^aBoldface indicate that this variant became predominant.

^bnt, nucleotide.

^cVariant A (synonymous → E) at position PrM 442 was detected in sample Cuba_553_2001 at a frequency of 0.1% (day 2).

^dRead coverage, the average number of reads that align to each base of the reference sequence.